Release minimap2-2.31 (r1302)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.github/workflows/ci.yaml

@@ -0,0 +1,68 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+
+jobs:
+  build-linux-x8664:
+    name: Linux x86_64
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout minimap2
+      uses: actions/checkout@v4
+
+    - name: Compile with ${{ matrix.compiler }}
+      run: |
+        make CC=${{ matrix.compiler }}
+        file minimap2 | grep x86-64
+
+  build-linux-aarch64:
+    name: Linux aarch64
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Compile with ${{ matrix.compiler }}
+      uses: uraimo/run-on-arch-action@v3
+      with:
+        arch: aarch64
+        distro: ubuntu22.04
+        githubToken: ${{ github.token }}
+        dockerRunArgs: |
+          --volume "${PWD}:/minimap2"
+        install: |
+          apt-get update -q -y
+          apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev file
+        run: |
+          cd /minimap2
+          make CC=${{ matrix.compiler }} arm_neon=1 aarch64=1 -j
+          file minimap2 | grep aarch64
+
+  build-mac-arm64:
+    name: Mac ARM64
+    runs-on: macos-14
+    strategy:
+      matrix:
+        compiler: [clang]
+
+    steps:
+    - name: Checkout minimap2
+      uses: actions/checkout@v4
+
+    - name: Compile with ${{ matrix.compiler }}
+      run: |
+        make CC=${{ matrix.compiler }} arm_neon=1 aarch64=1 -j
+        file minimap2 | grep arm64
+        

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lib/simde"]
+	path = lib/simde
+	url = https://github.com/nemequ/simde.git

.travis.yml

@@ -1,20 +0,0 @@
-matrix:
-  include:
-    - language: c
-      compiler: gcc
-      script: make
-    - language: c
-      compiler: clang
-      script: make
-    - language: python
-      python: "2.7"
-      before_install: pip install cython
-      script: python setup.py build_ext
-    - language: python
-      python: "3.5"
-      before_install: pip install cython
-      script: python setup.py build_ext
-    - language: python
-      python: "3.6"
-      before_install: pip install cython
-      script: python setup.py build_ext

FAQ.md

@@ -0,0 +1,46 @@
+#### 1. Alignment different with option `-a` or `-c`?
+
+Without `-a`, `-c` or `--cs`, minimap2 only finds *approximate* mapping
+locations without detailed base alignment. In particular, the start and end
+positions of the alignment are imprecise. With one of those options, minimap2
+will perform base alignment, which is generally more accurate but is much
+slower.
+
+#### 2. How to map Illumina short reads to noisy long reads?
+
+No good solutions. The better approach is to assemble short reads into contigs
+and then map noisy reads to contigs.
+
+#### 3. The output SAM doesn't have a header.
+
+By default, minimap2 indexes 4 billion reference bases (4Gb) in a batch and map
+all reads against each reference batch. Given a reference longer than 4Gb,
+minimap2 is unable to see all the sequences and thus can't produce a correct
+SAM header. In this case, minimap2 doesn't output any SAM header. There are two
+solutions to this issue. First, you may increase option `-I` to, for example,
+`-I8g` to index more reference bases in a batch. This is preferred if your
+machine has enough memory. Second, if your machines doesn't have enough memory
+to hold the reference index, you can use the `--split-prefix` option in a
+command line like:
+```sh
+minimap2 -ax map-ont --split-prefix=tmp ref.fa reads.fq
+```
+This second approach uses less memory, but it is slower and requires temporary
+disk space.
+
+#### 4. The output SAM is malformatted.
+
+This typically happens when you use nohup to wrap a minimap2 command line.
+Nohup is discouraged as it breaks piping. If you have to use nohup, please
+specify an output file with option `-o`.
+
+#### 5. How to output one alignment per read?
+
+You can use `--secondary=no` to suppress secondary alignments (aka multiple
+mappings), but you can't suppress supplementary alignment (aka split or
+chimeric alignment) this way. You can use samtools to filter out these
+alignments:
+```sh
+minimap2 -ax map-out ref.fa reads.fq | samtools view -F0x900
+```
+However, this is discouraged as supplementary alignment is informative.

LICENSE.txt

@@ -1,6 +1,7 @@
 The MIT License
 
-Copyright (c) 2017 Broad Institute, Inc.
+Copyright (c) 2018-     Dana-Farber Cancer Institute
+              2017-2018 Broad Institute, Inc.
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

MANIFEST.in

@@ -1,10 +1,9 @@
 include *.h
 include Makefile
 include ksw2_dispatch.c
-include getopt.c
 include main.c
 include README.md
-include python/mappy.c
+include sse2neon/emmintrin.h
 include python/cmappy.h
 include python/cmappy.pxd
 include python/mappy.pyx

Makefile

@@ -1,21 +1,41 @@
-CFLAGS=		-g -Wall -O2 -Wc++-compat
+CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 CPPFLAGS=	-DHAVE_KALLOC
 INCLUDES=
-OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o ksw2_ll_sse.o
+OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
+			lchain.o align.o hit.o seed.o jump.o map.o format.o pe.o esterr.o splitidx.o \
+			ksw2_ll_sse.o
 PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
-ifeq ($(arm_neon),)
-ifeq ($(sse2only),)
+ifneq ($(aarch64),)
+	arm_neon=1
+endif
+
+ifeq ($(arm_neon),) # if arm_neon is not defined
+ifeq ($(sse2only),) # if sse2only is not defined
 	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
-else
+else                # if sse2only is defined
 	OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
 endif
-else
-    OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
-    CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
-    INCLUDES+=-I sse2neon
+else				# if arm_neon is defined
+	OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
+    INCLUDES+=-Isse2neon
+ifeq ($(aarch64),)	#if aarch64 is not defined
+	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
+else				#if aarch64 is defined
+	CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
+endif
+endif
+
+ifneq ($(asan),)
+	CFLAGS+=-fsanitize=address
+	LIBS+=-fsanitize=address -ldl
+endif
+
+ifneq ($(tsan),)
+	CFLAGS+=-fsanitize=thread
+	LIBS+=-fsanitize=thread -ldl
 endif
 
 .PHONY:all extra clean depend
@@ -28,8 +48,8 @@ all:$(PROG)
 
 extra:all $(PROG_EXTRA)
 
-minimap2:main.o getopt.o libminimap2.a
-		$(CC) $(CFLAGS) main.o getopt.o -o $@ -L. -lminimap2 $(LIBS)
+minimap2:main.o libminimap2.a
+		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
 
 minimap2-lite:example.o libminimap2.a
 		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
@@ -37,31 +57,36 @@ minimap2-lite:example.o libminimap2.a
 libminimap2.a:$(OBJS)
 		$(AR) -csru $@ $(OBJS)
 
-sdust:sdust.c getopt.o kalloc.o kalloc.h kdq.h kvec.h kseq.h sdust.h
-		$(CC) -D_SDUST_MAIN $(CFLAGS) $< getopt.o kalloc.o -o $@ -lz
+sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
 
 # SSE-specific targets on x86/x86_64
 
+ifeq ($(arm_neon),)   # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
+ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
+endif
+
 ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extz2_sse2.o:ksw2_extz2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse41.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_extd2_sse2.o:ksw2_extd2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c -msse4 $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@
 
 ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
-		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
 
 # NEON-specific targets on ARM
 
@@ -77,30 +102,36 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
 # other non-file targets
 
 clean:
-		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg*
+		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* .eggs
 
 depend:
 		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
 
 # DO NOT DELETE
 
-align.o: minimap.h mmpriv.h bseq.h ksw2.h kalloc.h
+align.o: minimap.h mmpriv.h bseq.h kseq.h ksw2.h kalloc.h
 bseq.o: bseq.h kvec.h kalloc.h kseq.h
-chain.o: minimap.h mmpriv.h bseq.h kalloc.h
-esterr.o: mmpriv.h minimap.h bseq.h
+esterr.o: mmpriv.h minimap.h bseq.h kseq.h
 example.o: minimap.h kseq.h
-format.o: kalloc.h mmpriv.h minimap.h bseq.h
-getopt.o: getopt.h
-hit.o: mmpriv.h minimap.h bseq.h kalloc.h khash.h
-index.o: kthread.h bseq.h minimap.h mmpriv.h kvec.h kalloc.h khash.h
+format.o: kalloc.h mmpriv.h minimap.h bseq.h kseq.h
+hit.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h khash.h
+index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h ksw2.h kalloc.h kvec.h
+index.o: khash.h ksort.h
+jump.o: mmpriv.h minimap.h bseq.h kseq.h
 kalloc.o: kalloc.h
 ksw2_extd2_sse.o: ksw2.h kalloc.h
 ksw2_exts2_sse.o: ksw2.h kalloc.h
 ksw2_extz2_sse.o: ksw2.h kalloc.h
 ksw2_ll_sse.o: ksw2.h kalloc.h
-main.o: bseq.h minimap.h mmpriv.h getopt.h
-map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
-misc.o: minimap.h ksort.h
-pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
+kthread.o: kthread.h
+lchain.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h krmq.h
+main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
+map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h
+map.o: khash.h ksort.h
+misc.o: mmpriv.h minimap.h bseq.h kseq.h ksort.h
+options.o: mmpriv.h minimap.h bseq.h kseq.h
+pe.o: mmpriv.h minimap.h bseq.h kseq.h kvec.h kalloc.h ksort.h
 sdust.o: kalloc.h kdq.h kvec.h sdust.h
-sketch.o: kvec.h kalloc.h minimap.h
+seed.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h ksort.h
+sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
+splitidx.o: mmpriv.h minimap.h bseq.h kseq.h

Makefile.simde

@@ -0,0 +1,97 @@
+CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
+CPPFLAGS=	-DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
+INCLUDES=	-Ilib/simde
+OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \
+			ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
+PROG=		minimap2
+PROG_EXTRA=	sdust minimap2-lite
+LIBS=		-lm -lz -lpthread
+
+
+ifneq ($(arm_neon),) # if arm_neon is defined
+ifeq ($(aarch64),)   #if aarch64 is not defined
+	CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
+else                 #if aarch64 is defined
+	CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
+endif
+endif
+
+ifneq ($(asan),)
+	CFLAGS+=-fsanitize=address
+	LIBS+=-fsanitize=address
+endif
+
+ifneq ($(tsan),)
+	CFLAGS+=-fsanitize=thread
+	LIBS+=-fsanitize=thread
+endif
+
+.PHONY:all extra clean depend
+.SUFFIXES:.c .o
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+all:$(PROG)
+
+extra:all $(PROG_EXTRA)
+
+minimap2:main.o libminimap2.a
+		$(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
+
+minimap2-lite:example.o libminimap2.a
+		$(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+
+libminimap2.a:$(OBJS)
+		$(AR) -csru $@ $(OBJS)
+
+sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
+		$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
+
+ksw2_ll_simde.o:ksw2_ll_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ksw2_extz2_simde.o:ksw2_extz2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ksw2_extd2_simde.o:ksw2_extd2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
+		$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+
+# other non-file targets
+
+clean:
+		rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
+
+depend:
+		(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c)
+
+# DO NOT DELETE
+
+align.o: minimap.h mmpriv.h bseq.h kseq.h ksw2.h kalloc.h
+bseq.o: bseq.h kvec.h kalloc.h kseq.h
+chain.o: minimap.h mmpriv.h bseq.h kseq.h kalloc.h
+esterr.o: mmpriv.h minimap.h bseq.h kseq.h
+example.o: minimap.h kseq.h
+format.o: kalloc.h mmpriv.h minimap.h bseq.h kseq.h
+hit.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h khash.h
+index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h
+index.o: ksort.h
+kalloc.o: kalloc.h
+ksw2_extd2_sse.o: ksw2.h kalloc.h
+ksw2_exts2_sse.o: ksw2.h kalloc.h
+ksw2_extz2_sse.o: ksw2.h kalloc.h
+ksw2_ll_sse.o: ksw2.h kalloc.h
+kthread.o: kthread.h
+main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h
+map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h
+map.o: khash.h ksort.h
+misc.o: mmpriv.h minimap.h bseq.h kseq.h ksort.h
+options.o: mmpriv.h minimap.h bseq.h kseq.h
+pe.o: mmpriv.h minimap.h bseq.h kseq.h kvec.h kalloc.h ksort.h
+sdust.o: kalloc.h kdq.h kvec.h sdust.h
+self-chain.o: minimap.h kseq.h
+sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
+splitidx.o: mmpriv.h minimap.h bseq.h kseq.h

NEWS.md

@@ -1,3 +1,749 @@
+Release 2.31-r1302 (19 May 2026)
+--------------------------------
+
+Notable changes to minimap2:
+
+ * Bugfix: supplementary and secondary alignments were occasionally flagged
+   incorrectly.
+
+ * Bugfix: Smith-Waterman alignment for inversion alignment led to an
+   out-of-bound access in rare cases.
+
+Changes to paftools.js:
+
+ * New feature: new `sim2bed` subcommand to get a BED file from simulated
+   reads.
+
+ * New feature: new `badread2fa` subcommand to format reads simulated by
+   the Badread simulator.
+
+Change to the python binding:
+
+ * New feature: mappy optionally writes the `ds` tag.
+
+ * Bugfix: a use-after-free error (#1345)
+
+The two bugs in minimap2 had existed for years. They were caught by Jeremy Wang
+at UNC when he ported minimap2 to Rust. Due to the two bug fixes, this version
+occasionally produces alignment different from the last version.
+
+(2.31: 19 May 2026, r1302)
+
+
+
+Release 2.30-r1287 (15 June 2025)
+---------------------------------
+
+Notable changes:
+
+ * Improvement: consolidated `--spsc`.
+
+ * Deprecation: subcommands `splice2bed`, `gff2bed`, `gff2junc`, `junceval` and
+   `exoneval` in `paftools.js` are deprecated by minigff. They will remain
+   indefinitely for backward compatibility.
+
+(2.30: 15 June 2025, r1287)
+
+
+
+Release 2.29-r1283 (18 April 2025)
+----------------------------------
+
+Notable changes to minimap2:
+
+ * New feature: added the `splice:sr` preset for short RNA-seq read alignment.
+   Users may use `-j` to specify known gene annotation to improve spliced
+   alignment close to the ends of short reads. Also added `--write-junc` and
+   `--pass1` for 2-pass short-read RNA-seq alignment.
+
+ * Experimental feature: read splice scores from a file specified by `--spsc`
+   and consider the scores during base alignment. The feature makes it possible
+   to apply advanced splice models and to improve spliced alignment.
+
+ * Change: adjusted the mapping quality calculation for spliced alignment.
+
+ * Bugfixes: a) missing overlap alignment when base alignment is requested
+   (#969); b) incorrect summary information for long genomes (#1192); c)
+   missing parameter check for `--score-N` (#1226).
+
+ * Improvement: a) warn about absent junction files (#1229); b) report an error
+   if a wrong preset prefixed with "splice" is specified (#589).
+
+Notable changes to mappy:
+
+ * Improvement: allow passing read name (#1260)
+
+ * Improvement: exposed score for ambiguous bases (#1240)
+
+Minimap2 now supports short/long genomic/RNA-seq read alignment along with
+contig alignment and all-vs-all read overlapping. It produces identical genomic
+long-read or contig alignment to v2.27. Short genomic read alignment and the
+mapping quality of long RNA-seq read alignment may slightly differ in very rare
+cases.
+
+(2.29: 18 April 2025, r1283)
+
+
+
+Release 2.28-r1209 (27 March 2024)
+----------------------------------
+
+Notable changes to minimap2:
+
+ * Bugfix: `--MD` was not working properly due to the addition of `--ds` in the
+   last release (#1181 and #1182).
+
+ * New feature: added an experimental preset `lq:hqae` for aligning accurate
+   long reads back to their assembly. It has been observed that `map-hifi` and
+   `lr:hq` may produce many wrong alignments around centromeres when accurate
+   long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid
+   assembly constructed from them. This new preset produces much more accurate
+   alignment. It is still experimental and may be subjective to changes in
+   future.
+
+ * Change: reduced the default `--cap-kalloc` to 500m to lower the peak
+   memory consumption (#855).
+
+Notable changes to mappy:
+
+ * Bugfix: mappy option struct was out of sync with minimap2 (#1177).
+
+Minimap2 should output identical alignments to v2.27.
+
+(2.28: 27 March 2024, r1209)
+
+
+
+Release 2.27-r1193 (12 March 2024)
+----------------------------------
+
+Notable changes to minimap2:
+
+ * New feature: added the `lr:hq` preset for accurate long reads at ~1% error
+   rate. This was suggested by Oxford Nanopore developers (#1127). It is not
+   clear if this preset also works well for PacBio HiFi reads.
+
+ * New feature: added the `map-iclr` preset for Illumina Complete Long Reads
+   (#1069), provided by Illumina developers.
+
+ * New feature: added option `-b` to specify mismatch penalty for base
+   transitions (i.e. A-to-G or C-to-T changes).
+
+ * New feature: added option `--ds` to generate a new `ds:Z` tag that
+   indicates uncertainty in INDEL positions. It is an extension to `cs`. The
+   `mgutils-es6.js` script in minigraph parses `ds`.
+
+ * Bugfix: avoided a NULL pointer dereference (#1154). This would not have an
+   effect on most systems but would still be good to fix.
+
+ * Bugfix: reverted the value of `ms:i` to pre-2.22 versions (#1146). This was
+   an oversight. See fcd4df2 for details.
+
+Notable changes to paftools.js and mappy:
+
+ * New feature: expose `bw_long` to mappy's Aligner class (#1124).
+
+ * Bugfix: fixed several compatibility issues with k8 v1.0 (#1161 and #1166).
+   Subcommands "call", "pbsim2fq" and "mason2fq" were not working with v1.0.
+
+Minimap2 should output identical alignments to v2.26, except the ms tag.
+
+(2.27: 12 March 2024, r1193)
+
+
+
+Release 2.26-r1175 (29 April 2023)
+----------------------------------
+
+Fixed the broken Python package. This is the only change.
+
+(2.26: 25 April 2023, r1173)
+
+
+
+Release 2.25-r1173 (25 April 2023)
+----------------------------------
+
+Notable changes:
+
+ * Improvement: use the miniprot splice model for RNA-seq alignment by default.
+   This model considers non-GT-AG splice sites and leads to slightly higher
+   (<0.1%) accuracy and sensitivity on real human data.
+
+ * Change: increased the default `-I` to `8G` such that minimap2 would create a
+   uni-part index for a pair of mammalian genomes. This change may increase the
+   memory for all-vs-all read overlap alignment given large datasets.
+
+ * New feature: output the sequences in secondary alignments with option
+   `--secondary-seq` (#687).
+
+ * Bugfix: --rmq was not parsed correctly (#1010)
+
+ * Bugfix: possibly incorrect coordinate when applying end bonus to the target
+   sequence (#1025). This is a ksw2 bug. It does not affect minimap2 as
+   minimap2 is not using the affected feature.
+
+ * Improvement: incorporated several changes for better compatibility with
+   Windows (#1051) and for minimap2 integration at Oxford Nanopore Technologies
+   (#1048 and #1033).
+
+ * Improvement: output the HD-line in SAM output (#1019).
+
+ * Improvement: check minimap2 index file in mappy to prevent segmentation
+   fault for certain indices (#1008).
+
+For genomic sequences, minimap2 should give identical output to v2.24.
+Long-read RNA-seq alignment may occasionally differ from previous versions.
+
+(2.25: 25 April 2023, r1173)
+
+
+
+Release 2.24-r1122 (26 December 2021)
+-------------------------------------
+
+This release improves alignment around long poorly aligned regions. Older
+minimap2 may chain through such regions in rare cases which may result in
+missing alignments later. The issue has become worse since the the change of
+the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
+release provides a better solution with a X-drop-like heuristic and by enabling
+two-bandwidth chaining in the assembly mode.
+
+(2.24: 26 December 2021, r1122)
+
+
+
+Release 2.23-r1111 (18 November 2021)
+-------------------------------------
+
+Notable changes:
+
+ * Bugfix: fixed missing alignments around long inversions (#806 and #816).
+   This bug affected v2.19 through v2.22.
+
+ * Improvement: avoid extremely long mapping time for pathologic reads with
+   highly repeated k-mers not in the reference (#771). Use --q-occ-frac=0
+   to disable the new heuristic.
+
+ * Change: use --cap-kalloc=1g by default.
+
+(2.23: 18 November 2021, r1111)
+
+
+
+Release 2.22-r1101 (7 August 2021)
+----------------------------------
+
+When choosing the best alignment, this release uses logarithm gap penalty and
+query-specific mismatch penalty. It improves the sensitivity to long INDELs in
+repetitive regions.
+
+Other notable changes:
+
+ * Bugfix: fixed an indirect memory leak that may waste a large amount of
+   memory given highly repetitive reference such as a 16S RNA database (#749).
+   All versions of minimap2 have this issue.
+
+ * New feature: added --cap-kalloc to reduce the peak memory. This option is
+   not enabled by default but may become the default in future releases.
+
+Known issue:
+
+ * Minimap2 may take a long time to map a read (#771). So far it is not clear
+   if this happens to v2.18 and earlier versions.
+
+(2.22: 7 August 2021, r1101)
+
+
+
+Release 2.21-r1071 (6 July 2021)
+--------------------------------
+
+This release fixed a regression in short-read mapping introduced in v2.19
+(#776). It also fixed invalid comparisons of uninitialized variables, though
+these are harmless (#752). Long-read alignment should be identical to v2.20.
+
+(2.21: 6 July 2021, r1071)
+
+
+
+Release 2.20-r1061 (27 May 2021)
+--------------------------------
+
+This release fixed a bug in the Python module and improves the command-line
+compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset,
+users would get alignments more fragmented than v2.18. This could be an issue
+for existing pipelines specifying `-r`. This release resolves this issue.
+
+(2.20: 27 May 2021, r1061)
+
+
+
+Release 2.19-r1057 (26 May 2021)
+--------------------------------
+
+This release includes a few important improvements backported from unimap:
+
+ * Improvement: more contiguous alignment through long INDELs. This is enabled
+   by the minigraph chaining algorithm. All `asm*` presets now use the new
+   algorithm. They can find INDELs up to 100kb and may be faster for
+   chromosome-long contigs. The default mode and `map*` presets use this
+   algorithm to replace the long-join heuristic.
+
+ * Improvement: better alignment in highly repetitive regions by rescuing
+   high-occurrence seeds. If the distance between two adjacent seeds is too
+   large, attempt to choose a fraction of high-occurrence seeds in-between.
+   Minimap2 now produces fewer clippings and alignment break points in long
+   satellite regions.
+
+ * Improvement: allow to specify an interval of k-mer occurrences with `-U`.
+   For repeat-rich genomes, the automatic k-mer occurrence threshold determined
+   by `-f` may be too large and makes alignment impractically slow. The new
+   option protects against such cases. Enabled for `asm*` and `map-hifi`.
+
+ * New feature: added the `map-hifi` preset for maping PacBio High-Fidelity
+   (HiFi) reads.
+
+ * Change to the default: apply `--cap-sw-mem=100m` for genomic alignment.
+
+ * Bugfix: minimap2 could not generate an index file with `-xsr` (#734).
+
+This release represents the most signficant algorithmic change since v2.1 in
+2017. With features backported from unimap, minimap2 now has similar power to
+unimap for contig alignment. Unimap will remain an experimental project and is
+no longer recommended over minimap2. Sorry for reverting the recommendation in
+short time.
+
+(2.19: 26 May 2021, r1057)
+
+
+
+Release 2.18-r1015 (9 April 2021)
+---------------------------------
+
+This release fixes multiple rare bugs in minimap2 and adds additional
+functionality to paftools.js.
+
+Changes to minimap2:
+
+ * Bugfix: a rare segfault caused by an off-by-one error (#489)
+
+ * Bugfix: minimap2 segfaulted due to an uninitilized variable (#622 and #625).
+
+ * Bugfix: minimap2 parsed spaces as field separators in BED (#721). This led
+   to issues when the BED name column contains spaces.
+
+ * Bugfix: minimap2 `--split-prefix` did not work with long reference names
+   (#394).
+
+ * Bugfix: option `--junc-bonus` didn't work (#513)
+
+ * Bugfix: minimap2 didn't return 1 on I/O errors (#532)
+
+ * Bugfix: the `de:f` tag (sequence divergence) could be negative if there were
+   ambiguous bases
+
+ * Bugfix: fixed two undefined behaviors caused by calling memcpy() on
+   zero-length blocks (#443)
+
+ * Bugfix: there were duplicated SAM @SQ lines if option `--split-prefix` is in
+   use (#400 and #527)
+
+ * Bugfix: option -K had to be smaller than 2 billion (#491). This was caused
+   by a 32-bit integer overflow.
+
+ * Improvement: optionally compile against SIMDe (#597). Minimap2 should work
+   with IBM POWER CPUs, though this has not been tested. To compile with SIMDe,
+   please use `make -f Makefile.simde`.
+
+ * Improvement: more informative error message for I/O errors (#454) and for
+   FASTQ parsing errors (#510)
+
+ * Improvement: abort given malformatted RG line (#541)
+
+ * Improvement: better formula to estimate the `dv:f` tag (approximate sequence
+   divergence). See DOI:10.1101/2021.01.15.426881.
+
+ * New feature: added the `--mask-len` option to fine control the removal of
+   redundant hits (#659). The default behavior is unchanged.
+
+Changes to mappy:
+
+ * Bugfix: mappy caused segmentation fault if the reference index is not
+   present (#413).
+
+ * Bugfix: fixed a memory leak via 238b6bb3
+
+ * Change: always require Cython to compile the mappy module (#723). Older
+   mappy packages at PyPI bundled the C source code generated by Cython such
+   that end users did not need to install Cython to compile mappy. However, as
+   Python 3.9 is breaking backward compatibility, older mappy does not work
+   with Python 3.9 anymore. We have to add this Cython dependency as a
+   workaround.
+
+Changes to paftools.js:
+
+ * Bugfix: the "part10-" line from asmgene was wrong (#581)
+
+ * Improvement: compatibility with GTF files from GenBank (#422)
+
+ * New feature: asmgene also checks missing multi-copy genes
+
+ * New feature: added the misjoin command to evaluate large-scale misjoins and
+   megabase-long inversions.
+
+Although given the many bug fixes and minor improvements, the core algorithm
+stays the same. This version of minimap2 produces nearly identical alignments
+to v2.17 except very rare corner cases.
+
+Now unimap is recommended over minimap2 for aligning long contigs against a
+reference genome. It often takes less wall-clock time and is much more
+sensitive to long insertions and deletions.
+
+(2.18: 9 April 2021, r1015)
+
+
+
+Release 2.17-r941 (4 May 2019)
+------------------------------
+
+Changes since the last release:
+
+ * Fixed flawed CIGARs like `5I6D7I` (#392).
+
+ * Bugfix: TLEN should be 0 when either end is unmapped (#373 and #365).
+
+ * Bugfix: mappy is unable to write index (#372).
+
+ * Added option `--junc-bed` to load known gene annotations in the BED12
+   format. Minimap2 prefers annotated junctions over novel junctions (#197 and
+   #348). GTF can be converted to BED12 with `paftools.js gff2bed`.
+
+ * Added option `--sam-hit-only` to suppress unmapped hits in SAM (#377).
+
+ * Added preset `splice:hq` for high-quality CCS or mRNA sequences. It applies
+   better scoring and improves the sensitivity to small exons. This preset may
+   introduce false small introns, but the overall accuracy should be higher.
+
+This version produces nearly identical alignments to v2.16, except for CIGARs
+affected by the bug mentioned above.
+
+(2.17: 5 May 2019, r941)
+
+
+
+Release 2.16-r922 (28 February 2019)
+------------------------------------
+
+This release is 50% faster for mapping ultra-long nanopore reads at comparable
+accuracy. For short-read mapping, long-read overlapping and ordinary long-read
+mapping, the performance and accuracy remain similar. This speedup is achieved
+with a new heuristic to limit the number of chaining iterations (#324). Users
+can disable the heuristic by increasing a new option `--max-chain-iter` to a
+huge number.
+
+Other changes to minimap2:
+
+ * Implemented option `--paf-no-hit` to output unmapped query sequences in PAF.
+   The strand and reference name columns are both `*` at an unmapped line. The
+   hidden option is available in earlier minimap2 but had a different 2-column
+   output format instead of PAF.
+
+ * Fixed a bug that leads to wrongly calculated `de` tags when ambiguous bases
+   are involved (#309). This bug only affects v2.15.
+
+ * Fixed a bug when parsing command-line option `--splice` (#344). This bug was
+   introduced in v2.13.
+
+ * Fixed two division-by-zero cases (#326). They don't affect final alignments
+   because the results of the divisions are not used in both case.
+
+ * Added an option `-o` to output alignments to a specified file. It is still
+   recommended to use UNIX pipes for on-the-fly conversion or compression.
+
+ * Output a new `rl` tag to give the length of query regions harboring
+   repetitive seeds.
+
+Changes to paftool.js:
+
+ * Added a new option to convert the MD tag to the long form of the cs tag.
+
+Changes to mappy:
+
+ * Added the `mappy.Aligner.seq_names` method to return sequence names (#312).
+
+For NA12878 ultra-long reads, this release changes the alignments of <0.1% of
+reads in comparison to v2.15. All these reads have highly fragmented alignments
+and are likely to be problematic anyway. For shorter or well aligned reads,
+this release should produce mostly identical alignments to v2.15.
+
+(2.16: 28 February 2019, r922)
+
+
+
+Release 2.15-r905 (10 January 2019)
+-----------------------------------
+
+Changes to minimap2:
+
+ * Fixed a rare segmentation fault when option -H is in use (#307). This may
+   happen when there are very long homopolymers towards the 5'-end of a read.
+
+ * Fixed wrong CIGARs when option --eqx is used (#266).
+
+ * Fixed a typo in the base encoding table (#264). This should have no
+   practical effect.
+
+ * Fixed a typo in the example code (#265).
+
+ * Improved the C++ compatibility by removing "register" (#261). However,
+   minimap2 still can't be compiled in the pedantic C++ mode (#306).
+
+ * Output a new "de" tag for gap-compressed sequence divergence.
+
+Changes to paftools.js:
+
+ * Added "asmgene" to evaluate the completeness of an assembly by measuring the
+   uniquely mapped single-copy genes. This command learns the idea of BUSCO.
+
+ * Added "vcfpair" to call a phased VCF from phased whole-genome assemblies. An
+   earlier version of this script is used to produce the ground truth for the
+   syndip benchmark [PMID:30013044].
+
+This release produces identical alignment coordinates and CIGARs in comparison
+to v2.14. Users are advised to upgrade due to the several bug fixes.
+
+(2.15: 10 Janurary 2019, r905)
+
+
+
+Release 2.14-r883 (5 November 2018)
+-----------------------------------
+
+Notable changes:
+
+ * Fixed two minor bugs caused by typos (#254 and #266).
+
+ * Fixed a bug that made minimap2 abort when --eqx was used together with --MD
+   or --cs (#257).
+
+ * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may
+   take a lot of memory in the splicing mode. This may lead to issues when we
+   run minimap2 on a cluster with a hard memory limit. The new option avoids
+   unlimited memory usage at the cost of missing a few long introns.
+
+ * Conforming to C99 and C11 when possible (#261).
+
+ * Warn about malformatted FASTA or FASTQ (#252 and #255).
+
+This release occasionally produces base alignments different from v2.13. The
+overall alignment accuracy remain similar.
+
+(2.14: 5 November 2018, r883)
+
+
+
+Release 2.13-r850 (11 October 2018)
+-----------------------------------
+
+Changes to minimap2:
+
+ * Fixed wrongly formatted SAM when -L is in use (#231 and #233).
+
+ * Fixed an integer overflow in rare cases.
+
+ * Added --hard-mask-level to fine control split alignments (#244).
+
+ * Made --MD work with spliced alignment (#139).
+
+ * Replaced musl's getopt with ketopt for portability.
+
+ * Log peak memory usage on exit.
+
+This release should produce alignments identical to v2.12 and v2.11.
+
+(2.13: 11 October 2018, r850)
+
+
+
+Release 2.12-r827 (6 August 2018)
+---------------------------------
+
+Changes to minimap2:
+
+ * Added option --split-prefix to write proper alignments (correct mapping
+   quality and clustered query sequences) given a multi-part index (#141 and
+   #189; mostly by @hasindu2008).
+
+ * Fixed a memory leak when option -y is in use.
+
+Changes to mappy:
+
+ * Support the MD/cs tag (#183 and #203).
+
+ * Allow mappy to index a single sequence, to add extra flags and to change the
+   scoring system.
+
+Minimap2 should produce alignments identical to v2.11.
+
+(2.12: 6 August 2018, r827)
+
+
+
+Release 2.11-r797 (20 June 2018)
+--------------------------------
+
+Changes to minimap2:
+
+ * Improved alignment accuracy in low-complexity regions for SV calling. Thank
+   @armintoepfer for multiple offline examples.
+
+ * Added option --eqx to encode sequence match/mismatch with the =/X CIGAR
+   operators (#156, #157 and #175).
+
+ * When compiled with VC++, minimap2 generated wrong alignments due to a
+   comparison between a signed integer and an unsigned integer (#184). Also
+   fixed warnings reported by "clang -Wextra".
+
+ * Fixed incorrect anchor filtering due to a missing 64- to 32-bit cast.
+
+ * Fixed incorrect mapping quality for inversions (#148).
+
+ * Fixed incorrect alignment involving ambiguous bases (#155).
+
+ * Fixed incorrect presets: option `-r 2000` is intended to be used with
+   ava-ont, not ava-pb. The bug was introduced in 2.10.
+
+ * Fixed a bug when --for-only/--rev-only is used together with --sr or
+   --heap-sort=yes (#166).
+
+ * Fixed option -Y that was not working in the previous releases.
+
+ * Added option --lj-min-ratio to fine control the alignment of long gaps
+   found by the "long-join" heuristic (#128).
+
+ * Exposed `mm_idx_is_idx`, `mm_idx_load` and `mm_idx_dump` C APIs (#177).
+   Also fixed a bug when indexing without reference names (this feature is not
+   exposed to the command line).
+
+Changes to mappy:
+
+ * Added `__version__` (#165).
+
+ * Exposed the maximum fragment length parameter to mappy (#174).
+
+Changes to paftools:
+
+ * Don't crash when there is no "cg" tag (#153).
+
+ * Fixed wrong coverage report by "paftools.js call" (#145).
+
+This version may produce slightly different base-level alignment. The overall
+alignment statistics should remain similar.
+
+(2.11: 20 June 2018, r797)
+
+
+
+Release 2.10-r761 (27 March 2018)
+---------------------------------
+
+Changes to minimap2:
+
+ * Optionally output the MD tag for compatibility with existing tools (#63,
+   #118 and #137).
+
+ * Use SSE compiler flags more precisely to prevent compiling errors on certain
+   machines (#127).
+
+ * Added option --min-occ-floor to set a minimum occurrence threshold. Presets
+   intended for assembly-to-reference alignment set this option to 100. This
+   option alleviates issues with regions having high copy numbers (#107).
+
+ * Exit with non-zero code on file writing errors (e.g. disk full; #103 and
+   #132).
+
+ * Added option -y to copy FASTA/FASTQ comments in query sequences to the
+   output (#136).
+
+ * Added the asm20 preset for alignments between genomes at 5-10% sequence
+   divergence.
+
+ * Changed the band-width in the ava-ont preset from 500 to 2000. Oxford
+   Nanopore reads may contain long deletion sequencing errors that break
+   chaining.
+
+Changes to mappy, the Python binding:
+
+ * Fixed a typo in Align.seq() (#126).
+
+Changes to paftools.js, the companion script:
+
+ * Command sam2paf now converts the MD tag to cs.
+
+ * Support VCF output for assembly-to-reference variant calling (#109).
+
+This version should produce identical alignment for read overlapping, RNA-seq
+read mapping, and genomic read mapping. We have also added a cook book to show
+the variety uses of minimap2 on real datasets. Please see cookbook.md in the
+minimap2 source code directory.
+
+(2.10: 27 March 2017, r761)
+
+
+
+Release 2.9-r720 (23 February 2018)
+-----------------------------------
+
+This release fixed multiple minor bugs.
+
+* Fixed two bugs that lead to incorrect inversion alignment. Also improved the
+  sensitivity to small inversions by using double Z-drop cutoff (#112).
+
+* Fixed an issue that may cause the end of a query sequence unmapped (#104).
+
+* Added a mappy API to retrieve sequences from the index (#126) and to reverse
+  complement DNA sequences. Fixed a bug where the `best_n` parameter did not
+  work (#117).
+
+* Avoided segmentation fault given incorrect FASTQ input (#111).
+
+* Combined all auxiliary javascripts to paftools.js. Fixed several bugs in
+  these scripts at the same time.
+
+(2.9: 24 February 2018, r720)
+
+
+
+Release 2.8-r672 (1 February 2018)
+----------------------------------
+
+Notable changes in this release include:
+
+ * Speed up short-read alignment by ~10%. The overall mapping accuracy stays
+   the same, but the output alignments are not always identical to v2.7 due to
+   unstable sorting employed during chaining. Long-read alignment is not
+   affected by this change as the speedup is short-read specific.
+
+ * Mappy now supports paired-end short-read alignment (#87). Please see
+   python/README.rst for details.
+
+ * Added option --for-only and --rev-only to perform alignment against the
+   forward or the reverse strand of the reference genome only (#91).
+
+ * Alleviated the issue with undesired diagonal alignment in the self mapping
+   mode (#10). Even if the output is not ideal, it should not interfere with
+   other alignments. Fully resolving the issue is intricate and may require
+   additional heuristic thresholds.
+
+ * Enhanced error checking against incorrect input (#92 and #96).
+
+For long query sequences, minimap2 should output identical alignments to v2.7.
+
+(2.8: 1 February 2018, r672)
+
+
+
 Release 2.7-r654 (9 January 2018)
 ---------------------------------
 

README.md

@@ -1,28 +1,36 @@
 [![GitHub Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=social&logo=github&label=Download)](https://github.com/lh3/minimap2/releases)
 [![BioConda Install](https://img.shields.io/conda/dn/bioconda/minimap2.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/minimap2)
 [![PyPI](https://img.shields.io/pypi/v/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy)
-[![Build Status](https://travis-ci.org/lh3/minimap2.svg?branch=master)](https://travis-ci.org/lh3/minimap2)
+[![Build Status](https://github.com/lh3/minimap2/actions/workflows/ci.yaml/badge.svg)](https://github.com/lh3/minimap2/actions)
 ## <a name="started"></a>Getting Started
+**ALERT:** `minimap2.com` is a [phishing site](https://github.com/lh3/minimap2/issues/1316). Please don't use anything from that website.
 ```sh
 git clone https://github.com/lh3/minimap2
 cd minimap2 && make
 # long sequences against a reference genome
 ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
 # create an index first and then map
-./minimap2 -d MT-human.mmi test/MT-human.fa
-./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam
+./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa
+./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam
 # use presets (no test data)
-./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio genomic reads
+./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio CLR genomic reads
 ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
+./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19+)
+./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam       # Nanopore Q20 genomic reads (v2.27+)
 ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
-./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads
-./minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam  # Nanopore Direct RNA-seq
+./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
+./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore direct RNA-seq
+./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam    # PacBio Kinnex/Iso-seq (RNA-seq)
+./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam  # use annotated junctions
+./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam     # short-read RNA-seq (v2.29+)
+./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam
 ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf             # intra-species asm-to-asm alignment
 ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf     # PacBio read overlap
 ./minimap2 -x ava-ont reads.fa reads.fa > overlaps.paf    # Nanopore read overlap
 # man page for detailed command line options
 man ./minimap2.1
 ```
+
 ## Table of Contents
 
 - [Getting Started](#started)
@@ -33,12 +41,13 @@ man ./minimap2.1
     - [Map long noisy genomic reads](#map-long-genomic)
     - [Map long mRNA/cDNA reads](#map-long-splice)
     - [Find overlaps between long reads](#long-overlap)
-    - [Map short accurate genomic reads](#short-genomic)
+    - [Map short genomic reads](#short-genomic)
+    - [Map short RNA-seq reads](#short-rna-seq)
     - [Full genome/assembly alignment](#full-genome)
   - [Advanced features](#advanced)
     - [Working with >65535 CIGAR operations](#long-cigar)
     - [The cs optional tag](#cs)
-    - [Evaluation scripts](#eval)
+    - [Working with the PAF format](#paftools)
   - [Algorithm overview](#algo)
   - [Getting help](#help)
   - [Citing minimap2](#cite)
@@ -61,16 +70,16 @@ mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more
 accurate on simulated long reads and produces biologically meaningful alignment
 ready for downstream analyses. For >100bp Illumina short reads, minimap2 is
 three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data.
-Detailed evaluations are available from the [minimap2 preprint][preprint].
+Detailed evaluations are available from the [minimap2 paper][doi] or the
+[preprint][preprint].
 
 ### <a name="install"></a>Installation
 
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.7/minimap2-2.7_x64-linux.tar.bz2 \
-  | tar -jxvf -
-./minimap2-2.7_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.31/minimap2-2.31_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.31_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code
@@ -78,13 +87,20 @@ directory to compile. If you see compilation errors, try `make sse2only=1`
 to disable SSE4 code, which will make minimap2 slightly slower.
 
 Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
-compile, use `make arm_neon=1`.
+compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`. To
+compile for for 64 bit ARM architectures (such as ARMv8), use `make arm_neon=1
+aarch64=1`.
+
+Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
+implementation to the different SIMD instruction sets. To compile using SIMDe,
+use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
+with the ARM related command lines given above.
 
 ### <a name="general"></a>General usage
 
 Without any options, minimap2 takes a reference database and a query sequence
 file as input and produce approximate mapping, without base-level alignment
-(i.e. no CIGAR), in the [PAF format][paf]:
+(i.e. coordinates are only approximate and no CIGAR in output), in the [PAF format][paf]:
 ```sh
 minimap2 ref.fa query.fq > approx-mapping.paf
 ```
@@ -125,19 +141,22 @@ parameters at the same time. The default setting is the same as `map-ont`.
 #### <a name="map-long-genomic"></a>Map long noisy genomic reads
 
 ```sh
-minimap2 -ax map-pb  ref.fa pacbio-reads.fq > aln.sam   # for PacBio subreads
+minimap2 -ax map-pb  ref.fa pacbio-reads.fq > aln.sam   # for PacBio CLR reads
 minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam      # for Oxford Nanopore reads
+minimap2 -ax map-iclr ref.fa iclr-reads.fq > aln.sam    # for Illumina Complete Long Reads
 ```
 The difference between `map-pb` and `map-ont` is that `map-pb` uses
 homopolymer-compressed (HPC) minimizers as seeds, while `map-ont` uses ordinary
-minimizers as seeds. Emperical evaluation suggests HPC minimizers improve
-performance and sensitivity when aligning PacBio reads, but hurt when aligning
-Nanopore reads.
+minimizers as seeds. Empirical evaluation suggests HPC minimizers improve
+performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning
+Nanopore reads. `map-iclr` uses an adjusted alignment scoring matrix that
+accounts for the low overall error rate in the reads, with transversion errors
+being less frequent than transitions.
 
 #### <a name="map-long-splice"></a>Map long mRNA/cDNA reads
 
 ```sh
-minimap2 -ax splice -uf ref.fa iso-seq.fq > aln.sam          # PacBio Iso-seq/traditional cDNA
+minimap2 -ax splice:hq -uf ref.fa iso-seq.fq > aln.sam       # PacBio Iso-seq/traditional cDNA
 minimap2 -ax splice ref.fa nanopore-cdna.fa > aln.sam        # Nanopore 2D cDNA-seq
 minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam  # Nanopore Direct RNA-seq
 minimap2 -ax splice --splice-flank=no SIRV.fa SIRV-seq.fa    # mapping against SIRV control
@@ -156,9 +175,8 @@ or the last exons.
 
 Minimap2 rates an alignment by the score of the max-scoring sub-segment,
 *excluding* introns, and marks the best alignment as primary in SAM. When a
-spliced gene also has unspliced pseudogenes, minimap2 does not intentionally
-prefer spliced alignment, though in practice it more often marks the spliced
-alignment as the primary. By default, minimap2 outputs up to five secondary
+spliced gene also has unspliced pseudogenes, minimap2 slightly prefers
+the spliced alignment. By default, minimap2 outputs up to five secondary
 alignments (i.e. likely pseudogenes in the context of RNA-seq mapping). This
 can be tuned with option **-N**.
 
@@ -176,10 +194,27 @@ This is because SIRV does not honor the evolutionarily conservative splicing
 signal. If you are studying SIRV, you may apply `--splice-flank=no` to let
 minimap2 only model GT..AG, ignoring the additional base.
 
+Since v2.17, minimap2 can optionally take annotated genes as input and
+prioritize on annotated splice junctions. To use this feature, you can 
+```sh
+paftools.js gff2bed anno.gff > anno.bed
+minimap2 -ax splice --junc-bed anno.bed ref.fa query.fa > aln.sam
+```
+Here, `anno.gff` is the gene annotation in the GTF or GFF3 format (`gff2bed`
+automatically tests the format). The output of `gff2bed` is in the 12-column
+BED format, or the BED12 format. With the `--junc-bed` option, minimap2 adds a
+bonus score (tuned by `--junc-bonus`) if an aligned junction matches a junction
+in the annotation. Option `--junc-bed` also takes 5-column BED, including the
+strand field. In this case, each line indicates an oriented junction.
+
+**Note:** `--junc-bed` is intended for long noisy RNA-seq reads only.
+Applying the option to short RNA-seq reads would increase run time with little
+improvement to junction accuracy.
+
 #### <a name="long-overlap"></a>Find overlaps between long reads
 
 ```sh
-minimap2 -x ava-pb  reads.fq reads.fq > ovlp.paf    # PacBio read overlap
+minimap2 -x ava-pb  reads.fq reads.fq > ovlp.paf    # PacBio CLR read overlap
 minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf    # Oxford Nanopore read overlap
 ```
 Similarly, `ava-pb` uses HPC minimizers while `ava-ont` uses ordinary
@@ -188,7 +223,7 @@ the overlapping mode because it is slow and may produce false positive
 overlaps. However, if performance is not a concern, you may try to add `-a` or
 `-c` anyway.
 
-#### <a name="short-genomic"></a>Map short accurate genomic reads
+#### <a name="short-genomic"></a>Map short genomic reads
 
 ```sh
 minimap2 -ax sr ref.fa reads-se.fq > aln.sam           # single-end alignment
@@ -201,8 +236,18 @@ be paired if they are adjacent in the input stream and have the same name (with
 the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
 mixed.
 
-Minimap2 does not work well with short spliced reads. There are many capable
-RNA-seq mappers for short reads.
+#### <a name="short-rna-seq"></a>Map short RNA-seq reads
+
+```sh
+minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam           # single-end
+minimap2 -ax splice:sr ref.fa r1.fq.gz r2.fq.gz > aln.sam        # paired-end
+minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam  # use annotation
+# 2-pass alignment
+minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed
+minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam
+```
+The new preset `splice:sr` was added in v2.29. It functions similarly to `sr`
+except that it performs spliced alignment.
 
 #### <a name="full-genome"></a>Full genome/assembly alignment
 
@@ -226,10 +271,10 @@ To avoid this issue, you can add option `-L` at the minimap2 command line.
 This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR
 at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and
 sorting) still work with such BAM records; tools that read CIGAR will
-effectively ignore these records. It has been decided that future tools will
+effectively ignore these records. It has been decided that future tools
 will seamlessly recognize long-cigar records generated by option `-L`.
 
-**TD;DR**: if you work with ultra-long reads and use tools that only process
+**TL;DR**: if you work with ultra-long reads and use tools that only process
 BAM files, please add option `-L`.
 
 #### <a name="cs"></a>The cs optional tag
@@ -247,35 +292,24 @@ CGATCGATAAATAGAGTAG---GAATAGCA
 CGATCG---AATAGAGTAGGTCGAATtGCA
 ```
 is represented as `:6-ata:10+gtc:4*at:3`, where `:[0-9]+` represents an
-identical block, `-ata` represents a deltion, `+gtc` an insertion and `*at`
+identical block, `-ata` represents a deletion, `+gtc` an insertion and `*at`
 indicates reference base `a` is substituted with a query base `t`. It is
 similar to the `MD` SAM tag but is standalone and easier to parse.
 
 If `--cs=long` is used, the `cs` string also contains identical sequences in
 the alignment. The above example will become
 `=CGATCG-ata=AATAGAGTAG+gtc=GAAT*at=GCA`. The long form of `cs` encodes both
-reference and query sequences in one string.
+reference and query sequences in one string. The `cs` tag also encodes intron
+positions and splicing signals (see the [minimap2 manpage][manpage-cs] for
+details).
 
-#### <a name="eval"></a>Evaluation scripts
+#### <a name="paftools"></a>Working with the PAF format
 
-Minimap2 comes with several (java)scripts for evaluating the accuracy of
-minimap2. These scripts require the [k8][k8] javascript shell to run.
-Recent minimap2 binary release tar-balls contain a copy of k8 executable, a
-single file. Here are a few examples on how to use these scripts:
-
-```sh
-# Generate reads from PBSIM alignment (truth encoded in read names)
-k8 misc/sim-pbsim.js ref.fa.fai pbsim-aln.maf > pbsim-reads.fq
-# Generate reads from mason2 alignment (not tested for simulated SVs)
-k8 misc/sim-mason2.js mason2-aln.sam > mason2-reads.fq
-# Evaluate mapping accuracy with ROC-like curve
-k8 misc/sim-eval.js my-aln.sam.gz > result.txt
-k8 misc/sim-eval.js my-aln.paf.gz > result.txt
-# Collect alignment statistics
-k8 misc/mapstat.js my-aln.sam > result.txt
-# Compare spliced junctions to existing gene annotations
-k8 misc/intron-eval.js anno.gtf my-spliced-aln.sam > result.txt
-```
+Minimap2 also comes with a (java)script [paftools.js](misc/paftools.js) that
+processes alignments in the PAF format. It calls variants from
+assembly-to-reference alignment, lifts over BED files based on alignment,
+converts between formats and provides utilities for various evaluations. For
+details, please see [misc/README.md](misc/README.md).
 
 ### <a name="algo"></a>Algorithm overview
 
@@ -324,15 +358,22 @@ highlighted in bold. The description may help to tune minimap2 parameters.
 ### <a name="help"></a>Getting help
 
 Manpage [minimap2.1][manpage] provides detailed description of minimap2
-command line options and optional tags. If you encounter bugs or have further
-questions or requests, you can raise an issue at the [issue page][issue].
-There is not a specific mailing list for the time being.
+command line options and optional tags. The [FAQ](FAQ.md) page answers several
+frequently asked questions. If you encounter bugs or have further questions or
+requests, you can raise an issue at the [issue page][issue].  There is not a
+specific mailing list for the time being.
 
 ### <a name="cite"></a>Citing minimap2
 
-If you use minimap2 in your work, please consider to cite:
+If you use minimap2 in your work, please cite:
 
-> Li, H. (2017). Minimap2: fast pairwise alignment for long nucleotide sequences. [arXiv:1708.01492][preprint]
+> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.
+> *Bioinformatics*, **34**:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
+
+and/or:
+
+> Li, H. (2021). New strategies to improve minimap2 alignment accuracy.
+> *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
 
 ## <a name="dguide"></a>Developers' Guide
 
@@ -359,9 +400,11 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
   possible to add non-SIMD support, but it would make minimap2 slower by
   several times.
 
-In general, minimap2 is a young project with most code written since June, 2017.
-It may have bugs and room for improvements. Bug reports and suggestions are
-warmly welcomed.
+* Minimap2 does not work with a single query or database sequence ~2
+  billion bases or longer (2,147,483,647 to be exact). The total length of all
+  sequences can well exceed this threshold.
+
+* Minimap2 often misses small exons.
 
 
 
@@ -379,3 +422,8 @@ warmly welcomed.
 [issue]: https://github.com/lh3/minimap2/issues
 [k8]: https://github.com/attractivechaos/k8
 [manpage]: https://lh3.github.io/minimap2/minimap2.html
+[manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10
+[doi]: https://doi.org/10.1093/bioinformatics/bty191
+[doi2]: https://doi.org/10.1093/bioinformatics/btab705
+[simde]: https://github.com/nemequ/simde
+[unimap]: https://github.com/lh3/unimap

bseq.c

@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <assert.h>
+#define __STDC_LIMIT_MACROS
 #include "bseq.h"
 #include "kvec.h"
 #include "kseq.h"
@@ -14,7 +15,7 @@ unsigned char seq_comp_table[256] = {
 	 48,  49,  50,	51,	 52,  53,  54,	55,	 56,  57,  58,	59,	 60,  61,  62,	63,
 	 64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
 	'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z',	91,	 92,  93,  94,	95,
-	 64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+	 96, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
 	'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
 	128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
 	144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
@@ -38,7 +39,7 @@ mm_bseq_file_t *mm_bseq_open(const char *fn)
 {
 	mm_bseq_file_t *fp;
 	gzFile f;
-	f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(0, "r");
 	if (f == 0) return 0;
 	fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));
 	fp->fp = f;
@@ -53,21 +54,33 @@ void mm_bseq_close(mm_bseq_file_t *fp)
 	free(fp);
 }
 
-static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual)
+static inline char *kstrdup(const kstring_t *s)
+{
+	char *t;
+	t = (char*)malloc(s->l + 1);
+	memcpy(t, s->s, s->l + 1);
+	return t;
+}
+
+static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_comment)
 {
 	int i;
-	s->name = strdup(ks->name.s);
-	s->seq = strdup(ks->seq.s);
-	for (i = 0; i < ks->seq.l; ++i) // convert U to T
+	if (ks->name.l == 0)
+		fprintf(stderr, "[WARNING]\033[1;31m empty sequence name in the input.\033[0m\n");
+	s->name = kstrdup(&ks->name);
+	s->seq = kstrdup(&ks->seq);
+	for (i = 0; i < (int)ks->seq.l; ++i) // convert U to T
 		if (s->seq[i] == 'u' || s->seq[i] == 'U')
 			--s->seq[i];
-	s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
+	s->qual = with_qual && ks->qual.l? kstrdup(&ks->qual) : 0;
+	s->comment = with_comment && ks->comment.l? kstrdup(&ks->comment) : 0;
 	s->l_seq = ks->seq.l;
 }
 
-mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int frag_mode, int *n_)
+mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int *n_)
 {
 	int64_t size = 0;
+	int ret;
 	kvec_t(mm_bseq1_t) a = {0,0,0};
 	kseq_t *ks = fp->ks;
 	*n_ = 0;
@@ -77,17 +90,17 @@ mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
 		size = fp->s.l_seq;
 		memset(&fp->s, 0, sizeof(mm_bseq1_t));
 	}
-	while (kseq_read(ks) >= 0) {
+	while ((ret = kseq_read(ks)) >= 0) {
 		mm_bseq1_t *s;
 		assert(ks->seq.l <= INT32_MAX);
 		if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
 		kv_pushp(mm_bseq1_t, 0, a, &s);
-		kseq2bseq(ks, s, with_qual);
+		kseq2bseq(ks, s, with_qual, with_comment);
 		size += s->l_seq;
 		if (size >= chunk_size) {
 			if (frag_mode && a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
-				while (kseq_read(ks) >= 0) {
-					kseq2bseq(ks, &fp->s, with_qual);
+				while ((ret = kseq_read(ks)) >= 0) {
+					kseq2bseq(ks, &fp->s, with_qual, with_comment);
 					if (mm_qname_same(fp->s.name, a.a[a.n-1].name)) {
 						kv_push(mm_bseq1_t, 0, a, fp->s);
 						memset(&fp->s, 0, sizeof(mm_bseq1_t));
@@ -97,16 +110,25 @@ mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
 			break;
 		}
 	}
+	if (ret < -1) {
+		if (a.n) fprintf(stderr, "[WARNING]\033[1;31m failed to parse the FASTA/FASTQ record next to '%s'. Continue anyway.\033[0m\n", a.a[a.n-1].name);
+		else fprintf(stderr, "[WARNING]\033[1;31m failed to parse the first FASTA/FASTQ record. Continue anyway.\033[0m\n");
+	}
 	*n_ = a.n;
 	return a.a;
 }
 
-mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
+mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int frag_mode, int *n_)
+{
+	return mm_bseq_read3(fp, chunk_size, with_qual, 0, frag_mode, n_);
+}
+
+mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int *n_)
 {
 	return mm_bseq_read2(fp, chunk_size, with_qual, 0, n_);
 }
 
-mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_)
+mm_bseq1_t *mm_bseq_read_frag2(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_)
 {
 	int i;
 	int64_t size = 0;
@@ -114,15 +136,20 @@ mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int
 	*n_ = 0;
 	if (n_fp < 1) return 0;
 	while (1) {
+		int n_read = 0;
 		for (i = 0; i < n_fp; ++i)
-			if (kseq_read(fp[i]->ks) < 0)
-				break;
-		if (i != n_fp) break; // some file reaches the end
+			if (kseq_read(fp[i]->ks) >= 0)
+				++n_read;
+		if (n_read < n_fp) {
+			if (n_read > 0)
+				fprintf(stderr, "[W::%s]\033[1;31m query files have different number of records; extra records skipped.\033[0m\n", __func__);
+			break; // some file reaches the end
+		}
 		if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
 		for (i = 0; i < n_fp; ++i) {
 			mm_bseq1_t *s;
 			kv_pushp(mm_bseq1_t, 0, a, &s);
-			kseq2bseq(fp[i]->ks, s, with_qual);
+			kseq2bseq(fp[i]->ks, s, with_qual, with_comment);
 			size += s->l_seq;
 		}
 		if (size >= chunk_size) break;
@@ -131,6 +158,11 @@ mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int
 	return a.a;
 }
 
+mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int *n_)
+{
+	return mm_bseq_read_frag2(n_fp, fp, chunk_size, with_qual, 0, n_);
+}
+
 int mm_bseq_eof(mm_bseq_file_t *fp)
 {
 	return (ks_eof(fp->ks->f) && fp->s.seq == 0);

bseq.h

@@ -13,14 +13,16 @@ typedef struct mm_bseq_file_s mm_bseq_file_t;
 
 typedef struct {
 	int l_seq, rid;
-	char *name, *seq, *qual;
+	char *name, *seq, *qual, *comment;
 } mm_bseq1_t;
 
 mm_bseq_file_t *mm_bseq_open(const char *fn);
 void mm_bseq_close(mm_bseq_file_t *fp);
-mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int chunk_size, int with_qual, int frag_mode, int *n_);
-mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_);
-mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int chunk_size, int with_qual, int *n_);
+mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int *n_);
+mm_bseq1_t *mm_bseq_read2(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int frag_mode, int *n_);
+mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int64_t chunk_size, int with_qual, int *n_);
+mm_bseq1_t *mm_bseq_read_frag2(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_);
+mm_bseq1_t *mm_bseq_read_frag(int n_fp, mm_bseq_file_t **fp, int64_t chunk_size, int with_qual, int *n_);
 int mm_bseq_eof(mm_bseq_file_t *fp);
 
 extern unsigned char seq_nt4_table[256];

chain.c

@@ -1,157 +0,0 @@
-#include <stdint.h>
-#include <string.h>
-#include <stdio.h>
-#include "minimap.h"
-#include "mmpriv.h"
-#include "kalloc.h"
-
-static const char LogTable256[256] = {
-#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
-	-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
-	LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),
-	LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7)
-};
-
-static inline int ilog2_32(uint32_t v)
-{
-	register uint32_t t, tt;
-	if ((tt = v>>16)) return (t = tt>>8) ? 24 + LogTable256[t] : 16 + LogTable256[tt];
-	return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
-}
-
-mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
-{ // TODO: make sure this works when n has more than 32 bits
-	int32_t k, *f, *p, *t, *v, n_u, n_v;
-	int64_t i, j, st = 0;
-	uint64_t *u, *u2, sum_qspan = 0;
-	float avg_qspan;
-	mm128_t *b, *w;
-
-	if (_u) *_u = 0, *n_u_ = 0;
-	f = (int32_t*)kmalloc(km, n * 4);
-	p = (int32_t*)kmalloc(km, n * 4);
-	t = (int32_t*)kmalloc(km, n * 4);
-	v = (int32_t*)kmalloc(km, n * 4);
-	memset(t, 0, n * 4);
-
-	for (i = 0; i < n; ++i) sum_qspan += a[i].y>>32&0xff;
-	avg_qspan = (float)sum_qspan / n;
-
-	// fill the score and backtrack arrays
-	for (i = 0; i < n; ++i) {
-		uint64_t ri = a[i].x;
-		int64_t max_j = -1;
-		int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32&0xff; // NB: only 8 bits of span is used!!!
-		int32_t max_f = q_span, n_skip = 0, min_d;
-		int32_t sidi = (a[i].y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
-		while (st < i && ri - a[st].x > max_dist_x) ++st;
-		for (j = i - 1; j >= st; --j) {
-			int64_t dr = ri - a[j].x;
-			int32_t dq = qi - (int32_t)a[j].y, dd, sc, log_dd;
-			int32_t sidj = (a[j].y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
-			if ((sidi == sidj && dr == 0) || dq <= 0) continue; // don't skip if an anchor is used by multiple segments; see below
-			if ((sidi == sidj && dq > max_dist_y) || dq > max_dist_x) continue;
-			dd = dr > dq? dr - dq : dq - dr;
-			if (sidi == sidj && dd > bw) continue;
-			if (n_segs > 1 && !is_cdna && sidi == sidj && dr > max_dist_y) continue;
-			min_d = dq < dr? dq : dr;
-			sc = min_d > q_span? q_span : dq < dr? dq : dr;
-			log_dd = dd? ilog2_32(dd) : 0;
-			if (is_cdna || sidi != sidj) {
-				int c_log, c_lin;
-				c_lin = (int)(dd * .01 * avg_qspan);
-				c_log = log_dd;
-				if (sidi != sidj && dr == 0) ++sc; // possibly due to overlapping paired ends; give a minor bonus
-				else if (dr > dq || sidi != sidj) sc -= c_lin < c_log? c_lin : c_log;
-				else sc -= c_lin + (c_log>>1);
-			} else sc -= (int)(dd * .01 * avg_qspan) + (log_dd>>1);
-			sc += f[j];
-			if (sc > max_f) {
-				max_f = sc, max_j = j;
-				if (n_skip > 0) --n_skip;
-			} else if (t[j] == i) {
-				if (++n_skip > max_skip)
-					break;
-			}
-			if (p[j] >= 0) t[p[j]] = i;
-		}
-		f[i] = max_f, p[i] = max_j;
-		v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
-	}
-
-	// find the ending positions of chains
-	memset(t, 0, n * 4);
-	for (i = 0; i < n; ++i)
-		if (p[i] >= 0) t[p[i]] = 1;
-	for (i = n_u = 0; i < n; ++i)
-		if (t[i] == 0 && v[i] >= min_sc)
-			++n_u;
-	if (n_u == 0) {
-		kfree(km, a); kfree(km, f); kfree(km, p); kfree(km, t); kfree(km, v);
-		return 0;
-	}
-	u = (uint64_t*)kmalloc(km, n_u * 8);
-	for (i = n_u = 0; i < n; ++i) {
-		if (t[i] == 0 && v[i] >= min_sc) {
-			j = i;
-			while (j >= 0 && f[j] < v[j]) j = p[j]; // find the peak that maximizes f[]
-			if (j < 0) j = i; // TODO: this should really be assert(j>=0)
-			u[n_u++] = (uint64_t)f[j] << 32 | j;
-		}
-	}
-	radix_sort_64(u, u + n_u);
-	for (i = 0; i < n_u>>1; ++i) { // reverse, s.t. the highest scoring chain is the first
-		uint64_t t = u[i];
-		u[i] = u[n_u - i - 1], u[n_u - i - 1] = t;
-	}
-
-	// backtrack
-	memset(t, 0, n * 4);
-	for (i = n_v = k = 0; i < n_u; ++i) { // starting from the highest score
-		int32_t n_v0 = n_v, k0 = k;
-		j = (int32_t)u[i];
-		do {
-			v[n_v++] = j;
-			t[j] = 1;
-			j = p[j];
-		} while (j >= 0 && t[j] == 0);
-		if (j < 0) {
-			if (n_v - n_v0 >= min_cnt) u[k++] = u[i]>>32<<32 | (n_v - n_v0);
-		} else if ((int32_t)(u[i]>>32) - f[j] >= min_sc) {
-			if (n_v - n_v0 >= min_cnt) u[k++] = ((u[i]>>32) - f[j]) << 32 | (n_v - n_v0);
-		}
-		if (k0 == k) n_v = n_v0; // no new chain added, reset
-	}
-	*n_u_ = n_u = k, *_u = u; // NB: note that u[] may not be sorted by score here
-
-	// free temporary arrays
-	kfree(km, f); kfree(km, p); kfree(km, t);
-
-	// write the result to b[]
-	b = (mm128_t*)kmalloc(km, n_v * sizeof(mm128_t));
-	for (i = 0, k = 0; i < n_u; ++i) {
-		int32_t k0 = k, ni = (int32_t)u[i];
-		for (j = 0; j < ni; ++j)
-			b[k] = a[v[k0 + (ni - j - 1)]], ++k;
-	}
-	kfree(km, v);
-
-	// sort u[] and a[] by a[].x, such that adjacent chains may be joined (required by mm_join_long)
-	w = (mm128_t*)kmalloc(km, n_u * sizeof(mm128_t));
-	for (i = k = 0; i < n_u; ++i) {
-		w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
-		k += (int32_t)u[i];
-	}
-	radix_sort_128x(w, w + n_u);
-	u2 = (uint64_t*)kmalloc(km, n_u * 8);
-	for (i = k = 0; i < n_u; ++i) {
-		int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
-		u2[i] = u[j];
-		memcpy(&a[k], &b[w[i].y>>32], n * sizeof(mm128_t));
-		k += n;
-	}
-	memcpy(u, u2, n_u * 8);
-	memcpy(b, a, k * sizeof(mm128_t)); // write _a_ to _b_ and deallocate _a_ because _a_ is oversized, sometimes a lot
-	kfree(km, a); kfree(km, w); kfree(km, u2);
-	return b;
-}

code_of_conduct.md

@@ -0,0 +1,30 @@
+## Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all
+people who contribute through reporting issues, posting feature requests,
+updating documentation, submitting pull requests or patches, and other
+activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual
+language or imagery, derogatory comments or personal attacks, trolling, public
+or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct. Project maintainers or
+contributors who do not follow the Code of Conduct may be removed from the
+project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by opening an issue or contacting the maintainer via email.
+
+This Code of Conduct is adapted from the [Contributor Covenant][cc], [version
+1.0.0][v1].
+
+[cc]: http://contributor-covenant.org/
+[v1]: http://contributor-covenant.org/version/1/0/0/

cookbook.md

@@ -0,0 +1,243 @@
+## Table of Contents
+
+- [Introduction & Installation](#intro)
+- [Mapping Genomic Reads](#map-reads)
+  * [Mapping long reads](#map-pb)
+  * [Mapping Illumina paired-end reads](#map-sr)
+  * [Evaluating mapping accuracy with simulated reads (for developers)](#mapeval)
+- [Mapping Long RNA-seq Reads](#map-rna)
+  * [Mapping Nanopore 2D cDNA reads](#map-ont-cdna-2d)
+  * [Mapping Nanopore direct-RNA reads](#map-direct-rna)
+  * [Mapping PacBio Iso-seq reads](#map-iso-seq)
+- [Full-Genome Alignment](#genome-aln)
+  * [Intra-species assembly alignment](#asm-to-ref)
+  * [Cross-species full-genome alignment](#x-species)
+  * [Eyeballing alignment](#view-aln)
+  * [Calling variants from assembly-to-reference alignment](#asm-var)
+  * [Constructing self-homology map](#hom-map)
+  * [Lift Over (for developers)](#liftover)
+- [Read Overlap](#read-overlap)
+  * [Long-read overlap](#long-read-overlap)
+  * [Evaluating overlap sensitivity (for developers)](#ov-eval)
+
+## <a name="intro"></a>Introduction & Installation
+
+This cookbook walks you through a variety of applications of minimap2 and its
+companion script `paftools.js`. All data here are freely available from the
+minimap2 release page at version tag [v2.10][v2.10]. Some examples only work
+with v2.10 or later.
+
+To acquire the data used in this cookbook and to install minimap2 and paftools,
+please follow the command lines below:
+```sh
+# install minimap2 executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.31/minimap2-2.31_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.31_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+export PATH="$PATH:"`pwd`                               # put the current directory on PATH
+# download example datasets
+curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
+```
+
+## <a name="map-reads"></a>Mapping Genomic Reads
+
+### <a name="map-pb"></a>Mapping long reads
+```sh
+minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
+```
+Alternatively, you can create a minimap2 index first and then map:
+```sh
+minimap2 -x map-pb -d ecoli-pb.mmi ecoli_ref.fa                      # create an index
+minimap2 -ax map-pb ecoli-pb.mmi ecoli_p6_25x_canu.fa > mapped.sam
+```
+This will save you a couple of minutes when you map against the human genome.
+**HOWEVER**, key algorithm parameters such as the k-mer length and window
+size can't be changed after indexing. Minimap2 will give you a warning if
+parameters used in a pre-built index doesn't match parameters on the command
+line. **Please always make sure you are using an intended pre-built index.**
+
+### <a name="map-sr"></a>Mapping Illumina paired-end reads:
+```sh
+minimap2 -ax sr -t4 ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam
+```
+
+### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads (for developers)
+```sh
+minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval -
+```
+The output is:
+```
+Q       60      19712   0       0.000000000     19712
+Q       0       282     219     0.010953286     19994
+U       6
+```
+where a `U`-line gives the number of unmapped reads (for SAM input only); a
+`Q`-line gives:
+
+1. Mapping quality (mapQ) threshold
+2. Number of mapped reads between this threshold and the previous mapQ threshold.
+3. Number of wrong mappings in the same mapQ interval
+4. Accumulative mapping error rate
+5. Accumulative number of mappings
+
+For `paftools.js mapeval` to work, you need to encode the true read positions
+in read names in the right format. For [pbsim2][pbsim] and [mason2][mason2], we
+provide scripts to generate the right format. Simulated reads in this cookbook
+were created with the following command lines:
+```sh
+# in the pbsim2 source code directory:
+src/pbsim --depth 1 --length-min 5000 --length-mean 20000 --accuracy-mean 0.95 --hmm_model data/R94.model ../ecoli_ref.fa
+paftools.js pbsim2fq ../ecoli_ref.fa.fai sd_0001.maf > ../ecoli_pbsim.fa
+
+# mason2 simulation
+mason_simulator --illumina-prob-mismatch-scale 2.5 -ir ecoli_ref.fa -n 10000 -o tmp-l.fq -or tmp-r.fq -oa tmp.sam
+paftools.js mason2fq tmp.sam | seqtk seq -1 > ecoli_mason_1.fq
+paftools.js mason2fq tmp.sam | seqtk seq -2 > ecoli_mason_2.fq
+```
+
+
+
+## <a name="map-rna"></a>Mapping Long RNA-seq Reads
+
+### <a name="map-ont-cdna-2d"></a>Mapping Nanopore 2D cDNA reads
+```sh
+minimap2 -ax splice SIRV_E2.fa SIRV_ont-cdna.fa > aln.sam
+```
+You can compare the alignment to the true annotations with:
+```sh
+paftools.js junceval SIRV_E2C.gtf aln.sam
+```
+It gives the percentage of introns found in the annotation. For SIRV data, it
+is possible to achieve higher junction accuracy with
+```sh
+minimap2 -ax splice --splice-flank=no SIRV_E2.fa SIRV_ont-cdna.fa | paftools.js junceval SIRV_E2C.gtf
+```
+This is because minimap2 models one additional evolutionarily conserved base
+around a canonical junction, but SIRV doesn't honor this signal. Option
+`--splice-flank=no` asks minimap2 no to model this additional base.
+
+In the output a tag `ts:A:+` indicates that the read strand is the same as the
+transcript strand; `ts:A:-` indicates the read strand is opposite to the
+transcript strand. This tag is inferred from the GT-AG signal and is thus only
+available to spliced reads.
+
+### <a name="map-direct-rna"></a>Mapping Nanopore direct-RNA reads
+```sh
+minimap2 -ax splice -k14 -uf SIRV_E2.fa SIRV_ont-drna.fa > aln.sam
+```
+Direct-RNA reads are noisier, so we use a shorter k-mer for improved
+sensitivity. Here, option `-uf` forces minimap2 to map reads to the forward
+transcript strand only because direct-RNA reads are stranded. Again, applying
+`--splice-flank=no` helps junction accuracy for SIRV data.
+
+### <a name="map-iso-seq"></a>Mapping PacBio Iso-seq reads
+```sh
+minimap2 -ax splice -uf -C5 SIRV_E2.fa SIRV_iso-seq.fq > aln.sam
+```
+Option `-C5` reduces the penalty on non-canonical splicing sites. It helps
+to align such sites correctly for data with low error rate such as Iso-seq
+reads and traditional cDNAs. On this example, minimap2 makes one junction
+error. Applying `--splice-flank=no` fixes this alignment error.
+
+Note that the command line above is optimized for the final Iso-seq reads.
+PacBio's Iso-seq pipeline produces intermediate sequences at varying quality.
+For example, some intermediate reads are not stranded. For these reads, option
+`-uf` will lead to more errors. Please revise the minimap2 command line
+accordingly.
+
+
+
+## <a name="genome-aln"></a>Full-Genome Alignment
+
+### <a name="asm-to-ref"></a>Intra-species assembly alignment
+```sh
+# option "--cs" is recommended as paftools.js may need it
+minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa > ecoli_canu.paf
+```
+Here `ecoli_canu.fa` is the Canu assembly of `ecoli_p6_25x_canu.fa`. This
+command line outputs alignments in the [PAF format][paf]. Use `-a` instead of
+`-c` to get output in the SAM format.
+
+### <a name="x-species"></a>Cross-species full-genome alignment
+```sh
+minimap2 -cx asm20 --cs ecoli_ref.fa ecoli_O104:H4.fa > ecoli_O104:H4.paf
+sort -k6,6 -k8,8n ecoli_O104:H4.paf | paftools.js call -f ecoli_ref.fa -L10000 -l1000 - > out.vcf
+```
+Minimap2 has three presets for full-genome alignment: "asm5" for sequence
+divergence below 1%, "asm10" for divergence around a couple of percent and
+"asm20" for divergence not more than 10%. In theory, with the right setting,
+minimap2 should work for sequence pairs with sequence divergence up to ~15%,
+but this has not been carefully evaluated.
+
+### <a name="view-aln"></a>Eyeballing alignment
+```sh
+# option "--cs" required; minimap2-r741 or higher required for the "asm20" preset
+minimap2 -cx asm20 --cs ecoli_ref.fa ecoli_O104:H4.fa | paftools.js view - | less -S
+```
+This prints the alignment in a BLAST-like format.
+
+### <a name="asm-var"></a>Calling variants from assembly-to-reference alignment
+```sh
+# don't forget the "--cs" option; otherwise it doesn't work
+minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa \
+  | sort -k6,6 -k8,8n \
+  | paftools.js call -f ecoli_ref.fa - > out.vcf
+```
+Without option `-f`, `paftools.js call` outputs in a custom format. In this
+format, lines starting with `R` give the regions covered by one contig only.
+This information is not available in the VCF output.
+
+### <a name="hom-map"></a>Constructing self-homology map
+```sh
+minimap2 -DP -k19 -w19 -m200 ecoli_ref.fa ecoli_ref.fa > out.paf
+```
+Option `-D` asks minimap2 to ignore anchors from perfect self match and `-P`
+outputs all chains. For large nomes, we don't recommend to perform base-level
+alignment (with `-c`, `-a` or `--cs`) when `-P` is applied. This is because
+base-alignment is slow and occasionally gives wrong alignments close to the
+diagonal of a dotter plot. For E. coli, though, base-alignment is still fast.
+
+### <a name="liftover"></a>Lift over (for developers)
+```sh
+minimap2 -cx asm5 --cs ecoli_ref.fa ecoli_canu.fa > ecoli_canu.paf
+echo -e 'tig00000001\t200000\t300000' | paftools.js liftover ecoli_canu.paf -
+```
+This lifts over a region on query sequences to one or multiple regions on
+reference sequences. Note that this paftools.js command may not be efficient
+enough to lift millions of regions.
+
+
+
+## <a name="read-overlap"></a>Read Overlap
+
+### <a name="long-read-overlap"></a>Long read overlap
+```sh
+# For pacbio reads:
+minimap2 -x ava-pb ecoli_p6_25x_canu.fa ecoli_p6_25x_canu.fa > overlap.paf
+# For Nanopore reads (ava-ont also works with PacBio but not as good):
+minimap2 -x ava-ont -r 10000 ecoli_p6_25x_canu.fa ecoli_p6_25x_canu.fa > overlap.paf
+# If you have miniasm installed:
+miniasm -f ecoli_p6_25x_canu.fa overlap.paf > asm.gfa
+```
+Here we explicitly applied `-r 10000`. We are considering to set this as the
+default for the `ava-ont` mode as this seems to improve the contiguity for
+nanopore read assembly (Loman, personal communication).
+
+*Minimap2 doesn't work well with short-read overlap.*
+
+### <a name="ov-eval"></a>Evaluating overlap sensitivity (for developers)
+
+```sh
+# read to reference mapping
+minimap2 -cx map-pb ecoli_ref.fa ecoli_p6_25x_canu.fa > to-ref.paf
+# evaluate overlap sensitivity
+sort -k6,6 -k8,8n to-ref.paf | paftools.js ov-eval - overlap.paf
+```
+You can see that for PacBio reads, minimap2 achieves higher overlap sensitivity
+with `-x ava-pb` (99% vs 93% with `-x ava-ont`).
+
+
+
+[pbsim]: https://github.com/yukiteruono/pbsim2
+[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
+[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
+[v2.10]: https://github.com/lh3/minimap2/releases/tag/v2.10

esterr.c

@@ -59,6 +59,6 @@ void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const
 		n_tot = en - st + 1;
 		if (r->qs > avg_k && r->rs > avg_k) ++n_tot;
 		if (qlen - r->qs > avg_k && l_ref - r->re > avg_k) ++n_tot;
-		r->div = logf((float)n_tot / n_match) / avg_k;
+		r->div = n_match >= n_tot? 0.0f : (float)(1.0 - pow((double)n_match / n_tot, 1.0 / avg_k));
 	}
 }

example.c

@@ -35,6 +35,8 @@ int main(int argc, char *argv[])
 	while ((mi = mm_idx_reader_read(r, n_threads)) != 0) { // traverse each part of the index
 		mm_mapopt_update(&mopt, mi); // this sets the maximum minimizer occurrence; TODO: set a better default in mm_mapopt_init()!
 		mm_tbuf_t *tbuf = mm_tbuf_init(); // thread buffer; for multi-threading, allocate one tbuf for each thread
+		gzrewind(f);
+		kseq_rewind(ks);
 		while (kseq_read(ks) >= 0) { // each kseq_read() call reads one query sequence
 			mm_reg1_t *reg;
 			int j, i, n_reg;
@@ -45,7 +47,7 @@ int main(int argc, char *argv[])
 				printf("%s\t%d\t%d\t%d\t%c\t", ks->name.s, ks->seq.l, r->qs, r->qe, "+-"[r->rev]);
 				printf("%s\t%d\t%d\t%d\t%d\t%d\t%d\tcg:Z:", mi->seq[r->rid].name, mi->seq[r->rid].len, r->rs, r->re, r->mlen, r->blen, r->mapq);
 				for (i = 0; i < r->p->n_cigar; ++i) // IMPORTANT: this gives the CIGAR in the aligned regions. NO soft/hard clippings!
-					printf("%d%c", r->p->cigar[i]>>4, "MIDSHN"[r->p->cigar[i]&0xf]);
+					printf("%d%c", r->p->cigar[i]>>4, MM_CIGAR_STR[r->p->cigar[i]&0xf]);
 				putchar('\n');
 				free(r->p);
 			}

format.c

@@ -79,11 +79,11 @@ static char *mm_escape(char *s)
 	return s;
 }
 
-static void sam_write_rg_line(kstring_t *str, const char *s)
+static int sam_write_rg_line(kstring_t *str, const char *s)
 {
 	char *p, *q, *r, *rg_line = 0;
 	memset(mm_rg_id, 0, 256);
-	if (s == 0) return;
+	if (s == 0) return 0;
 	if (strstr(s, "@RG") != s) {
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line is not started with @RG\n");
 		goto err_set_rg;
@@ -92,7 +92,8 @@ static void sam_write_rg_line(kstring_t *str, const char *s)
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n");
 		goto err_set_rg;
 	}
-	rg_line = strdup(s);
+	rg_line = (char*)malloc(strlen(s) + 1);
+	strcpy(rg_line, s);
 	mm_escape(rg_line);
 	if ((p = strstr(rg_line, "\tID:")) == 0) {
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] no ID within the read group line\n");
@@ -107,20 +108,24 @@ static void sam_write_rg_line(kstring_t *str, const char *s)
 	for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
 		*r++ = *q;
 	mm_sprintf_lite(str, "%s\n", rg_line);
+	return 0;
 
 err_set_rg:
 	free(rg_line);
+	return -1;
 }
 
-void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
+int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int argc, char *argv[])
 {
 	kstring_t str = {0,0,0};
+	int ret = 0;
+	mm_sprintf_lite(&str, "@HD\tVN:1.6\tSO:unsorted\tGO:query\n");
 	if (idx) {
 		uint32_t i;
 		for (i = 0; i < idx->n_seq; ++i)
-			printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
+			mm_sprintf_lite(&str, "@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
 	}
-	if (rg) sam_write_rg_line(&str, rg);
+	if (rg) ret = sam_write_rg_line(&str, rg);
 	mm_sprintf_lite(&str, "@PG\tID:minimap2\tPN:minimap2");
 	if (ver) mm_sprintf_lite(&str, "\tVN:%s", ver);
 	if (argc > 1) {
@@ -129,36 +134,57 @@ void mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int
 		for (i = 1; i < argc; ++i)
 			mm_sprintf_lite(&str, " %s", argv[i]);
 	}
-	mm_sprintf_lite(&str, "\n");
-	fputs(str.s, stdout);
+	mm_err_puts(str.s);
 	free(str.s);
+	return ret;
 }
 
-static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden)
+static void write_indel_ds(kstring_t *str, int64_t len, const uint8_t *seq, int64_t ll, int64_t lr) // write an indel to ds; adapted from minigraph
 {
-	extern unsigned char seq_nt4_table[256];
-	int i, q_off, t_off;
-	uint8_t *qseq, *tseq;
-	char *tmp;
-	if (r->p == 0) return;
-	mm_sprintf_lite(s, "\tcs:Z:");
-	qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
-	tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
-	tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
-	mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
-	if (!r->rev) {
-		for (i = r->qs; i < r->qe; ++i)
-			qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
+	int64_t i;
+	if (ll + lr >= len) {
+		mm_sprintf_lite(str, "[");
+		for (i = 0; i < len; ++i)
+			mm_sprintf_lite(str, "%c", "acgtn"[seq[i]]);
+		mm_sprintf_lite(str, "]");
 	} else {
-		for (i = r->qs; i < r->qe; ++i) {
-			uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
-			qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
+		int64_t k = 0;
+		if (ll > 0) {
+			mm_sprintf_lite(str, "[");
+			for (i = 0; i < ll; ++i)
+				mm_sprintf_lite(str, "%c", "acgtn"[seq[k+i]]);
+			mm_sprintf_lite(str, "]");
+			k += ll;
+		}
+		for (i = 0; i < len - lr - ll; ++i)
+			mm_sprintf_lite(str, "%c", "acgtn"[seq[k+i]]);
+		k += len - lr - ll;
+		if (lr > 0) {
+			mm_sprintf_lite(str, "[");
+			for (i = 0; i < lr; ++i)
+				mm_sprintf_lite(str, "%c", "acgtn"[seq[k+i]]);
+			mm_sprintf_lite(str, "]");
 		}
 	}
-	for (i = q_off = t_off = 0; i < r->p->n_cigar; ++i) {
+}
+
+static void write_cs_ds_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp, int no_iden, int is_ds, int write_tag)
+{
+	int i, q_off, t_off, q_len = 0, t_len = 0;
+	if (write_tag) mm_sprintf_lite(s, "\t%cs:Z:", is_ds? 'd' : 'c');
+	for (i = 0; i < (int)r->p->n_cigar; ++i) {
+		int op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
+		if (op == MM_CIGAR_MATCH || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH)
+			q_len += len, t_len += len;
+		else if (op == MM_CIGAR_INS)
+			q_len += len;
+		else if (op == MM_CIGAR_DEL || op == MM_CIGAR_N_SKIP)
+			t_len += len;
+	}
+	for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) {
 		int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
-		assert(op >= 0 && op <= 3);
-		if (op == 0) {
+		assert((op >= MM_CIGAR_MATCH && op <= MM_CIGAR_N_SKIP) || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH);
+		if (op == MM_CIGAR_MATCH || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH) {
 			int l_tmp = 0;
 			for (j = 0; j < len; ++j) {
 				if (qseq[q_off + j] != tseq[t_off + j]) {
@@ -179,17 +205,45 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
 				} else mm_sprintf_lite(s, ":%d", l_tmp);
 			}
 			q_off += len, t_off += len;
-		} else if (op == 1) {
-			for (j = 0, tmp[len] = 0; j < len; ++j)
-				tmp[j] = "acgtn"[qseq[q_off + j]];
-			mm_sprintf_lite(s, "+%s", tmp);
+		} else if (op == MM_CIGAR_INS) {
+			if (is_ds) {
+				int z, ll, lr, y = q_off;
+				for (z = 1; z <= len; ++z)
+					if (y - z < 0 || qseq[y + len - z] != qseq[y - z])
+						break;
+				lr = z - 1;
+				for (z = 0; z < len; ++z)
+					if (y + len + z >= q_len || qseq[y + len + z] != qseq[y + z])
+						break;
+				ll = z;
+				mm_sprintf_lite(s, "+");
+				write_indel_ds(s, len, &qseq[y], ll, lr);
+			} else {
+				for (j = 0, tmp[len] = 0; j < len; ++j)
+					tmp[j] = "acgtn"[qseq[q_off + j]];
+				mm_sprintf_lite(s, "+%s", tmp);
+			}
 			q_off += len;
-		} else if (op == 2) {
-			for (j = 0, tmp[len] = 0; j < len; ++j)
-				tmp[j] = "acgtn"[tseq[t_off + j]];
-			mm_sprintf_lite(s, "-%s", tmp);
+		} else if (op == MM_CIGAR_DEL) {
+			if (is_ds) {
+				int z, ll, lr, x = t_off;
+				for (z = 1; z <= len; ++z)
+					if (x - z < 0 || tseq[x + len - z] != tseq[x - z])
+						break;
+				lr = z - 1;
+				for (z = 0; z < len; ++z)
+					if (x + len + z >= t_len || tseq[x + z] != tseq[x + len + z])
+						break;
+				ll = z;
+				mm_sprintf_lite(s, "-");
+				write_indel_ds(s, len, &tseq[x], ll, lr);
+			} else {
+				for (j = 0, tmp[len] = 0; j < len; ++j)
+					tmp[j] = "acgtn"[tseq[t_off + j]];
+				mm_sprintf_lite(s, "-%s", tmp);
+			}
 			t_off += len;
-		} else {
+		} else { // intron
 			assert(len >= 2);
 			mm_sprintf_lite(s, "~%c%c%d%c%c", "acgtn"[tseq[t_off]], "acgtn"[tseq[t_off+1]],
 				len, "acgtn"[tseq[t_off+len-2]], "acgtn"[tseq[t_off+len-1]]);
@@ -197,48 +251,220 @@ static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_
 		}
 	}
 	assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
+}
+
+static inline void revcomp_splice(uint8_t s[2])
+{
+	uint8_t c = s[1] < 4? 3 - s[1] : 4;
+	s[1] = s[0] < 4? 3 - s[0] : 4;
+	s[0] = c;
+}
+
+void mm_write_junc(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
+{
+	int32_t i, t_off, swritten = 0;
+	s->l = 0;
+	if (!r->is_spliced || r->p == 0) return; // no junctions
+	if (r->p->trans_strand != 1 && r->p->trans_strand != 2) return; // no preferred strand
+	for (i = 0, t_off = r->rs; i < (int)r->p->n_cigar; ++i) {
+		int op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
+		if (op == MM_CIGAR_MATCH || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH || op == MM_CIGAR_DEL) {
+			t_off += len;
+		} else if (op == MM_CIGAR_N_SKIP) { // intron
+			uint8_t donor[2], acceptor[2];
+			int32_t score1 = 0, score2 = 0, rev;
+			assert(len >= 2);
+			rev = (r->p->trans_strand == 2) ^ r->rev;
+			if (!rev) {
+				mm_idx_getseq(mi, r->rid, t_off, t_off + 2, donor);
+				mm_idx_getseq(mi, r->rid, t_off + len - 2, t_off + len, acceptor);
+			} else {
+				mm_idx_getseq(mi, r->rid, t_off, t_off + 2, acceptor);
+				mm_idx_getseq(mi, r->rid, t_off + len - 2, t_off + len, donor);
+				revcomp_splice(donor);
+				revcomp_splice(acceptor);
+			}
+			//fprintf(stderr, "%c%c-%c%c\n", "ACGTN"[donor[0]], "ACGTN"[donor[1]], "ACGTN"[acceptor[0]], "ACGTN"[acceptor[1]]);
+			if (donor[0] == 2 && donor[1] == 3) score1 = 3;
+			else if (donor[0] == 2 && donor[1] == 1) score1 = 2;
+			else if (donor[0] == 0 && donor[1] == 3) score1 = 1;
+			if (acceptor[0] == 0 && acceptor[1] == 2) score2 = 3;
+			else if (acceptor[0] == 0 && acceptor[1] == 1) score2 = 1;
+			if (swritten) mm_sprintf_lite(s, "\n");
+			else swritten = 1;
+			mm_sprintf_lite(s, "%s\t%d\t%d\t%s\t%d\t%c", mi->seq[r->rid].name, t_off, t_off + len, t->name, score1 + score2, "+-"[rev]);
+			t_off += len;
+		}
+	}
+	assert(t_off == r->re);
+}
+
+static void write_MD_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq, const mm_reg1_t *r, char *tmp, int write_tag)
+{
+	int i, q_off, t_off, l_MD = 0;
+	if (write_tag) mm_sprintf_lite(s, "\tMD:Z:");
+	for (i = q_off = t_off = 0; i < (int)r->p->n_cigar; ++i) {
+		int j, op = r->p->cigar[i]&0xf, len = r->p->cigar[i]>>4;
+		assert((op >= MM_CIGAR_MATCH && op <= MM_CIGAR_N_SKIP) || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH);
+		if (op == MM_CIGAR_MATCH || op == MM_CIGAR_EQ_MATCH || op == MM_CIGAR_X_MISMATCH) {
+			for (j = 0; j < len; ++j) {
+				if (qseq[q_off + j] != tseq[t_off + j]) {
+					mm_sprintf_lite(s, "%d%c", l_MD, "ACGTN"[tseq[t_off + j]]);
+					l_MD = 0;
+				} else ++l_MD;
+			}
+			q_off += len, t_off += len;
+		} else if (op == MM_CIGAR_INS) {
+			q_off += len;
+		} else if (op == MM_CIGAR_DEL) {
+			for (j = 0, tmp[len] = 0; j < len; ++j)
+				tmp[j] = "ACGTN"[tseq[t_off + j]];
+			mm_sprintf_lite(s, "%d^%s", l_MD, tmp);
+			l_MD = 0;
+			t_off += len;
+		} else if (op == MM_CIGAR_N_SKIP) {
+			t_off += len;
+		}
+	}
+	if (l_MD > 0) mm_sprintf_lite(s, "%d", l_MD);
+	assert(t_off == r->re - r->rs && q_off == r->qe - r->qs);
+}
+
+static void write_cs_ds_or_MD(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int no_iden, int is_MD, int is_ds, int write_tag, int is_qstrand)
+{
+	extern unsigned char seq_nt4_table[256];
+	int i;
+	uint8_t *qseq, *tseq;
+	char *tmp;
+	if (r->p == 0) return;
+	qseq = (uint8_t*)kmalloc(km, r->qe - r->qs);
+	tseq = (uint8_t*)kmalloc(km, r->re - r->rs);
+	tmp = (char*)kmalloc(km, r->re - r->rs > r->qe - r->qs? r->re - r->rs + 1 : r->qe - r->qs + 1);
+	if (is_qstrand) {
+		mm_idx_getseq2(mi, r->rev, r->rid, r->rs, r->re, tseq);
+		for (i = r->qs; i < r->qe; ++i)
+			qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
+	} else {
+		mm_idx_getseq(mi, r->rid, r->rs, r->re, tseq);
+		if (!r->rev) {
+			for (i = r->qs; i < r->qe; ++i)
+				qseq[i - r->qs] = seq_nt4_table[(uint8_t)t->seq[i]];
+		} else {
+			for (i = r->qs; i < r->qe; ++i) {
+				uint8_t c = seq_nt4_table[(uint8_t)t->seq[i]];
+				qseq[r->qe - i - 1] = c >= 4? 4 : 3 - c;
+			}
+		}
+	}
+	if (is_MD) write_MD_core(s, tseq, qseq, r, tmp, write_tag);
+	else write_cs_ds_core(s, tseq, qseq, r, tmp, no_iden, is_ds, write_tag);
 	kfree(km, qseq); kfree(km, tseq); kfree(km, tmp);
 }
 
+int mm_gen_cs_ds_or_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int is_MD, int is_ds, int no_iden, int is_qstrand)
+{
+	mm_bseq1_t t;
+	kstring_t str;
+	str.s = *buf, str.l = 0, str.m = *max_len;
+	t.l_seq = strlen(seq);
+	t.seq = (char*)seq;
+	write_cs_ds_or_MD(km, &str, mi, &t, r, no_iden, is_MD, is_ds, 0, is_qstrand);
+	*max_len = str.m;
+	*buf = str.s;
+	return str.l;
+}
+
+int mm_gen_cs_or_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int is_MD, int no_iden, int is_qstrand)
+{
+	return mm_gen_cs_ds_or_MD(km, buf, max_len, mi, r, seq, is_MD, 0, no_iden, is_qstrand);
+}
+
+int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden)
+{
+	return mm_gen_cs_or_MD(km, buf, max_len, mi, r, seq, 0, no_iden, 0);
+}
+
+int mm_gen_ds(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden)
+{
+	return mm_gen_cs_ds_or_MD(km, buf, max_len, mi, r, seq, 0, 1, no_iden, 0);
+}
+
+int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq)
+{
+	return mm_gen_cs_or_MD(km, buf, max_len, mi, r, seq, 1, 0, 0);
+}
+
 static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
 {
 	int type;
 	if (r->id == r->parent) type = r->inv? 'I' : 'P';
 	else type = r->inv? 'i' : 'S';
 	if (r->p) {
-		mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->blen - r->mlen + r->p->n_ambi, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
+		mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->blen - r->mlen + r->p->n_ambi, r->p->dp_max0, r->p->dp_score, r->p->n_ambi);
 		if (r->p->trans_strand == 1 || r->p->trans_strand == 2)
 			mm_sprintf_lite(s, "\tts:A:%c", "?+-?"[r->p->trans_strand]);
 	}
 	mm_sprintf_lite(s, "\ttp:A:%c\tcm:i:%d\ts1:i:%d", type, r->cnt, r->score);
 	if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
-	if (r->div >= 0.0f && r->div <= 1.0f) {
-		char buf[8];
+	if (r->p) {
+		char buf[16];
+		double div;
+		div = 1.0 - mm_event_identity(r);
+		if (div == 0.0) buf[0] = '0', buf[1] = 0;
+		else snprintf(buf, 16, "%.4f", 1.0 - mm_event_identity(r));
+		mm_sprintf_lite(s, "\tde:f:%s", buf);
+	} else if (r->div >= 0.0f && r->div <= 1.0f) {
+		char buf[16];
 		if (r->div == 0.0f) buf[0] = '0', buf[1] = 0;
-		else sprintf(buf, "%.4f", r->div);
+		else snprintf(buf, 16, "%.4f", r->div);
 		mm_sprintf_lite(s, "\tdv:f:%s", buf);
 	}
 	if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);
 }
 
-void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag)
+void mm_write_paf4(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag, int rep_len, int n_seg, int seg_idx)
 {
 	s->l = 0;
-	mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
+	mm_sprintf_lite(s, "%s", t->name);
+	if ((opt_flag & MM_F_FRAG_MODE) && n_seg >= 2 && seg_idx >= 0)
+		mm_sprintf_lite(s, "/%d", seg_idx + 1);
+	if (r == 0) {
+		mm_sprintf_lite(s, "\t%d\t0\t0\t*\t*\t0\t0\t0\t0\t0\t0", t->l_seq);
+		if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len);
+		return;
+	}
+	mm_sprintf_lite(s, "\t%d\t%d\t%d\t%c\t", t->l_seq, r->qs, r->qe, "+-"[r->rev]);
 	if (mi->seq[r->rid].name) mm_sprintf_lite(s, "%s", mi->seq[r->rid].name);
 	else mm_sprintf_lite(s, "%d", r->rid);
-	mm_sprintf_lite(s, "\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
+	mm_sprintf_lite(s, "\t%d", mi->seq[r->rid].len);
+	if ((opt_flag & MM_F_QSTRAND) && r->rev)
+		mm_sprintf_lite(s, "\t%d\t%d", mi->seq[r->rid].len - r->re, mi->seq[r->rid].len - r->rs);
+	else
+		mm_sprintf_lite(s, "\t%d\t%d", r->rs, r->re);
 	mm_sprintf_lite(s, "\t%d\t%d", r->mlen, r->blen);
 	mm_sprintf_lite(s, "\t%d", r->mapq);
 	write_tags(s, r);
+	if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len);
 	if (r->p && (opt_flag & MM_F_OUT_CG)) {
 		uint32_t k;
 		mm_sprintf_lite(s, "\tcg:Z:");
 		for (k = 0; k < r->p->n_cigar; ++k)
-			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
+			mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, MM_CIGAR_STR[r->p->cigar[k]&0xf]);
 	}
-	if (r->p && (opt_flag & MM_F_OUT_CS))
-		write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
+	if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_DS|MM_F_OUT_MD)))
+		write_cs_ds_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), !!(opt_flag&MM_F_OUT_MD), !!(opt_flag&MM_F_OUT_DS), 1, !!(opt_flag&MM_F_QSTRAND));
+	if ((opt_flag & MM_F_COPY_COMMENT) && t->comment)
+		mm_sprintf_lite(s, "\t%s", t->comment);
+}
+
+void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag, int rep_len)
+{
+	mm_write_paf4(s, mi, t, r, km, opt_flag, rep_len, 0, 0);
+}
+
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag)
+{
+	mm_write_paf3(s, mi, t, r, km, opt_flag, -1);
 }
 
 static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
@@ -265,7 +491,7 @@ static inline const mm_reg1_t *get_sam_pri(int n_regs, const mm_reg1_t *regs)
 	return NULL;
 }
 
-static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, const mm_reg1_t *r, int opt_flag)
+static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, const mm_reg1_t *r, int64_t opt_flag)
 {
 	if (r->p == 0) {
 		mm_sprintf_lite(s, "*");
@@ -274,27 +500,30 @@ static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, co
 		clip_len[0] = r->rev? qlen - r->qe : r->qs;
 		clip_len[1] = r->rev? r->qs : qlen - r->qe;
 		if (in_tag) {
-			int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 5 : 4;
+			int clip_char = (((sam_flag&0x800) || ((sam_flag&0x100) && (opt_flag&MM_F_SECONDARY_SEQ))) &&
+							 !(opt_flag&MM_F_SOFTCLIP)) ? 5 : 4;
 			mm_sprintf_lite(s, "\tCG:B:I");
 			if (clip_len[0]) mm_sprintf_lite(s, ",%u", clip_len[0]<<4|clip_char);
 			for (k = 0; k < r->p->n_cigar; ++k)
 				mm_sprintf_lite(s, ",%u", r->p->cigar[k]);
 			if (clip_len[1]) mm_sprintf_lite(s, ",%u", clip_len[1]<<4|clip_char);
 		} else {
-			int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 'H' : 'S';
+			int clip_char = (((sam_flag&0x800) || ((sam_flag&0x100) && (opt_flag&MM_F_SECONDARY_SEQ))) &&
+							 !(opt_flag&MM_F_SOFTCLIP)) ? 'H' : 'S';
+			assert(clip_len[0] < qlen && clip_len[1] < qlen);
 			if (clip_len[0]) mm_sprintf_lite(s, "%d%c", clip_len[0], clip_char);
 			for (k = 0; k < r->p->n_cigar; ++k)
-				mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
+				mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, MM_CIGAR_STR[r->p->cigar[k]&0xf]);
 			if (clip_len[1]) mm_sprintf_lite(s, "%d%c", clip_len[1], clip_char);
 		}
 	}
 }
 
-void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int opt_flag)
+void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int64_t opt_flag, int rep_len)
 {
 	const int max_bam_cigar_op = 65535;
 	int flag, n_regs = n_regss[seg_idx], cigar_in_tag = 0;
-	int this_rid = -1, this_pos = -1, this_rev = 0;
+	int this_rid = -1, this_pos = -1;
 	const mm_reg1_t *regs = regss[seg_idx], *r_prev = NULL, *r_next;
 	const mm_reg1_t *r = n_regs > 0 && reg_idx < n_regs && reg_idx >= 0? &regs[reg_idx] : NULL;
 
@@ -343,7 +572,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 			mm_sprintf_lite(s, "\t%s\t%d\t0\t*", mi->seq[this_rid].name, this_pos+1);
 		} else mm_sprintf_lite(s, "\t*\t0\t0\t*");
 	} else {
-		this_rid = r->rid, this_pos = r->rs, this_rev = r->rev;
+		this_rid = r->rid, this_pos = r->rs;
 		mm_sprintf_lite(s, "\t%s\t%d\t%d\t", mi->seq[r->rid].name, r->rs+1, r->mapq);
 		if ((opt_flag & MM_F_LONG_CIGAR) && r->p && r->p->n_cigar > max_bam_cigar_op - 2) {
 			int n_cigar = r->p->n_cigar;
@@ -353,9 +582,11 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 				cigar_in_tag = 1;
 		}
 		if (cigar_in_tag) {
-			if (flag & 0x100) mm_sprintf_lite(s, "0S"); // secondary alignment
-			else if (flag & 0x800) mm_sprintf_lite(s, "%dS", r->re - r->rs); // supplementary alignment
-			else mm_sprintf_lite(s, "%dS", t->l_seq);
+			int slen;
+			if ((flag & 0x900) == 0 || (opt_flag & MM_F_SOFTCLIP)) slen = t->l_seq;
+			else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)) slen = 0;
+			else slen = r->qe - r->qs;
+			mm_sprintf_lite(s, "%dS%dN", slen, r->re - r->rs);
 		} else write_sam_cigar(s, flag, 0, t->l_seq, r, opt_flag);
 	}
 
@@ -364,17 +595,17 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 		int tlen = 0;
 		if (this_rid >= 0 && r_next) {
 			if (this_rid == r_next->rid) {
-				int this_pos5 = r && r->rev? r->re - 1 : this_pos;
-				int next_pos5 = r_next->rev? r_next->re - 1 : r_next->rs;
-				tlen = next_pos5 - this_pos5;
+				if (r) {
+					int this_pos5 = r->rev? r->re - 1 : this_pos;
+					int next_pos5 = r_next->rev? r_next->re - 1 : r_next->rs;
+					tlen = next_pos5 - this_pos5;
+				}
 				mm_sprintf_lite(s, "\t=\t");
 			} else mm_sprintf_lite(s, "\t%s\t", mi->seq[r_next->rid].name);
 			mm_sprintf_lite(s, "%d\t", r_next->rs + 1);
 		} else if (r_next) { // && this_rid < 0
 			mm_sprintf_lite(s, "\t%s\t%d\t", mi->seq[r_next->rid].name, r_next->rs + 1);
 		} else if (this_rid >= 0) { // && r_next == NULL
-			int this_pos5 = this_rev? r->re - 1 : this_pos; // this_rev is only true when r != NULL
-			tlen = this_pos - this_pos5; // next_pos5 will be this_pos
 			mm_sprintf_lite(s, "\t=\t%d\t", this_pos + 1); // next segment will take r's coordinate
 		} else mm_sprintf_lite(s, "\t*\t0\t"); // neither has coordinates
 		if (tlen > 0) ++tlen;
@@ -394,7 +625,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 			mm_sprintf_lite(s, "\t");
 			if (t->qual) sam_write_sq(s, t->qual, t->l_seq, r->rev, 0);
 			else mm_sprintf_lite(s, "*");
-		} else if (flag & 0x100) {
+		} else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)){
 			mm_sprintf_lite(s, "*\t*");
 		} else {
 			sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
@@ -434,15 +665,24 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 				}
 			}
 		}
-		if (r->p && (opt_flag & MM_F_OUT_CS))
-			write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
+		if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_DS|MM_F_OUT_MD)))
+			write_cs_ds_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD, !!(opt_flag&MM_F_OUT_DS), 1, 0);
 		if (cigar_in_tag)
 			write_sam_cigar(s, flag, 1, t->l_seq, r, opt_flag);
 	}
+	if (rep_len >= 0) mm_sprintf_lite(s, "\trl:i:%d", rep_len);
+
+	if ((opt_flag & MM_F_COPY_COMMENT) && t->comment)
+		mm_sprintf_lite(s, "\t%s", t->comment);
 
 	s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
 }
 
+void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int64_t opt_flag)
+{
+	mm_write_sam3(s, mi, t, seg_idx, reg_idx, n_seg, n_regss, regss, km, opt_flag, -1);
+}
+
 void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs)
 {
 	int i;

getopt.c

@@ -1,216 +0,0 @@
-#include <stddef.h>
-#include <stdio.h>
-#include <string.h>
-#include "getopt.h"
-
-char *optarg;
-int optind=1, opterr=1, optopt, __optpos, optreset=0;
-
-#define optpos __optpos
-
-static void __getopt_msg(const char *a, const char *b, const char *c, size_t l)
-{
-	FILE *f = stderr;
-#if !defined(WIN32) && !defined(_WIN32)
-	flockfile(f);
-#endif
-	fputs(a, f);
-	fwrite(b, strlen(b), 1, f);
-	fwrite(c, 1, l, f);
-	fputc('\n', f);
-#if !defined(WIN32) && !defined(_WIN32)
-	funlockfile(f);
-#endif
-}
-
-int getopt(int argc, char * const argv[], const char *optstring)
-{
-	int i, c, d;
-	int k, l;
-	char *optchar;
-
-	if (!optind || optreset) {
-		optreset = 0;
-		__optpos = 0;
-		optind = 1;
-	}
-
-	if (optind >= argc || !argv[optind])
-		return -1;
-
-	if (argv[optind][0] != '-') {
-		if (optstring[0] == '-') {
-			optarg = argv[optind++];
-			return 1;
-		}
-		return -1;
-	}
-
-	if (!argv[optind][1])
-		return -1;
-
-	if (argv[optind][1] == '-' && !argv[optind][2])
-		return optind++, -1;
-
-	if (!optpos) optpos++;
-	c = argv[optind][optpos], k = 1;
-	optchar = argv[optind]+optpos;
-	optopt = c;
-	optpos += k;
-
-	if (!argv[optind][optpos]) {
-		optind++;
-		optpos = 0;
-	}
-
-	if (optstring[0] == '-' || optstring[0] == '+')
-		optstring++;
-
-	i = 0;
-	d = 0;
-	do {
-		d = optstring[i], l = 1;
-		if (l>0) i+=l; else i++;
-	} while (l && d != c);
-
-	if (d != c) {
-		if (optstring[0] != ':' && opterr)
-			__getopt_msg(argv[0], ": unrecognized option: ", optchar, k);
-		return '?';
-	}
-	if (optstring[i] == ':') {
-		if (optstring[i+1] == ':') optarg = 0;
-		else if (optind >= argc) {
-			if (optstring[0] == ':') return ':';
-			if (opterr) __getopt_msg(argv[0],
-				": option requires an argument: ",
-				optchar, k);
-			return '?';
-		}
-		if (optstring[i+1] != ':' || optpos) {
-			optarg = argv[optind++] + optpos;
-			optpos = 0;
-		}
-	}
-	return c;
-}
-
-static void permute(char *const *argv, int dest, int src)
-{
-	char **av = (char **)argv;
-	char *tmp = av[src];
-	int i;
-	for (i=src; i>dest; i--)
-		av[i] = av[i-1];
-	av[dest] = tmp;
-}
-
-static int __getopt_long_core(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx, int longonly)
-{
-	optarg = 0;
-	if (longopts && argv[optind][0] == '-' &&
-		((longonly && argv[optind][1] && argv[optind][1] != '-') ||
-		 (argv[optind][1] == '-' && argv[optind][2])))
-	{
-		int colon = optstring[optstring[0]=='+'||optstring[0]=='-']==':';
-		int i, cnt, match = -1;
-		char *opt;
-		for (cnt=i=0; longopts[i].name; i++) {
-			const char *name = longopts[i].name;
-			opt = argv[optind]+1;
-			if (*opt == '-') opt++;
-			for (; *name && *name == *opt; name++, opt++);
-			if (*opt && *opt != '=') continue;
-			match = i;
-			if (!*name) {
-				cnt = 1;
-				break;
-			}
-			cnt++;
-		}
-		if (cnt==1) {
-			i = match;
-			optind++;
-			optopt = longopts[i].val;
-			if (*opt == '=') {
-				if (!longopts[i].has_arg) {
-					if (colon || !opterr)
-						return '?';
-					__getopt_msg(argv[0],
-						": option does not take an argument: ",
-						longopts[i].name,
-						strlen(longopts[i].name));
-					return '?';
-				}
-				optarg = opt+1;
-			} else if (longopts[i].has_arg == required_argument) {
-				if (!(optarg = argv[optind])) {
-					if (colon) return ':';
-					if (!opterr) return '?';
-					__getopt_msg(argv[0],
-						": option requires an argument: ",
-						longopts[i].name,
-						strlen(longopts[i].name));
-					return '?';
-				}
-				optind++;
-			}
-			if (idx) *idx = i;
-			if (longopts[i].flag) {
-				*longopts[i].flag = longopts[i].val;
-				return 0;
-			}
-			return longopts[i].val;
-		}
-		if (argv[optind][1] == '-') {
-			if (!colon && opterr)
-				__getopt_msg(argv[0], cnt ?
-					": option is ambiguous: " :
-					": unrecognized option: ",
-					argv[optind]+2,
-					strlen(argv[optind]+2));
-			optind++;
-			return '?';
-		}
-	}
-	return getopt(argc, argv, optstring);
-}
-
-static int __getopt_long(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx, int longonly)
-{
-	int ret, skipped, resumed;
-	if (!optind || optreset) {
-		optreset = 0;
-		__optpos = 0;
-		optind = 1;
-	}
-	if (optind >= argc || !argv[optind]) return -1;
-	skipped = optind;
-	if (optstring[0] != '+' && optstring[0] != '-') {
-		int i;
-		for (i=optind; ; i++) {
-			if (i >= argc || !argv[i]) return -1;
-			if (argv[i][0] == '-' && argv[i][1]) break;
-		}
-		optind = i;
-	}
-	resumed = optind;
-	ret = __getopt_long_core(argc, argv, optstring, longopts, idx, longonly);
-	if (resumed > skipped) {
-		int i, cnt = optind-resumed;
-		for (i=0; i<cnt; i++)
-			permute(argv, skipped, optind-1);
-		optind = skipped + cnt;
-	}
-	return ret;
-}
-
-int getopt_long(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx)
-{
-	return __getopt_long(argc, argv, optstring, longopts, idx, 0);
-}
-
-int getopt_long_only(int argc, char *const *argv, const char *optstring, const struct option *longopts, int *idx)
-{
-	return __getopt_long(argc, argv, optstring, longopts, idx, 1);
-}

getopt.h

@@ -1,53 +0,0 @@
-/*
-  Copyright 2005-2014 Rich Felker, et al.
-  
-  Permission is hereby granted, free of charge, to any person obtaining
-  a copy of this software and associated documentation files (the
-  "Software"), to deal in the Software without restriction, including
-  without limitation the rights to use, copy, modify, merge, publish,
-  distribute, sublicense, and/or sell copies of the Software, and to
-  permit persons to whom the Software is furnished to do so, subject to
-  the following conditions:
-  
-  The above copyright notice and this permission notice shall be
-  included in all copies or substantial portions of the Software.
-  
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-  CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-  TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-*/
-
-#ifndef _GETOPT_H
-#define _GETOPT_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-int getopt(int, char * const [], const char *);
-extern char *optarg;
-extern int optind, opterr, optopt, optreset;
-
-struct option {
-	const char *name;
-	int has_arg;
-	int *flag;
-	int val;
-};
-
-int getopt_long(int, char *const *, const char *, const struct option *, int *);
-int getopt_long_only(int, char *const *, const char *, const struct option *, int *);
-
-#define no_argument        0
-#define required_argument  1
-#define optional_argument  2
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif

hit.c

@@ -20,14 +20,14 @@ static inline void mm_cal_fuzzy_len(mm_reg1_t *r, const mm128_t *a)
 	}
 }
 
-static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
+static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a, int is_qstrand)
 { // NB: r->as and r->cnt MUST BE set correctly for this function to work
 	int32_t k = r->as, q_span = (int32_t)(a[k].y>>32&0xff);
 	r->rev = a[k].x>>63;
 	r->rid = a[k].x<<1>>33;
 	r->rs = (int32_t)a[k].x + 1 > q_span? (int32_t)a[k].x + 1 - q_span : 0; // NB: target span may be shorter, so this test is necessary
 	r->re = (int32_t)a[k + r->cnt - 1].x + 1;
-	if (!r->rev) {
+	if (!r->rev || is_qstrand) {
 		r->qs = (int32_t)a[k].y + 1 - q_span;
 		r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
 	} else {
@@ -49,13 +49,13 @@ static inline uint64_t hash64(uint64_t key)
 	return key;
 }
 
-mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
+mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a, int is_qstrand) // convert chains to hits
 {
 	mm128_t *z, tmp;
 	mm_reg1_t *r;
 	int i, k;
 
-	if (n_u == 0) return 0;
+	if (n_u <= 0) return 0;
 
 	// sort by score
 	z = (mm128_t*)kmalloc(km, n_u * 16);
@@ -81,31 +81,48 @@ mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u,
 		ri->cnt = (int32_t)z[i].y;
 		ri->as = z[i].y >> 32;
 		ri->div = -1.0f;
-		mm_reg_set_coor(ri, qlen, a);
+		mm_reg_set_coor(ri, qlen, a, is_qstrand);
 	}
 	kfree(km, z);
 	return r;
 }
 
-void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
+void mm_mark_alt(const mm_idx_t *mi, int n, mm_reg1_t *r)
+{
+	int i;
+	if (mi->n_alt == 0) return;
+	for (i = 0; i < n; ++i)
+		if (mi->seq[r[i].rid].is_alt)
+			r[i].is_alt = 1;
+}
+
+static inline int mm_alt_score(int score, float alt_diff_frac)
+{
+	if (score < 0) return score;
+	score = (int)(score * (1.0 - alt_diff_frac) + .499);
+	return score > 0? score : 1;
+}
+
+void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a, int is_qstrand)
 {
 	if (n <= 0 || n >= r->cnt) return;
 	*r2 = *r;
 	r2->id = -1;
 	r2->sam_pri = 0;
 	r2->p = 0;
+	r2->split_inv = 0;
 	r2->cnt = r->cnt - n;
 	r2->score = (int32_t)(r->score * ((float)r2->cnt / r->cnt) + .499);
 	r2->as = r->as + n;
 	if (r->parent == r->id) r2->parent = MM_PARENT_TMP_PRI;
-	mm_reg_set_coor(r2, qlen, a);
+	mm_reg_set_coor(r2, qlen, a, is_qstrand);
 	r->cnt -= r2->cnt;
 	r->score -= r2->score;
-	mm_reg_set_coor(r, qlen, a);
+	mm_reg_set_coor(r, qlen, a, is_qstrand);
 	r->split |= 1, r2->split |= 2;
 }
 
-void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff) // and compute mm_reg1_t::subsc
+void mm_set_parent(void *km, float mask_level, int mask_len, int n, mm_reg1_t *r, int sub_diff, int hard_mask_level, float alt_diff_frac) // and compute mm_reg1_t::subsc
 {
 	int i, j, k, *w;
 	uint64_t *cov;
@@ -117,6 +134,7 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
 	for (i = 1, k = 1; i < n; ++i) {
 		mm_reg1_t *ri = &r[i];
 		int si = ri->qs, ei = ri->qe, n_cov = 0, uncov_len = 0;
+		if (hard_mask_level) goto skip_uncov;
 		for (j = 0; j < k; ++j) { // traverse existing primary hits to find overlapping hits
 			mm_reg1_t *rp = &r[w[j]];
 			int sj = rp->qs, ej = rp->qe;
@@ -131,25 +149,29 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
 			int j, x = si;
 			radix_sort_64(cov, cov + n_cov);
 			for (j = 0; j < n_cov; ++j) {
-				if (cov[j]>>32 > x) uncov_len += (cov[j]>>32) - x;
+				if ((int)(cov[j]>>32) > x) uncov_len += (cov[j]>>32) - x;
 				x = (int32_t)cov[j] > x? (int32_t)cov[j] : x;
 			}
 			if (ei > x) uncov_len += ei - x;
 		}
+skip_uncov:
 		for (j = 0; j < k; ++j) { // traverse existing primary hits again
 			mm_reg1_t *rp = &r[w[j]];
 			int sj = rp->qs, ej = rp->qe, min, max, ol;
 			if (ej <= si || sj >= ei) continue; // no overlap
 			min = ej - sj < ei - si? ej - sj : ei - si;
 			max = ej - sj > ei - si? ej - sj : ei - si;
-			ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si); // overlap length
-			if ((float)ol / min - (float)uncov_len / max > mask_level) {
-				int cnt_sub = 0;
+			ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si); // overlap length; TODO: this can be simplified
+			if ((float)ol / min - (float)uncov_len / max > mask_level && uncov_len <= mask_len) { // then this is a secondary hit
+				int cnt_sub = 0, sci = ri->score;
 				ri->parent = rp->parent;
-				rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
+				if (!rp->is_alt && ri->is_alt) sci = mm_alt_score(sci, alt_diff_frac);
+				rp->subsc = rp->subsc > sci? rp->subsc : sci;
 				if (ri->cnt >= rp->cnt) cnt_sub = 1;
 				if (rp->p && ri->p && (rp->rid != ri->rid || rp->rs != ri->rs || rp->re != ri->re || ol != min)) { // the last condition excludes identical hits after DP
-					rp->p->dp_max2 = rp->p->dp_max2 > ri->p->dp_max? rp->p->dp_max2 : ri->p->dp_max;
+					sci = ri->p->dp_max;
+					if (!rp->is_alt && ri->is_alt) sci = mm_alt_score(sci, alt_diff_frac);
+					rp->p->dp_max2 = rp->p->dp_max2 > sci? rp->p->dp_max2 : sci;
 					if (rp->p->dp_max - ri->p->dp_max <= sub_diff) cnt_sub = 1;
 				}
 				if (cnt_sub) ++rp->n_sub;
@@ -163,9 +185,9 @@ set_parent_test:
 	kfree(km, w);
 }
 
-void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r)
+void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac)
 {
-	int32_t i, n_aux, n = *n_regs;
+	int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0;
 	mm128_t *aux;
 	mm_reg1_t *t;
 
@@ -174,14 +196,18 @@ void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r)
 	t = (mm_reg1_t*)kmalloc(km, n * sizeof(mm_reg1_t));
 	for (i = n_aux = 0; i < n; ++i) {
 		if (r[i].inv || r[i].cnt > 0) { // squeeze out elements with cnt==0 (soft deleted)
-			assert(r[i].p);
-			aux[n_aux].x = (uint64_t)r[i].p->dp_max << 32 | r[i].hash;
+			int score;
+			if (r[i].p) score = r[i].p->dp_max, has_cigar = 1;
+			else score = r[i].score, no_cigar = 1;
+			if (r[i].is_alt) score = mm_alt_score(score, alt_diff_frac);
+			aux[n_aux].x = (uint64_t)score << 32 | r[i].hash;
 			aux[n_aux++].y = i;
 		} else if (r[i].p) {
 			free(r[i].p);
 			r[i].p = 0;
 		}
 	}
+	assert(has_cigar + no_cigar == 1);
 	radix_sort_128x(aux, aux + n_aux);
 	for (i = n_aux - 1; i >= 0; --i)
 		t[n_aux - 1 - i] = r[aux[i].y];
@@ -226,35 +252,63 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
 	mm_set_sam_pri(n_regs, regs);
 }
 
-void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r)
+void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int check_strand, int min_strand_sc, int *n_, mm_reg1_t *r)
 {
 	if (pri_ratio > 0.0f && *n_ > 0) {
 		int i, k, n = *n_, n_2nd = 0;
-		for (i = k = 0; i < n; ++i) {
+		uint8_t *keep = (uint8_t*)kmalloc(km, n);
+		for (i = 0; i < n; ++i) {
 			int p = r[i].parent;
+			keep[i] = 0;
 			if (p == i || r[i].inv) { // primary or inversion
-				r[k++] = r[i];
+				keep[i] = 1;
 			} else if ((r[i].score >= r[p].score * pri_ratio || r[i].score + min_diff >= r[p].score) && n_2nd < best_n) {
 				if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].rid == r[p].rid && r[i].rs == r[p].rs && r[i].re == r[p].re)) // not identical hits
-					r[k++] = r[i], ++n_2nd;
-				else if (r[i].p) free(r[i].p);
-			} else if (r[i].p) free(r[i].p);
+					keep[i] = 1, ++n_2nd;
+			} else if (check_strand && n_2nd < best_n && r[i].score > min_strand_sc && r[i].rev != r[p].rev) {
+				r[i].strand_retained = 1;
+				keep[i] = 1, ++n_2nd;
+			}
 		}
+		for (i = k = 0; i < n; ++i) {
+			if (keep[i]) r[k++] = r[i];
+			else if (r[i].p) free(r[i].p);
+		}
+		kfree(km, keep);
 		if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
 		*n_ = k;
 	}
 }
 
-void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs)
+int mm_filter_strand_retained(int n_regs, mm_reg1_t *r)
+{
+	int i, k;
+	uint8_t *keep = (uint8_t*)malloc(n_regs);
+	for (i = 0; i < n_regs; ++i) {
+		int p = r[i].parent;
+		keep[i] = (!r[i].strand_retained || r[i].div < r[p].div * 5.0f || r[i].div < 0.01f);
+	}
+	for (i = k = 0; i < n_regs; ++i) {
+		if (keep[i]) {
+			if (k < i) r[k++] = r[i];
+			else ++k;
+		}
+	}
+	free(keep);
+	return k;
+}
+
+void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs)
 { // NB: after this call, mm_reg1_t::parent can be -1 if its parent filtered out
 	int i, k;
 	for (i = k = 0; i < *n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
 		int flt = 0;
 		if (!r->inv && !r->seg_split && r->cnt < opt->min_cnt) flt = 1;
-		if (r->p) {
+		if (r->p) { // these filters are only applied when base-alignment is available
 			if (r->mlen < opt->min_chain_score) flt = 1;
 			else if (r->p->dp_max < opt->min_dp_max) flt = 1;
+			else if (r->qs > qlen * opt->max_clip_ratio && qlen - r->qe > qlen * opt->max_clip_ratio) flt = 1;
 			if (flt) free(r->p);
 		}
 		if (!flt) {
@@ -285,63 +339,6 @@ int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
 	return as;
 }
 
-void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
-{
-	int i, n_aux, n_regs = *n_regs_, n_drop = 0;
-	uint64_t *aux;
-
-	if (n_regs < 2) return; // nothing to join
-	mm_squeeze_a(km, n_regs, regs, a);
-
-	aux = (uint64_t*)kmalloc(km, n_regs * 8);
-	for (i = n_aux = 0; i < n_regs; ++i)
-		if (regs[i].parent == i || regs[i].parent < 0)
-			aux[n_aux++] = (uint64_t)regs[i].as << 32 | i;
-	radix_sort_64(aux, aux + n_aux);
-
-	for (i = n_aux - 1; i >= 1; --i) {
-		mm_reg1_t *r0 = &regs[(int32_t)aux[i-1]], *r1 = &regs[(int32_t)aux[i]];
-		mm128_t *a0e, *a1s;
-		int max_gap, min_gap, sc_thres;
-
-		// test
-		if (r0->as + r0->cnt != r1->as) continue; // not adjacent in a[]
-		if (r0->rid != r1->rid || r0->rev != r1->rev) continue; // make sure on the same target and strand
-		a0e = &a[r0->as + r0->cnt - 1];
-		a1s = &a[r1->as];
-		if (a1s->x <= a0e->x || (int32_t)a1s->y <= (int32_t)a0e->y) continue; // keep colinearity
-		max_gap = min_gap = (int32_t)a1s->y - (int32_t)a0e->y;
-		max_gap = max_gap > a1s->x - a0e->x? max_gap : a1s->x - a0e->x;
-		min_gap = min_gap < a1s->x - a0e->x? min_gap : a1s->x - a0e->x;
-		if (max_gap > opt->max_join_long || min_gap > opt->max_join_short) continue;
-		sc_thres = (int)((float)opt->min_join_flank_sc / opt->max_join_long * max_gap + .499);
-		if (r0->score < sc_thres || r1->score < sc_thres) continue; // require good flanking chains
-		if (r0->re - r0->rs < max_gap>>1 || r0->qe - r0->qs < max_gap>>1) continue; // require enough flanking length
-		if (r1->re - r1->rs < max_gap>>1 || r1->qe - r1->qs < max_gap>>1) continue;
-
-		// all conditions satisfied; join
-		a[r1->as].y |= MM_SEED_LONG_JOIN;
-		r0->cnt += r1->cnt, r0->score += r1->score;
-		mm_reg_set_coor(r0, qlen, a);
-		r1->cnt = 0;
-		r1->parent = r0->id;
-		++n_drop;
-	}
-	kfree(km, aux);
-
-	if (n_drop > 0) { // then fix the hits hierarchy
-		for (i = 0; i < n_regs; ++i) { // adjust the mm_reg1_t::parent
-			mm_reg1_t *r = &regs[i];
-			if (r->parent >= 0 && r->id != r->parent) { // fix for secondary hits only
-				if (regs[r->parent].parent >= 0 && regs[r->parent].parent != r->parent)
-					r->parent = regs[r->parent].parent;
-			}
-		}
-		mm_filter_regs(km, opt, n_regs_, regs);
-		mm_sync_regs(km, *n_regs_, regs);
-	}
-}
-
 mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int n_regs0, const mm_reg1_t *regs0, int *n_regs, mm_reg1_t **regs, const mm128_t *a)
 {
 	int s, i, j, acc_qlen[MM_MAX_SEG+1], qlen_sum = 0;
@@ -388,10 +385,12 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
 		}
 	}
 	for (s = 0; s < n_segs; ++s) {
-		regs[s] = mm_gen_regs(km, hash, qlens[s], seg[s].n_u, seg[s].u, seg[s].a);
+		regs[s] = mm_gen_regs(km, hash, qlens[s], seg[s].n_u, seg[s].u, seg[s].a, 0);
 		n_regs[s] = seg[s].n_u;
-		for (i = 0; i < n_regs[s]; ++i)
+		for (i = 0; i < n_regs[s]; ++i) {
 			regs[s][i].seg_split = 1;
+			regs[s][i].seg_id = s;
+		}
 	}
 	return seg;
 }
@@ -404,15 +403,45 @@ void mm_seg_free(void *km, int n_segs, mm_seg_t *segs)
 	kfree(km, segs);
 }
 
-void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr)
+static void mm_set_inv_mapq(void *km, int n_regs, mm_reg1_t *regs)
+{
+	int i, n_aux;
+	mm128_t *aux;
+	if (n_regs < 3) return;
+	for (i = 0; i < n_regs; ++i)
+		if (regs[i].inv) break;
+	if (i == n_regs) return; // no inversion hits
+
+	aux = (mm128_t*)kmalloc(km, n_regs * 16);
+	for (i = n_aux = 0; i < n_regs; ++i)
+		if (regs[i].parent == i || regs[i].parent < 0)
+			aux[n_aux].y = i, aux[n_aux++].x = (uint64_t)regs[i].rid << 32 | regs[i].rs;
+	radix_sort_128x(aux, aux + n_aux);
+
+	for (i = 1; i < n_aux - 1; ++i) {
+		mm_reg1_t *inv = &regs[aux[i].y];
+		if (inv->inv) {
+			mm_reg1_t *l = &regs[aux[i-1].y];
+			mm_reg1_t *r = &regs[aux[i+1].y];
+			inv->mapq = l->mapq < r->mapq? l->mapq : r->mapq;
+		}
+	}
+	kfree(km, aux);
+}
+
+void mm_set_mapq2(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr, int is_splice)
 {
 	static const float q_coef = 40.0f;
 	int64_t sum_sc = 0;
 	float uniq_ratio;
-	int i;
-	for (i = 0; i < n_regs; ++i)
+	int i, n_2nd_splice = 0;
+	if (n_regs == 0) return;
+	for (i = 0; i < n_regs; ++i) {
 		if (regs[i].parent == regs[i].id)
 			sum_sc += regs[i].score;
+		else if (regs[i].is_spliced)
+			++n_2nd_splice;
+	}
 	uniq_ratio = (float)sum_sc / (sum_sc + rep_len);
 	for (i = 0; i < n_regs; ++i) {
 		mm_reg1_t *r = &regs[i];
@@ -425,13 +454,18 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
 			pen_cm = pen_s1 < pen_cm? pen_s1 : pen_cm;
 			subsc = r->subsc > min_chain_sc? r->subsc : min_chain_sc;
 			if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0) {
-				float identity = (float)r->mlen / r->blen;
-				float x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score0;
+				float x, identity = (float)r->mlen / r->blen;
+				if (is_sr && is_splice)
+					x = (float)r->p->dp_max2 / r->p->dp_max; // ignore chaining score; for short RNA-seq reads, unspliced chaining score tends to be higher
+				else
+					x = (float)r->p->dp_max2 * subsc / r->p->dp_max / r->score0;
 				mapq = (int)(identity * pen_cm * q_coef * (1.0f - x * x) * logf((float)r->p->dp_max / match_sc));
 				if (!is_sr) {
 					int mapq_alt = (int)(6.02f * identity * identity * (r->p->dp_max - r->p->dp_max2) / match_sc + .499f); // BWA-MEM like mapQ, mostly for short reads
 					mapq = mapq < mapq_alt? mapq : mapq_alt; // in case the long-read heuristic fails
 				}
+				if (is_splice && is_sr && r->is_spliced && n_2nd_splice == 0)
+					mapq += 10;
 			} else {
 				float x = (float)subsc / r->score0;
 				if (r->p) {
@@ -447,4 +481,5 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
 			if (r->p && r->p->dp_max > r->p->dp_max2 && r->mapq == 0) r->mapq = 1;
 		} else r->mapq = 0;
 	}
+	mm_set_inv_mapq(km, n_regs, regs);
 }

index.c

@@ -7,10 +7,12 @@
 #endif
 #include <fcntl.h>
 #include <stdio.h>
+#define __STDC_LIMIT_MACROS
 #include "kthread.h"
 #include "bseq.h"
 #include "minimap.h"
 #include "mmpriv.h"
+#include "ksw2.h"
 #include "kvec.h"
 #include "khash.h"
 
@@ -19,6 +21,8 @@
 KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
 typedef khash_t(idx) idxhash_t;
 
+KHASH_MAP_INIT_STR(str, uint32_t)
+
 #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
 
 typedef struct mm_idx_bucket_s {
@@ -28,14 +32,20 @@ typedef struct mm_idx_bucket_s {
 	void *h;     // hash table indexing _p_ and minimizers appearing once
 } mm_idx_bucket_t;
 
-void mm_idxopt_init(mm_idxopt_t *opt)
-{
-	memset(opt, 0, sizeof(mm_idxopt_t));
-	opt->k = 15, opt->w = 10, opt->flag = 0;
-	opt->bucket_bits = 14;
-	opt->mini_batch_size = 50000000;
-	opt->batch_size = 4000000000ULL;
-}
+typedef struct {
+	int32_t st, en, cnt;
+	int32_t score:30, strand:2;
+} mm_idx_intv1_t;
+
+typedef struct mm_idx_intv_s {
+	int32_t n, m;
+	mm_idx_intv1_t *a;
+} mm_idx_intv_t;
+
+typedef struct mm_idx_jjump_s {
+	int32_t n, m;
+	mm_idx_jjump1_t *a;
+} mm_idx_jjump_t;
 
 mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
 {
@@ -51,12 +61,26 @@ mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
 
 void mm_idx_destroy(mm_idx_t *mi)
 {
-	int i;
+	uint32_t i;
 	if (mi == 0) return;
-	for (i = 0; i < 1<<mi->b; ++i) {
-		free(mi->B[i].p);
-		free(mi->B[i].a.a);
-		kh_destroy(idx, (idxhash_t*)mi->B[i].h);
+	if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
+	if (mi->B) {
+		for (i = 0; i < 1U<<mi->b; ++i) {
+			free(mi->B[i].p);
+			free(mi->B[i].a.a);
+			kh_destroy(idx, (idxhash_t*)mi->B[i].h);
+		}
+	}
+	if (mi->spsc) free(mi->spsc);
+	if (mi->I) {
+		for (i = 0; i < mi->n_seq; ++i)
+			free(mi->I[i].a);
+		free(mi->I);
+	}
+	if (mi->J) {
+		for (i = 0; i < mi->n_seq; ++i)
+			free(mi->J[i].a);
+		free(mi->J);
 	}
 	if (!mi->km) {
 		for (i = 0; i < mi->n_seq; ++i)
@@ -87,14 +111,15 @@ const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
 
 void mm_idx_stat(const mm_idx_t *mi)
 {
-	int i, n = 0, n1 = 0;
+	int64_t n = 0, n1 = 0;
+	uint32_t i;
 	uint64_t sum = 0, len = 0;
 	fprintf(stderr, "[M::%s] kmer size: %d; skip: %d; is_hpc: %d; #seq: %d\n", __func__, mi->k, mi->w, mi->flag&MM_I_HPC, mi->n_seq);
 	for (i = 0; i < mi->n_seq; ++i)
 		len += mi->seq[i].len;
-	for (i = 0; i < 1<<mi->b; ++i)
+	for (i = 0; i < 1U<<mi->b; ++i)
 		if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
-	for (i = 0; i < 1<<mi->b; ++i) {
+	for (i = 0; i < 1U<<mi->b; ++i) {
 		idxhash_t *h = (idxhash_t*)mi->B[i].h;
 		khint_t k;
 		if (h == 0) continue;
@@ -104,8 +129,36 @@ void mm_idx_stat(const mm_idx_t *mi)
 				if (kh_key(h, k)&1) ++n1;
 			}
 	}
-	fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
-			__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
+	fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %ld (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n",
+			__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), (long)n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len);
+}
+
+int mm_idx_index_name(mm_idx_t *mi)
+{
+	khash_t(str) *h;
+	uint32_t i;
+	int has_dup = 0, absent;
+	if (mi->h) return 0;
+	h = kh_init(str);
+	for (i = 0; i < mi->n_seq; ++i) {
+		khint_t k;
+		k = kh_put(str, h, mi->seq[i].name, &absent);
+		if (absent) kh_val(h, k) = i;
+		else has_dup = 1;
+	}
+	mi->h = h;
+	if (has_dup && mm_verbose >= 2)
+		fprintf(stderr, "[WARNING] some database sequences have identical sequence names\n");
+	return has_dup;
+}
+
+int mm_idx_name2id(const mm_idx_t *mi, const char *name)
+{
+	khash_t(str) *h = (khash_t(str)*)mi->h;
+	khint_t k;
+	if (h == 0) return -2;
+	k = kh_get(str, h, name);
+	return k == kh_end(h)? -1 : kh_val(h, k);
 }
 
 int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
@@ -120,6 +173,28 @@ int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, ui
 	return en - st;
 }
 
+int mm_idx_getseq_rev(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+{
+	uint64_t i, st1, en1;
+	const mm_idx_seq_t *s;
+	if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
+	s = &mi->seq[rid];
+	if (en > s->len) en = s->len;
+	st1 = s->offset + (s->len - en);
+	en1 = s->offset + (s->len - st);
+	for (i = st1; i < en1; ++i) {
+		uint8_t c = mm_seq4_get(mi->S, i);
+		seq[en1 - i - 1] = c < 4? 3 - c : c;
+	}
+	return en - st;
+}
+
+int mm_idx_getseq2(const mm_idx_t *mi, int is_rev, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
+{
+	if (is_rev) return mm_idx_getseq_rev(mi, rid, st, en, seq);
+	else return mm_idx_getseq(mi, rid, st, en, seq);
+}
+
 int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
 {
 	int i;
@@ -129,6 +204,7 @@ int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
 	if (f <= 0.) return INT32_MAX;
 	for (i = 0; i < 1<<mi->b; ++i)
 		if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
+	if (n == 0) return INT32_MAX;
 	a = (uint32_t*)malloc(n * 4);
 	for (i = n = 0; i < 1<<mi->b; ++i) {
 		idxhash_t *h = (idxhash_t*)mi->B[i].h;
@@ -149,7 +225,8 @@ int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
 
 static void worker_post(void *g, long i, int tid)
 {
-	int j, start_a, start_p, n, n_keys;
+	int n, n_keys;
+	size_t j, start_a, start_p;
 	idxhash_t *h;
 	mm_idx_t *mi = (mm_idx_t*)g;
 	mm_idx_bucket_t *b = &mi->B[i];
@@ -177,7 +254,7 @@ static void worker_post(void *g, long i, int tid)
 			int absent;
 			mm128_t *p = &b->a.a[j-1];
 			itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
-			assert(absent && j - start_a == n);
+			assert(absent && j == start_a + n);
 			if (n == 1) {
 				kh_key(h, itr) |= 1;
 				kh_val(h, itr) = p->y;
@@ -193,7 +270,7 @@ static void worker_post(void *g, long i, int tid)
 		} else ++n;
 	}
 	b->h = h;
-	assert(b->n == start_p);
+	assert(b->n == (int32_t)start_p);
 
 	// deallocate and clear b->a
 	kfree(0, b->a.a);
@@ -274,6 +351,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
 				} else seq->name = 0;
 				seq->len = s->seq[i].l_seq;
 				seq->offset = p->sum_len;
+				seq->is_alt = 0;
 				// copy the sequence
 				if (!(p->mi->flag & MM_I_NO_SEQ)) {
 					for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
@@ -313,7 +391,7 @@ mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini
 	pipeline_t pl;
 	if (fp == 0 || mm_bseq_eof(fp)) return 0;
 	memset(&pl, 0, sizeof(pipeline_t));
-	pl.mini_batch_size = mini_batch_size < batch_size? mini_batch_size : batch_size;
+	pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
 	pl.batch_size = batch_size;
 	pl.fp = fp;
 	pl.mi = mm_idx_init(w, k, b, flag);
@@ -345,7 +423,9 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
 	uint64_t sum_len = 0;
 	mm128_v a = {0,0,0};
 	mm_idx_t *mi;
+	khash_t(str) *h;
 	int i, flag = 0;
+
 	if (n <= 0) return 0;
 	for (i = 0; i < n; ++i) // get the total length
 		sum_len += strlen(seq[i]);
@@ -356,16 +436,21 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
 	mi->n_seq = n;
 	mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
 	mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
+	mi->h = h = kh_init(str);
 	for (i = 0, sum_len = 0; i < n; ++i) {
 		const char *s = seq[i];
 		mm_idx_seq_t *p = &mi->seq[i];
 		uint32_t j;
 		if (name && name[i]) {
+			int absent;
 			p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
 			strcpy(p->name, name[i]);
+			kh_put(str, h, p->name, &absent);
+			assert(absent);
 		}
 		p->offset = sum_len;
 		p->len = strlen(s);
+		p->is_alt = 0;
 		for (j = 0; j < p->len; ++j) {
 			int c = seq_nt4_table[(uint8_t)s[j]];
 			uint64_t o = sum_len + j;
@@ -390,17 +475,20 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
 void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
 {
 	uint64_t sum_len = 0;
-	uint32_t x[5];
-	int i;
+	uint32_t x[5], i;
 
 	x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->flag;
 	fwrite(MM_IDX_MAGIC, 1, 4, fp);
 	fwrite(x, 4, 5, fp);
 	for (i = 0; i < mi->n_seq; ++i) {
-		uint8_t l;
-		l = strlen(mi->seq[i].name);
-		fwrite(&l, 1, 1, fp);
-		fwrite(mi->seq[i].name, 1, l, fp);
+		if (mi->seq[i].name) {
+			uint8_t l = strlen(mi->seq[i].name);
+			fwrite(&l, 1, 1, fp);
+			fwrite(mi->seq[i].name, 1, l, fp);
+		} else {
+			uint8_t l = 0;
+			fwrite(&l, 1, 1, fp);
+		}
 		fwrite(&mi->seq[i].len, 4, 1, fp);
 		sum_len += mi->seq[i].len;
 	}
@@ -427,9 +515,8 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
 
 mm_idx_t *mm_idx_load(FILE *fp)
 {
-	int i;
 	char magic[4];
-	uint32_t x[5];
+	uint32_t x[5], i;
 	uint64_t sum_len = 0;
 	mm_idx_t *mi;
 
@@ -443,11 +530,14 @@ mm_idx_t *mm_idx_load(FILE *fp)
 		uint8_t l;
 		mm_idx_seq_t *s = &mi->seq[i];
 		fread(&l, 1, 1, fp);
-		s->name = (char*)kmalloc(mi->km, l + 1);
-		fread(s->name, 1, l, fp);
-		s->name[l] = 0;
+		if (l) {
+			s->name = (char*)kmalloc(mi->km, l + 1);
+			fread(s->name, 1, l, fp);
+			s->name[l] = 0;
+		}
 		fread(&s->len, 4, 1, fp);
 		s->offset = sum_len;
+		s->is_alt = 0;
 		sum_len += s->len;
 	}
 	for (i = 0; i < 1<<mi->b; ++i) {
@@ -481,14 +571,19 @@ mm_idx_t *mm_idx_load(FILE *fp)
 int64_t mm_idx_is_idx(const char *fn)
 {
 	int fd, is_idx = 0;
-	off_t ret, off_end;
+	int64_t ret, off_end;
 	char magic[4];
 
 	if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
 	fd = open(fn, O_RDONLY);
 	if (fd < 0) return -1; // error
+#ifdef WIN32
+	if ((off_end = _lseeki64(fd, 0, SEEK_END)) >= 4) {
+		_lseeki64(fd, 0, SEEK_SET);
+#else
 	if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
 		lseek(fd, 0, SEEK_SET);
+#endif // WIN32
 		ret = read(fd, magic, 4);
 		if (ret == 4 && strncmp(magic, MM_IDX_MAGIC, 4) == 0)
 			is_idx = 1;
@@ -534,7 +629,7 @@ mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
 		mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
 	if (mi) {
 		if (r->fp_out) mm_idx_dump(r->fp_out, mi);
-		++r->n_parts;
+		mi->index = r->n_parts++;
 	}
 	return mi;
 }
@@ -543,3 +638,437 @@ int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases
 {
 	return r->is_idx? (feof(r->fp.idx) || ftell(r->fp.idx) == r->idx_size) : mm_bseq_eof(r->fp.seq);
 }
+
+#include <ctype.h>
+#include <zlib.h>
+#include "ksort.h"
+#include "kseq.h"
+KSTREAM_DECLARE(gzFile, gzread)
+
+int mm_idx_alt_read(mm_idx_t *mi, const char *fn)
+{
+	int n_alt = 0;
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t str = {0,0,0};
+	fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	if (fp == 0) return -1;
+	ks = ks_init(fp);
+	if (mi->h == 0) mm_idx_index_name(mi);
+	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
+		char *p;
+		int id;
+		for (p = str.s; *p && !isspace(*p); ++p) { }
+		*p = 0;
+		id = mm_idx_name2id(mi, str.s);
+		if (id >= 0) mi->seq[id].is_alt = 1, ++n_alt;
+	}
+	mi->n_alt = n_alt;
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s] found %d ALT contigs\n", __func__, n_alt);
+	return n_alt;
+}
+
+/***************
+ * BED reading *
+ ***************/
+
+#define sort_key_bed(a) ((a).st)
+KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
+
+#define sort_key_end(a) ((a).en)
+KRADIX_SORT_INIT(end, mm_idx_intv1_t, sort_key_end, 4)
+
+static mm_idx_intv_t *mm_idx_bed_read_core(const mm_idx_t *mi, const char *fn, int read_junc, int min_sc)
+{
+	gzFile fp;
+	kstream_t *ks;
+	kstring_t str = {0,0,0};
+	mm_idx_intv_t *I;
+
+	fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	if (fp == 0) return 0;
+	I = CALLOC(mm_idx_intv_t, mi->n_seq);
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
+		mm_idx_intv_t *r;
+		mm_idx_intv1_t t = {-1,-1,-1,-1,0};
+		char *p, *q, *bl, *bs;
+		int32_t i, id = -1, n_blk = 0;
+		for (p = q = str.s, i = 0;; ++p) {
+			if (*p == 0 || *p == '\t') {
+				int32_t c = *p;
+				*p = 0;
+				if (i == 0) { // chr
+					id = mm_idx_name2id(mi, q);
+					if (id < 0) break; // unknown name; TODO: throw a warning
+				} else if (i == 1) { // start
+					t.st = atol(q); // TODO: watch out integer overflow!
+					if (t.st < 0) break;
+				} else if (i == 2) { // end
+					t.en = atol(q);
+					if (t.en < 0) break;
+				} else if (i == 4) { // BED score
+					t.score = *q >= '0' && *q <= '9'? atol(q) : -1;
+				} else if (i == 5) { // strand
+					t.strand = *q == '+'? 1 : *q == '-'? -1 : 0;
+				} else if (i == 9) {
+					if (!isdigit(*q)) break;
+					n_blk = atol(q);
+				} else if (i == 10) {
+					bl = q;
+				} else if (i == 11) {
+					bs = q;
+					break;
+				}
+				if (c == 0) break;
+				++i, q = p + 1;
+			}
+		}
+		if (id < 0 || t.st < 0 || t.st >= t.en) continue; // contig ID not found, or other problems
+		if (min_sc > 0 && t.score < min_sc) continue;
+		r = &I[id];
+		if (i >= 11 && read_junc) { // BED12
+			int32_t st, sz, en;
+			st = strtol(bs, &bs, 10); ++bs;
+			sz = strtol(bl, &bl, 10); ++bl;
+			en = t.st + st + sz;
+			for (i = 1; i < n_blk; ++i) {
+				mm_idx_intv1_t s = t;
+				if (r->n == r->m) {
+					r->m = r->m? r->m + (r->m>>1) : 16;
+					r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+				}
+				st = strtol(bs, &bs, 10); ++bs;
+				sz = strtol(bl, &bl, 10); ++bl;
+				s.st = en, s.en = t.st + st;
+				en = t.st + st + sz;
+				if (s.en > s.st) r->a[r->n++] = s;
+			}
+		} else {
+			if (r->n == r->m) {
+				r->m = r->m? r->m + (r->m>>1) : 16;
+				r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+			}
+			r->a[r->n++] = t;
+		}
+	}
+	free(str.s);
+	ks_destroy(ks);
+	gzclose(fp);
+	return I;
+}
+
+static mm_idx_intv_t *mm_idx_bed_read_merge(const mm_idx_t *mi, const char *fn, int read_junc, int min_sc)
+{
+	long n = 0, n0 = 0;
+	int32_t i;
+	mm_idx_intv_t *I;
+	I = mm_idx_bed_read_core(mi, fn, read_junc, min_sc);
+	if (I == 0) return 0;
+	for (i = 0; i < mi->n_seq; ++i) {
+		int32_t j, j0, k;
+		mm_idx_intv_t *intv = &I[i];
+		n0 += intv->n;
+		radix_sort_bed(intv->a, intv->a + intv->n); // sort by st
+		for (j = 1, j0 = 0; j <= intv->n; ++j) { // sort by st and then by end
+			if (j == intv->n || intv->a[j].st != intv->a[j0].st) {
+				radix_sort_end(intv->a + j0, intv->a + j);
+				j0 = j;
+			}
+		}
+		for (j = 1, j0 = 0, k = 0; j <= intv->n; ++j) { // merge intervals with the same (st, en)
+			if (j == intv->n || intv->a[j].st != intv->a[j0].st || intv->a[j].en != intv->a[j0].en) {
+				intv->a[k] = intv->a[j0];
+				intv->a[k++].cnt = j - j0;
+				j0 = j;
+			}
+		}
+		intv->a = REALLOC(mm_idx_intv1_t, intv->a, k);
+		intv->n = intv->m = k;
+		n += k;
+	}
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[%s] read %ld introns, %ld of which are non-redundant\n", __func__, n0, n);
+	return I;
+}
+
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
+{
+	if (mi->h == 0) mm_idx_index_name(mi);
+	mi->I = mm_idx_bed_read_merge(mi, fn, read_junc, -1);
+	return 0;
+}
+
+int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s)
+{
+	int32_t i, left, right;
+	mm_idx_intv_t *r;
+	memset(s, 0, en - st);
+	if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1;
+	r = &mi->I[ctg];
+	left = 0, right = r->n;
+	while (right > left) {
+		int32_t mid = left + ((right - left) >> 1);
+		if (r->a[mid].st >= st) right = mid;
+		else left = mid + 1;
+	}
+	for (i = left; i < r->n; ++i) {
+		if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
+			if (r->a[i].strand > 0) {
+				s[r->a[i].st - st] |= 1, s[r->a[i].en - 1 - st] |= 2;
+			} else {
+				s[r->a[i].st - st] |= 8, s[r->a[i].en - 1 - st] |= 4;
+			}
+		}
+	}
+	return left;
+}
+
+/*********************************
+ * Reading junctions for jumping *
+ *********************************/
+
+#define sort_key_jj(a) ((a).off)
+KRADIX_SORT_INIT(jj, mm_idx_jjump1_t, sort_key_jj, 4)
+
+#define sort_key_jj2(a) ((a).off2)
+KRADIX_SORT_INIT(jj2, mm_idx_jjump1_t, sort_key_jj2, 4)
+
+static void sort_jjump(mm_idx_jjump_t *jj2)
+{
+	int32_t j0, j, k;
+	if (jj2 == 0 || jj2->n == 0) return;
+	radix_sort_jj(jj2->a, jj2->a + jj2->n);
+	for (j0 = 0, j = 1; j <= jj2->n; ++j) {
+		if (j == jj2->n || jj2->a[j0].off != jj2->a[j].off) {
+			radix_sort_jj2(jj2->a + j0, jj2->a + j);
+			j0 = j;
+		}
+	}
+	// the actual merge
+	for (j0 = 0, j = 1, k = 0; j <= jj2->n; ++j) {
+		if (j == jj2->n || jj2->a[j0].off != jj2->a[j].off || jj2->a[j0].off2 != jj2->a[j].off2) {
+			int32_t t, cnt = 0;
+			uint16_t flag = 0;
+			for (t = j0; t < j; ++t) cnt += jj2->a[t].cnt, flag |= jj2->a[t].flag;
+			jj2->a[k] = jj2->a[j0];
+			jj2->a[k].cnt = cnt;
+			jj2->a[k++].flag = flag;
+			j0 = j;
+		}
+	}
+	jj2->n = k;
+	jj2->a = REALLOC(mm_idx_jjump1_t, jj2->a, k);
+}
+
+static mm_idx_jjump_t *mm_idx_bed2jjump(const mm_idx_t *mi, const mm_idx_intv_t *I, uint16_t flag)
+{
+	int32_t i;
+	mm_idx_jjump_t *J;
+	J = CALLOC(mm_idx_jjump_t, mi->n_seq);
+	for (i = 0; i < mi->n_seq; ++i) {
+		int32_t j, k;
+		const mm_idx_intv_t *intv = &I[i];
+		mm_idx_jjump_t *jj = &J[i];
+		jj->n = intv->n * 2;
+		jj->a = CALLOC(mm_idx_jjump1_t, jj->n);
+		for (j = k = 0; j < intv->n; ++j) {
+			jj->a[k].off = intv->a[j].st, jj->a[k].off2 = intv->a[j].en, jj->a[k].cnt = intv->a[j].cnt, jj->a[k].strand = intv->a[j].strand, jj->a[k++].flag = flag;
+			jj->a[k].off = intv->a[j].en, jj->a[k].off2 = intv->a[j].st, jj->a[k].cnt = intv->a[j].cnt, jj->a[k].strand = intv->a[j].strand, jj->a[k++].flag = flag;
+		}
+		sort_jjump(jj);
+	}
+	return J;
+}
+
+static mm_idx_jjump_t *mm_idx_jjump_merge(const mm_idx_t *mi, const mm_idx_jjump_t *J0, const mm_idx_jjump_t *J1)
+{
+	int32_t i;
+	mm_idx_jjump_t *J2;
+	J2 = CALLOC(mm_idx_jjump_t, mi->n_seq);
+	for (i = 0; i < mi->n_seq; ++i) {
+		int32_t j, k;
+		const mm_idx_jjump_t *jj0 = &J0[i], *jj1 = &J1[i];
+		mm_idx_jjump_t *jj2 = &J2[i];
+		jj2->n = jj0->n + jj1->n;
+		jj2->a = CALLOC(mm_idx_jjump1_t, jj2->n);
+		for (j = k = 0; j < jj0->n; ++j) jj2->a[k++] = jj0->a[j];
+		for (j = 0; j < jj1->n; ++j) jj2->a[k++] = jj1->a[j];
+		sort_jjump(jj2);
+	}
+	return J2;
+}
+
+int mm_idx_jjump_read(mm_idx_t *mi, const char *fn, int flag, int min_sc)
+{
+	int32_t i, j, n_anno = 0, n_misc = 0;
+	mm_idx_intv_t *I;
+	mm_idx_jjump_t *J;
+	if (mi->h == 0) mm_idx_index_name(mi);
+	I = mm_idx_bed_read_merge(mi, fn, 1, min_sc);
+	J = mm_idx_bed2jjump(mi, I, flag);
+	for (i = 0; i < mi->n_seq; ++i) free(I[i].a);
+	free(I);
+	if (mi->J) {
+		mm_idx_jjump_t *J2;
+		J2 = mm_idx_jjump_merge(mi, mi->J, J);
+		for (i = 0; i < mi->n_seq; ++i) {
+			free(mi->J[i].a); free(J[i].a);
+		}
+		free(mi->J); free(J);
+		mi->J = J2;
+	} else mi->J = J;
+	for (i = 0; i < mi->n_seq; ++i) {
+		for (j = 0; j < mi->J[i].n; ++j)
+			if (mi->J[i].a[j].flag & MM_JUNC_ANNO) ++n_anno;
+			else ++n_misc;
+	}
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[%s] there are %d annotated and %d other splice positions in the index\n", __func__, n_anno, n_misc);
+	return 0;
+}
+
+static int32_t mm_idx_jump_get_core(int32_t n, const mm_idx_jjump1_t *a, int32_t x) // similar to mm_idx_find_intv()
+{
+	int32_t s = 0, e = n;
+	if (n == 0) return -1;
+	if (x < a[0].off) return -1;
+	while (s < e) {
+		int32_t mid = s + (e - s) / 2;
+		if (x >= a[mid].off && (mid + 1 >= n || x < a[mid+1].off)) return mid;
+		else if (x < a[mid].off) e = mid;
+		else s = mid + 1;
+	}
+	assert(0);
+}
+
+const mm_idx_jjump1_t *mm_idx_jump_get(const mm_idx_t *db, int32_t cid, int32_t st, int32_t en, int32_t *n)
+{
+	mm_idx_jjump_t *s;
+	int32_t l, r;
+	*n = 0;
+	if (cid >= db->n_seq || cid < 0 || db->J == 0) return 0;
+	if (en < 0 || en > db->seq[cid].len) en = db->seq[cid].len;
+	s = &db->J[cid];
+	if (s->n == 0) return 0;
+	l = mm_idx_jump_get_core(s->n, s->a, st);
+	r = mm_idx_jump_get_core(s->n, s->a, en);
+	*n = r - l;
+	return &s->a[l + 1];
+}
+
+/****************
+ * splice score *
+ ****************/
+
+typedef struct mm_idx_spsc_s {
+	uint32_t n, m;
+	uint64_t *a; // pos<<56 | score<<1 | acceptor
+} mm_idx_spsc_t;
+
+int32_t mm_idx_spsc_read2(mm_idx_t *idx, const char *fn, int32_t max_sc, float scale)
+{
+	gzFile fp;
+	kstring_t str = {0,0,0};
+	kstream_t *ks;
+	int32_t dret, j;
+	int64_t n_read = 0;
+
+	fp = fn && strcmp(fn, "-") != 0? gzopen(fn, "rb") : gzdopen(0, "rb");
+	if (fp == 0) return -1;
+	if (idx->h == 0) mm_idx_index_name(idx);
+	if (max_sc > 63) max_sc = 63;
+	idx->spsc = Kcalloc(0, mm_idx_spsc_t, idx->n_seq * 2);
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+		mm_idx_spsc_t *s;
+		char *p, *q, *name = 0;
+		int32_t i, type = -1, strand = 0, cid = -1, score = -1;
+		int64_t pos = -1;
+		for (i = 0, p = q = str.s;; ++p) {
+			if (*p == '\t' || *p == 0) {
+				int c = *p;
+				*p = 0;
+				if (i == 0) {
+					name = q;
+				} else if (i == 1) {
+					pos = atol(q);
+				} else if (i == 2) {
+					strand = *q == '+'? 1 : '-'? -1 : 0;
+				} else if (i == 3) {
+					type = *q == 'D'? 0 : *q == 'A'? 1 : -1;
+				} else if (i == 4) {
+					score = atoi(q);
+					break;
+				}
+				if (c == 0) break;
+				q = p + 1, ++i;
+			}
+		}
+		if (i < 4) continue; // not enough fields
+		if (scale > 0.0f && scale < 1.0f)
+			score = score > 0.0f? (int)(score * scale + .499) : (int)(score * scale - .499);
+		if (score > max_sc) score = max_sc;
+		if (score < -max_sc) score = -max_sc;
+		cid = mm_idx_name2id(idx, name);
+		if (cid < 0 || type < 0 || strand == 0 || pos < 0) continue; // FIXME: give a warning!
+		s = &idx->spsc[cid << 1 | (strand > 0? 0 : 1)];
+		Kgrow(0, uint64_t, s->a, s->n, s->m);
+		if (pos > 0 && pos < idx->seq[cid].len) { // ignore scores at the ends
+			s->a[s->n++] = (uint64_t)pos << 8 | (score + KSW_SPSC_OFFSET) << 1 | type;
+			++n_read;
+		}
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	for (j = 0; j < idx->n_seq * 2; ++j) {
+		mm_idx_spsc_t *s = &idx->spsc[j];
+		if (s->n > 0)
+			radix_sort_64(s->a, s->a + s->n);
+	}
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s] read %ld splice scores\n", __func__, (long)n_read);
+	return 0;
+}
+
+int32_t mm_idx_spsc_read(mm_idx_t *idx, const char *fn, int32_t max_sc)
+{
+	return mm_idx_spsc_read2(idx, fn, max_sc, 1.0f);
+}
+
+static int32_t mm_idx_find_intv(int32_t n, const uint64_t *a, int64_t x)
+{
+	int32_t s = 0, e = n;
+	if (n == 0) return -1;
+	if (x < a[0]>>8) return -1;
+	while (s < e) {
+		int32_t mid = s + (e - s) / 2;
+		if (x >= a[mid]>>8 && (mid + 1 >= n || x < a[mid+1]>>8)) return mid;
+		else if (x < a[mid]>>8) e = mid;
+		else s = mid + 1;
+	}
+	assert(0);
+}
+
+int64_t mm_idx_spsc_get(const mm_idx_t *db, int32_t cid, int64_t st, int64_t en, int32_t rev, uint8_t *sc)
+{
+	const mm_idx_spsc_t *s;
+	if (cid >= db->n_seq || cid < 0 || db->spsc == 0) return -1;
+	if (en < 0 || en > db->seq[cid].len) en = db->seq[cid].len;
+	memset(sc, 0xff, en - st);
+	s = &db->spsc[cid << 1 | (!!rev)];
+	if (s->n > 0) {
+		int32_t j, l, r;
+		l = mm_idx_find_intv(s->n, s->a, st);
+		r = mm_idx_find_intv(s->n, s->a, en);
+		for (j = l + 1; j <= r; ++j) {
+			int64_t x = (s->a[j]>>8) - st;
+			uint8_t score = s->a[j] & 0xff;
+			assert(x <= en - st);
+			if (x == en - st) continue;
+			if (sc[x] == 0xff || sc[x] < score) sc[x] = score;
+		}
+	}
+	return en - st;
+}

jump.c

@@ -0,0 +1,201 @@
+#include <stdio.h>
+#include "mmpriv.h"
+#include "kalloc.h"
+
+#define MM_MIN_EXON_LEN 20
+
+static int32_t mm_jump_check(void *km, const mm_idx_t *mi, int32_t qlen, const uint8_t *qseq0, const mm_reg1_t *r, int32_t ext, int32_t is_left) // TODO: check close N
+{
+	int32_t clip, clen, e = !r->rev ^ !is_left; // 0 for left of the alignment; 1 for right
+	uint32_t cigar;
+	if (!r->p || r->p->n_cigar <= 0) return -1; // only working with CIGAR
+	clip = e == 0? r->qs : qlen - r->qe;
+	cigar = r->p->cigar[is_left? 0 : r->p->n_cigar - 1];
+	clen = (cigar&0xf) == MM_CIGAR_MATCH? cigar>>4 : 0;
+	if (clen <= ext) return -1;
+	if (is_left) {
+		if (clip >= r->rs) return -1; // no space to jump
+	} else {
+		if (clip >= mi->seq[r->rid].len - r->re) return -1; // no space to jump
+	}
+	return 0;
+}
+
+static uint8_t *mm_jump_get_qseq_seq(void *km, int32_t qlen, const uint8_t *qseq0, const mm_reg1_t *r, int32_t is_left, int32_t ql0, uint8_t *qseq)
+{
+	extern unsigned char seq_nt4_table[256];
+	int32_t i, k = 0;
+	if (!r->rev) {
+		if (is_left)
+			for (i = 0; i < ql0; ++i)
+				qseq[k++] = seq_nt4_table[(uint8_t)qseq0[i]];
+		else
+			for (i = qlen - ql0; i < qlen; ++i)
+				qseq[k++] = seq_nt4_table[(uint8_t)qseq0[i]];
+	} else {
+		if (is_left)
+			for (i = qlen - 1; i >= qlen - ql0; --i) {
+				uint8_t c = seq_nt4_table[(uint8_t)qseq0[i]];
+				qseq[k++] = c >= 4? c : 3 - c;
+			}
+		else
+			for (i = ql0 - 1; i >= 0; --i) {
+				uint8_t c = seq_nt4_table[(uint8_t)qseq0[i]];
+				qseq[k++] = c >= 4? c : 3 - c;
+			}
+	}
+	return qseq;
+}
+
+static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq0, mm_reg1_t *r, int32_t ts_strand)
+{
+	uint8_t *tseq = 0, *qseq = 0;
+	int32_t i, n, l, i0, m, mm0;
+	int32_t i0_anno = -1, n_anno = 0, mm0_anno = 0, i0_misc = -1, n_misc = 0, mm0_misc = 0;
+	int32_t ext = 1 + (opt->b + opt->a - 1) / opt->a + 1;
+	int32_t clip = !r->rev? r->qs : qlen - r->qe;
+	int32_t extt = clip < ext? clip : ext;
+	const mm_idx_jjump1_t *a;
+
+	if (mm_jump_check(km, mi, qlen, qseq0, r, ext + MM_MIN_EXON_LEN, 1) < 0) return;
+	a = mm_idx_jump_get(mi, r->rid, r->rs - extt, r->rs + ext, &n);
+	if (n == 0) return;
+
+	for (i = 0; i < n; ++i) { // traverse possible jumps
+		const mm_idx_jjump1_t *ai = &a[i];
+		int32_t tlen, tl1, j, mm1, mm2;
+		assert(ai->off >= r->rs - extt && ai->off <= r->rs + ext);
+		if (ts_strand * ai->strand < 0) continue; // wrong strand
+		if (ai->off2 >= ai->off) continue; // wrong direction
+		if (ai->off - ai->off2 < 6) continue; // intron too small
+		if (ai->off2 < clip + ext) continue; // not long enough
+		if (tseq == 0) {
+			tseq = Kcalloc(km, uint8_t, (clip + ext) * 2); // tseq and qseq are allocated together
+			qseq = tseq + clip + ext;
+			mm_jump_get_qseq_seq(km, qlen, qseq0, r, 1, clip + ext, qseq);
+		}
+		tl1 = clip + (ai->off - r->rs);
+		tlen = mm_idx_getseq2(mi, 0, r->rid, ai->off, r->rs + ext, &tseq[tl1]);
+		assert(tlen == r->rs + ext - ai->off);
+		tlen = mm_idx_getseq2(mi, 0, r->rid, ai->off2 - tl1, ai->off2, tseq);
+		assert(tlen == tl1);
+		for (j = 0, mm1 = 0; j < tl1; ++j)
+			if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
+				++mm1;
+		for (mm2 = 0; j < clip + ext; ++j)
+			if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
+				++mm2;
+		if (mm1 == 0 && mm2 <= 1) {
+			if (ai->flag & MM_JUNC_ANNO)
+				i0_anno = i, mm0_anno = mm1 + mm2, ++n_anno; // i0 points to the rightmost i
+			else
+				i0_misc = i, mm0_misc = mm1 + mm2, ++n_misc;
+		}
+	}
+	if (n_anno > 0) m = n_anno, i0 = i0_anno, mm0 = mm0_anno;
+	else m = n_misc, i0 = i0_misc, mm0 = mm0_misc;
+	kfree(km, tseq);
+
+	l = m > 0? a[i0].off - r->rs : 0; // may be negative
+	if (m == 1 && clip + l >= opt->jump_min_match) { // add one more exon
+		mm_enlarge_cigar(r, 2);
+		memmove(r->p->cigar + 2, r->p->cigar, r->p->n_cigar * 4);
+		r->p->cigar[0] = (clip + l) << 4 | MM_CIGAR_MATCH;
+		r->p->cigar[1] = (a[i0].off - a[i0].off2) << 4 | MM_CIGAR_N_SKIP;
+		r->p->cigar[2] = ((r->p->cigar[2]>>4) - l) << 4 | MM_CIGAR_MATCH;
+		r->p->n_cigar += 2;
+		r->rs = a[i0].off2 - (clip + l);
+		if (!r->rev) r->qs = 0;
+		else r->qe = qlen;
+		r->blen += clip, r->mlen += clip - mm0;
+		r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
+		r->p->dp_max += (clip - mm0) * opt->a - mm0 * opt->b;
+		if (!r->is_spliced) r->is_spliced = 1, r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
+	} else if (m > 0 && a[i0].off > r->rs) { // trim by l; l is always positive
+		r->p->cigar[0] -= l << 4 | MM_CIGAR_MATCH;
+		r->rs += l;
+		if (!r->rev) r->qs += l;
+		else r->qe -= l;
+	}
+}
+
+static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq0, mm_reg1_t *r, int32_t ts_strand)
+{
+	uint8_t *tseq = 0, *qseq = 0;
+	int32_t i, n, l, i0, m, mm0;
+	int32_t i0_anno = -1, n_anno = 0, mm0_anno = 0, i0_misc = -1, n_misc = 0, mm0_misc = 0;
+	int32_t ext = 1 + (opt->b + opt->a - 1) / opt->a + 1;
+	int32_t clip = !r->rev? qlen - r->qe : r->qs;
+	int32_t extt = clip < ext? clip : ext;
+	const mm_idx_jjump1_t *a;
+
+	if (mm_jump_check(km, mi, qlen, qseq0, r, ext + MM_MIN_EXON_LEN, 0) < 0) return;
+	a = mm_idx_jump_get(mi, r->rid, r->re - ext, r->re + extt, &n);
+	if (n == 0) return;
+
+	for (i = 0; i < n; ++i) { // traverse possible jumps
+		const mm_idx_jjump1_t *ai = &a[i];
+		int32_t tlen, tl1, j, mm1, mm2;
+		assert(ai->off >= r->re - ext && ai->off <= r->re + extt);
+		if (ts_strand * ai->strand < 0) continue; // wrong strand
+		if (ai->off2 <= ai->off) continue; // wrong direction
+		if (ai->off2 - ai->off < 6) continue; // intron too small
+		if (ai->off2 + clip + ext > mi->seq[r->rid].len) continue; // not long enough
+		if (tseq == 0) {
+			tseq = Kcalloc(km, uint8_t, (clip + ext) * 2); // tseq and qseq are allocated together
+			qseq = tseq + clip + ext;
+			mm_jump_get_qseq_seq(km, qlen, qseq0, r, 0, clip + ext, qseq);
+		}
+		tl1 = clip + (r->re - ai->off);
+		tlen = mm_idx_getseq2(mi, 0, r->rid, r->re - ext, ai->off, tseq);
+		assert(tlen == ai->off - (r->re - ext));
+		tlen = mm_idx_getseq2(mi, 0, r->rid, ai->off2, ai->off2 + tl1, &tseq[clip + ext - tl1]);
+		assert(tlen == tl1);
+		for (j = 0, mm2 = 0; j < clip + ext - tl1; ++j)
+			if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
+				++mm2;
+		for (mm1 = 0; j < clip + ext; ++j)
+			if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
+				++mm1;
+		if (mm1 == 0 && mm2 <= 1) {
+			if (ai->flag & MM_JUNC_ANNO) {
+				if (i0_anno < 0) i0_anno = i, mm0_anno = mm1 + mm2;
+				++n_anno;
+			} else {
+				if (i0_misc < 0) i0_misc = i, mm0_misc = mm1 + mm2;
+				++n_misc;
+			}
+		}
+	}
+	if (n_anno > 0) m = n_anno, i0 = i0_anno, mm0 = mm0_anno;
+	else m = n_misc, i0 = i0_misc, mm0 = mm0_misc;
+	kfree(km, tseq);
+
+	l = m > 0? r->re - a[i0].off : 0; // may be negative
+	if (m == 1 && clip + l >= opt->jump_min_match) { // add one more exon
+		mm_enlarge_cigar(r, 2);
+		r->p->cigar[r->p->n_cigar - 1] = ((r->p->cigar[r->p->n_cigar - 1]>>4) - l) << 4 | MM_CIGAR_MATCH;
+		r->p->cigar[r->p->n_cigar] = (a[i0].off2 - a[i0].off) << 4 | MM_CIGAR_N_SKIP;
+		r->p->cigar[r->p->n_cigar + 1] = (clip + l) << 4 | MM_CIGAR_MATCH;
+		r->p->n_cigar += 2;
+		r->re = a[i0].off2 + (clip + l);
+		if (!r->rev) r->qe = qlen;
+		else r->qs = 0;
+		r->blen += clip, r->mlen += clip - mm0;
+		r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
+		r->p->dp_max += (clip - mm0) * opt->a - mm0 * opt->b;
+		if (!r->is_spliced) r->is_spliced = 1, r->p->dp_max += (opt->a + opt->b) + ((opt->a + opt->b) >> 1);
+	} else if (m > 0 && r->re > a[i0].off) { // trim by l; l is always positive
+		r->p->cigar[r->p->n_cigar - 1] -= l << 4 | MM_CIGAR_MATCH;
+		r->re -= l;
+		if (!r->rev) r->qe -= l;
+		else r->qs += l;
+	}
+}
+
+void mm_jump_split(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq, mm_reg1_t *r, int32_t ts_strand)
+{
+	assert((opt->flag & MM_F_EQX) == 0);
+	mm_jump_split_left(km,  mi, opt, qlen, qseq, r, ts_strand);
+	mm_jump_split_right(km, mi, opt, qlen, qseq, r, ts_strand);
+}

kalloc.c

@@ -18,15 +18,14 @@
  *       |                           |                 |                               |
  *       p=p->ptr->ptr->ptr->ptr     p->ptr            p->ptr->ptr                     p->ptr->ptr->ptr
  */
-
-#define MIN_CORE_SIZE 0x80000
-
 typedef struct header_t {
 	size_t size;
 	struct header_t *ptr;
 } header_t;
 
 typedef struct {
+	void *par;
+	size_t min_core_size;
 	header_t base, *loop_head, *core_head; /* base is a zero-sized block always kept in the loop */
 } kmem_t;
 
@@ -36,31 +35,40 @@ static void panic(const char *s)
 	abort();
 }
 
-void *km_init(void)
+void *km_init2(void *km_par, size_t min_core_size)
 {
-	return calloc(1, sizeof(kmem_t));
+	kmem_t *km;
+	km = (kmem_t*)kcalloc(km_par, 1, sizeof(kmem_t));
+	km->par = km_par;
+	if (km_par) km->min_core_size = min_core_size > 0? min_core_size : ((kmem_t*)km_par)->min_core_size - 2;
+	else km->min_core_size = min_core_size > 0? min_core_size : 0x80000;
+	return (void*)km;
 }
 
+void *km_init(void) { return km_init2(0, 0); }
+
 void km_destroy(void *_km)
 {
 	kmem_t *km = (kmem_t*)_km;
+	void *km_par;
 	header_t *p, *q;
 	if (km == NULL) return;
+	km_par = km->par;
 	for (p = km->core_head; p != NULL;) {
 		q = p->ptr;
-		free(p);
+		kfree(km_par, p);
 		p = q;
 	}
-	free(km);
+	kfree(km_par, km);
 }
 
 static header_t *morecore(kmem_t *km, size_t nu)
 {
 	header_t *q;
 	size_t bytes, *p;
-	nu = (nu + 1 + (MIN_CORE_SIZE - 1)) / MIN_CORE_SIZE * MIN_CORE_SIZE; /* the first +1 for core header */
+	nu = (nu + 1 + (km->min_core_size - 1)) / km->min_core_size * km->min_core_size; /* the first +1 for core header */
 	bytes = nu * sizeof(header_t);
-	q = (header_t*)malloc(bytes);
+	q = (header_t*)kmalloc(km->par, bytes);
 	if (!q) panic("[morecore] insufficient memory");
 	q->ptr = km->core_head, q->size = nu, km->core_head = q;
 	p = (size_t*)(q + 1);
@@ -125,7 +133,7 @@ void *kmalloc(void *_km, size_t n_bytes)
 
 	if (n_bytes == 0) return 0;
 	if (km == NULL) return malloc(n_bytes);
-	n_units = (n_bytes + sizeof(size_t) + sizeof(header_t) - 1) / sizeof(header_t) + 1;
+	n_units = (n_bytes + sizeof(size_t) + sizeof(header_t) - 1) / sizeof(header_t); /* header+n_bytes requires at least this number of units */
 
 	if (!(q = km->loop_head)) /* the first time when kmalloc() is called, intialize it */
 		q = km->loop_head = km->base.ptr = &km->base;
@@ -160,22 +168,32 @@ void *kcalloc(void *_km, size_t count, size_t size)
 void *krealloc(void *_km, void *ap, size_t n_bytes) // TODO: this can be made more efficient in principle
 {
 	kmem_t *km = (kmem_t*)_km;
-	size_t n_units, *p, *q;
+	size_t cap, *p, *q;
 
 	if (n_bytes == 0) {
 		kfree(km, ap); return 0;
 	}
 	if (km == NULL) return realloc(ap, n_bytes);
 	if (ap == NULL) return kmalloc(km, n_bytes);
-	n_units = (n_bytes + sizeof(size_t) + sizeof(header_t) - 1) / sizeof(header_t);
 	p = (size_t*)ap - 1;
-	if (*p >= n_units) return ap; /* TODO: this prevents shrinking */
+	cap = (*p) * sizeof(header_t) - sizeof(size_t);
+	if (cap >= n_bytes) return ap; /* TODO: this prevents shrinking */
 	q = (size_t*)kmalloc(km, n_bytes);
-	memcpy(q, ap, (*p - 1) * sizeof(header_t));
+	memcpy(q, ap, cap);
 	kfree(km, ap);
 	return q;
 }
 
+void *krelocate(void *km, void *ap, size_t n_bytes)
+{
+	void *p;
+	if (km == 0 || ap == 0) return ap;
+	p = kmalloc(km, n_bytes);
+	memcpy(p, ap, n_bytes);
+	kfree(km, ap);
+	return p;
+}
+
 void km_stat(const void *_km, km_stat_t *s)
 {
 	kmem_t *km = (kmem_t*)_km;
@@ -196,3 +214,11 @@ void km_stat(const void *_km, km_stat_t *s)
 		s->largest = s->largest > size? s->largest : size;
 	}
 }
+
+void km_stat_print(const void *km)
+{
+	km_stat_t st;
+	km_stat(km, &st);
+	fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
+			st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
+}

kalloc.h

@@ -13,15 +13,83 @@ typedef struct {
 
 void *kmalloc(void *km, size_t size);
 void *krealloc(void *km, void *ptr, size_t size);
+void *krelocate(void *km, void *ap, size_t n_bytes);
 void *kcalloc(void *km, size_t count, size_t size);
 void kfree(void *km, void *ptr);
 
 void *km_init(void);
+void *km_init2(void *km_par, size_t min_core_size);
 void km_destroy(void *km);
 void km_stat(const void *_km, km_stat_t *s);
+void km_stat_print(const void *km);
 
 #ifdef __cplusplus
 }
 #endif
 
+#define Kmalloc(km, type, cnt)       ((type*)kmalloc((km), (cnt) * sizeof(type)))
+#define Kcalloc(km, type, cnt)       ((type*)kcalloc((km), (cnt), sizeof(type)))
+#define Krealloc(km, type, ptr, cnt) ((type*)krealloc((km), (ptr), (cnt) * sizeof(type)))
+
+#define Kgrow(km, type, ptr, __i, __m) do { \
+		if ((__i) >= (__m)) { \
+			(__m) = (__i) + 1; \
+			(__m) += ((__m)>>1) + 16; \
+			(ptr) = Krealloc(km, type, ptr, (__m)); \
+		} \
+	} while (0)
+
+#define Kexpand(km, type, a, m) do { \
+		(m) = (m) >= 4? (m) + ((m)>>1) : 16; \
+		(a) = Krealloc(km, type, (a), (m)); \
+	} while (0)
+
+#define KMALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))kmalloc((km), (len) * sizeof(*(ptr))))
+#define KCALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))kcalloc((km), (len), sizeof(*(ptr))))
+#define KREALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))krealloc((km), (ptr), (len) * sizeof(*(ptr))))
+
+#define KEXPAND(km, a, m) do { \
+		(m) = (m) >= 4? (m) + ((m)>>1) : 16; \
+		KREALLOC((km), (a), (m)); \
+	} while (0)
+
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
+#define KALLOC_POOL_INIT2(SCOPE, name, kmptype_t) \
+	typedef struct { \
+		size_t cnt, n, max; \
+		kmptype_t **buf; \
+		void *km; \
+	} kmp_##name##_t; \
+	SCOPE kmp_##name##_t *kmp_init_##name(void *km) { \
+		kmp_##name##_t *mp; \
+		mp = Kcalloc(km, kmp_##name##_t, 1); \
+		mp->km = km; \
+		return mp; \
+	} \
+	SCOPE void kmp_destroy_##name(kmp_##name##_t *mp) { \
+		size_t k; \
+		for (k = 0; k < mp->n; ++k) kfree(mp->km, mp->buf[k]); \
+		kfree(mp->km, mp->buf); kfree(mp->km, mp); \
+	} \
+	SCOPE kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \
+		++mp->cnt; \
+		if (mp->n == 0) return (kmptype_t*)kcalloc(mp->km, 1, sizeof(kmptype_t)); \
+		return mp->buf[--mp->n]; \
+	} \
+	SCOPE void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \
+		--mp->cnt; \
+		if (mp->n == mp->max) Kexpand(mp->km, kmptype_t*, mp->buf, mp->max); \
+		mp->buf[mp->n++] = p; \
+	}
+
+#define KALLOC_POOL_INIT(name, kmptype_t) \
+	KALLOC_POOL_INIT2(static inline klib_unused, name, kmptype_t)
+
 #endif

ketopt.h

@@ -0,0 +1,120 @@
+#ifndef KETOPT_H
+#define KETOPT_H
+
+#include <string.h> /* for strchr() and strncmp() */
+
+#define ko_no_argument       0
+#define ko_required_argument 1
+#define ko_optional_argument 2
+
+typedef struct {
+	int ind;   /* equivalent to optind */
+	int opt;   /* equivalent to optopt */
+	char *arg; /* equivalent to optarg */
+	int longidx; /* index of a long option; or -1 if short */
+	/* private variables not intended for external uses */
+	int i, pos, n_args;
+} ketopt_t;
+
+typedef struct {
+	char *name;
+	int has_arg;
+	int val;
+} ko_longopt_t;
+
+static ketopt_t KETOPT_INIT = { 1, 0, 0, -1, 1, 0, 0 };
+
+static void ketopt_permute(char *argv[], int j, int n) /* move argv[j] over n elements to the left */
+{
+	int k;
+	char *p = argv[j];
+	for (k = 0; k < n; ++k)
+		argv[j - k] = argv[j - k - 1];
+	argv[j - k] = p;
+}
+
+/**
+ * Parse command-line options and arguments
+ *
+ * This fuction has a similar interface to GNU's getopt_long(). Each call
+ * parses one option and returns the option name.  s->arg points to the option
+ * argument if present. The function returns -1 when all command-line arguments
+ * are parsed. In this case, s->ind is the index of the first non-option
+ * argument.
+ *
+ * @param s         status; shall be initialized to KETOPT_INIT on the first call
+ * @param argc      length of argv[]
+ * @param argv      list of command-line arguments; argv[0] is ignored
+ * @param permute   non-zero to move options ahead of non-option arguments
+ * @param ostr      option string
+ * @param longopts  long options
+ *
+ * @return ASCII for a short option; ko_longopt_t::val for a long option; -1 if
+ *         argv[] is fully processed; '?' for an unknown option or an ambiguous
+ *         long option; ':' if an option argument is missing
+ */
+static int ketopt(ketopt_t *s, int argc, char *argv[], int permute, const char *ostr, const ko_longopt_t *longopts)
+{
+	int opt = -1, i0, j;
+	if (permute) {
+		while (s->i < argc && (argv[s->i][0] != '-' || argv[s->i][1] == '\0'))
+			++s->i, ++s->n_args;
+	}
+	s->arg = 0, s->longidx = -1, i0 = s->i;
+	if (s->i >= argc || argv[s->i][0] != '-' || argv[s->i][1] == '\0') {
+		s->ind = s->i - s->n_args;
+		return -1;
+	}
+	if (argv[s->i][0] == '-' && argv[s->i][1] == '-') { /* "--" or a long option */
+		if (argv[s->i][2] == '\0') { /* a bare "--" */
+			ketopt_permute(argv, s->i, s->n_args);
+			++s->i, s->ind = s->i - s->n_args;
+			return -1;
+		}
+		s->opt = 0, opt = '?', s->pos = -1;
+		if (longopts) { /* parse long options */
+			int k, n_exact = 0, n_partial = 0;
+			const ko_longopt_t *o = 0, *o_exact = 0, *o_partial = 0;
+			for (j = 2; argv[s->i][j] != '\0' && argv[s->i][j] != '='; ++j) {} /* find the end of the option name */
+			for (k = 0; longopts[k].name != 0; ++k)
+				if (strncmp(&argv[s->i][2], longopts[k].name, j - 2) == 0) {
+					if (longopts[k].name[j - 2] == 0) ++n_exact, o_exact = &longopts[k];
+					else ++n_partial, o_partial = &longopts[k];
+				}
+			if (n_exact > 1 || (n_exact == 0 && n_partial > 1)) return '?';
+			o = n_exact == 1? o_exact : n_partial == 1? o_partial : 0;
+			if (o) {
+				s->opt = opt = o->val, s->longidx = o - longopts;
+				if (argv[s->i][j] == '=') s->arg = &argv[s->i][j + 1];
+				if (o->has_arg == 1 && argv[s->i][j] == '\0') {
+					if (s->i < argc - 1) s->arg = argv[++s->i];
+					else opt = ':'; /* missing option argument */
+				}
+			}
+		}
+	} else { /* a short option */
+		char *p;
+		if (s->pos == 0) s->pos = 1;
+		opt = s->opt = argv[s->i][s->pos++];
+		p = strchr((char*)ostr, opt);
+		if (p == 0) {
+			opt = '?'; /* unknown option */
+		} else if (p[1] == ':') {
+			if (argv[s->i][s->pos] == 0) {
+				if (s->i < argc - 1) s->arg = argv[++s->i];
+				else opt = ':'; /* missing option argument */
+			} else s->arg = &argv[s->i][s->pos];
+			s->pos = -1;
+		}
+	}
+	if (s->pos < 0 || argv[s->i][s->pos] == 0) {
+		++s->i, s->pos = 0;
+		if (s->n_args > 0) /* permute */
+			for (j = i0; j < s->i; ++j)
+				ketopt_permute(argv, j, s->n_args);
+	}
+	s->ind = s->i - s->n_args;
+	return opt;
+}
+
+#endif

krmq.h

@@ -0,0 +1,474 @@
+/* The MIT License
+
+   Copyright (c) 2019 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* An example:
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include "krmq.h"
+
+struct my_node {
+  char key;
+  KRMQ_HEAD(struct my_node) head;
+};
+#define my_cmp(p, q) (((q)->key < (p)->key) - ((p)->key < (q)->key))
+KRMQ_INIT(my, struct my_node, head, my_cmp)
+
+int main(void) {
+  const char *str = "MNOLKQOPHIA"; // from wiki, except a duplicate
+  struct my_node *root = 0;
+  int i, l = strlen(str);
+  for (i = 0; i < l; ++i) {        // insert in the input order
+    struct my_node *q, *p = malloc(sizeof(*p));
+    p->key = str[i];
+    q = krmq_insert(my, &root, p, 0);
+    if (p != q) free(p);           // if already present, free
+  }
+  krmq_itr_t(my) itr;
+  krmq_itr_first(my, root, &itr);  // place at first
+  do {                             // traverse
+    const struct my_node *p = krmq_at(&itr);
+    putchar(p->key);
+    free((void*)p);                // free node
+  } while (krmq_itr_next(my, &itr));
+  putchar('\n');
+  return 0;
+}
+*/
+
+#ifndef KRMQ_H
+#define KRMQ_H
+
+#ifdef __STRICT_ANSI__
+#define inline __inline__
+#endif
+
+#define KRMQ_MAX_DEPTH 64
+
+#define krmq_size(head, p) ((p)? (p)->head.size : 0)
+#define krmq_size_child(head, q, i) ((q)->head.p[(i)]? (q)->head.p[(i)]->head.size : 0)
+
+#define KRMQ_HEAD(__type) \
+	struct { \
+		__type *p[2], *s; \
+		signed char balance; /* balance factor */ \
+		unsigned size; /* #elements in subtree */ \
+	}
+
+#define __KRMQ_FIND(suf, __scope, __type, __head,  __cmp) \
+	__scope __type *krmq_find_##suf(const __type *root, const __type *x, unsigned *cnt_) { \
+		const __type *p = root; \
+		unsigned cnt = 0; \
+		while (p != 0) { \
+			int cmp; \
+			cmp = __cmp(x, p); \
+			if (cmp >= 0) cnt += krmq_size_child(__head, p, 0) + 1; \
+			if (cmp < 0) p = p->__head.p[0]; \
+			else if (cmp > 0) p = p->__head.p[1]; \
+			else break; \
+		} \
+		if (cnt_) *cnt_ = cnt; \
+		return (__type*)p; \
+	} \
+	__scope __type *krmq_interval_##suf(const __type *root, const __type *x, __type **lower, __type **upper) { \
+		const __type *p = root, *l = 0, *u = 0; \
+		while (p != 0) { \
+			int cmp; \
+			cmp = __cmp(x, p); \
+			if (cmp < 0) u = p, p = p->__head.p[0]; \
+			else if (cmp > 0) l = p, p = p->__head.p[1]; \
+			else { l = u = p; break; } \
+		} \
+		if (lower) *lower = (__type*)l; \
+		if (upper) *upper = (__type*)u; \
+		return (__type*)p; \
+	}
+
+#define __KRMQ_RMQ(suf, __scope, __type, __head,  __cmp, __lt2) \
+	__scope __type *krmq_rmq_##suf(const __type *root, const __type *lo, const __type *up) { /* CLOSED interval */ \
+		const __type *p = root, *path[2][KRMQ_MAX_DEPTH], *min; \
+		int plen[2] = {0, 0}, pcmp[2][KRMQ_MAX_DEPTH], i, cmp, lca; \
+		if (root == 0) return 0; \
+		while (p) { \
+			cmp = __cmp(lo, p); \
+			path[0][plen[0]] = p, pcmp[0][plen[0]++] = cmp; \
+			if (cmp < 0) p = p->__head.p[0]; \
+			else if (cmp > 0) p = p->__head.p[1]; \
+			else break; \
+		} \
+		p = root; \
+		while (p) { \
+			cmp = __cmp(up, p); \
+			path[1][plen[1]] = p, pcmp[1][plen[1]++] = cmp; \
+			if (cmp < 0) p = p->__head.p[0]; \
+			else if (cmp > 0) p = p->__head.p[1]; \
+			else break; \
+		} \
+		for (i = 0; i < plen[0] && i < plen[1]; ++i) /* find the LCA */ \
+			if (path[0][i] == path[1][i] && pcmp[0][i] <= 0 && pcmp[1][i] >= 0) \
+				break; \
+		if (i == plen[0] || i == plen[1]) return 0; /* no elements in the closed interval */ \
+		lca = i, min = path[0][lca]; \
+		for (i = lca + 1; i < plen[0]; ++i) { \
+			if (pcmp[0][i] <= 0) { \
+				if (__lt2(path[0][i], min)) min = path[0][i]; \
+				if (path[0][i]->__head.p[1] && __lt2(path[0][i]->__head.p[1]->__head.s, min)) \
+					min = path[0][i]->__head.p[1]->__head.s; \
+			} \
+		} \
+		for (i = lca + 1; i < plen[1]; ++i) { \
+			if (pcmp[1][i] >= 0) { \
+				if (__lt2(path[1][i], min)) min = path[1][i]; \
+				if (path[1][i]->__head.p[0] && __lt2(path[1][i]->__head.p[0]->__head.s, min)) \
+					min = path[1][i]->__head.p[0]->__head.s; \
+			} \
+		} \
+		return (__type*)min; \
+	}
+
+#define __KRMQ_ROTATE(suf, __type, __head, __lt2) \
+	/* */ \
+	static inline void krmq_update_min_##suf(__type *p, const __type *q, const __type *r) { \
+		p->__head.s = !q || __lt2(p, q->__head.s)? p : q->__head.s; \
+		p->__head.s = !r || __lt2(p->__head.s, r->__head.s)? p->__head.s : r->__head.s; \
+	} \
+	/* one rotation: (a,(b,c)q)p => ((a,b)p,c)q */ \
+	static inline __type *krmq_rotate1_##suf(__type *p, int dir) { /* dir=0 to left; dir=1 to right */ \
+		int opp = 1 - dir; /* opposite direction */ \
+		__type *q = p->__head.p[opp], *s = p->__head.s; \
+		unsigned size_p = p->__head.size; \
+		p->__head.size -= q->__head.size - krmq_size_child(__head, q, dir); \
+		q->__head.size = size_p; \
+		krmq_update_min_##suf(p, p->__head.p[dir], q->__head.p[dir]); \
+		q->__head.s = s; \
+		p->__head.p[opp] = q->__head.p[dir]; \
+		q->__head.p[dir] = p; \
+		return q; \
+	} \
+	/* two consecutive rotations: (a,((b,c)r,d)q)p => ((a,b)p,(c,d)q)r */ \
+	static inline __type *krmq_rotate2_##suf(__type *p, int dir) { \
+		int b1, opp = 1 - dir; \
+		__type *q = p->__head.p[opp], *r = q->__head.p[dir], *s = p->__head.s; \
+		unsigned size_x_dir = krmq_size_child(__head, r, dir); \
+		r->__head.size = p->__head.size; \
+		p->__head.size -= q->__head.size - size_x_dir; \
+		q->__head.size -= size_x_dir + 1; \
+		krmq_update_min_##suf(p, p->__head.p[dir], r->__head.p[dir]); \
+		krmq_update_min_##suf(q, q->__head.p[opp], r->__head.p[opp]); \
+		r->__head.s = s; \
+		p->__head.p[opp] = r->__head.p[dir]; \
+		r->__head.p[dir] = p; \
+		q->__head.p[dir] = r->__head.p[opp]; \
+		r->__head.p[opp] = q; \
+		b1 = dir == 0? +1 : -1; \
+		if (r->__head.balance == b1) q->__head.balance = 0, p->__head.balance = -b1; \
+		else if (r->__head.balance == 0) q->__head.balance = p->__head.balance = 0; \
+		else q->__head.balance = b1, p->__head.balance = 0; \
+		r->__head.balance = 0; \
+		return r; \
+	}
+
+#define __KRMQ_INSERT(suf, __scope, __type, __head, __cmp, __lt2) \
+	__scope __type *krmq_insert_##suf(__type **root_, __type *x, unsigned *cnt_) { \
+		unsigned char stack[KRMQ_MAX_DEPTH]; \
+		__type *path[KRMQ_MAX_DEPTH]; \
+		__type *bp, *bq; \
+		__type *p, *q, *r = 0; /* _r_ is potentially the new root */ \
+		int i, which = 0, top, b1, path_len; \
+		unsigned cnt = 0; \
+		bp = *root_, bq = 0; \
+		/* find the insertion location */ \
+		for (p = bp, q = bq, top = path_len = 0; p; q = p, p = p->__head.p[which]) { \
+			int cmp; \
+			cmp = __cmp(x, p); \
+			if (cmp >= 0) cnt += krmq_size_child(__head, p, 0) + 1; \
+			if (cmp == 0) { \
+				if (cnt_) *cnt_ = cnt; \
+				return p; \
+			} \
+			if (p->__head.balance != 0) \
+				bq = q, bp = p, top = 0; \
+			stack[top++] = which = (cmp > 0); \
+			path[path_len++] = p; \
+		} \
+		if (cnt_) *cnt_ = cnt; \
+		x->__head.balance = 0, x->__head.size = 1, x->__head.p[0] = x->__head.p[1] = 0, x->__head.s = x; \
+		if (q == 0) *root_ = x; \
+		else q->__head.p[which] = x; \
+		if (bp == 0) return x; \
+		for (i = 0; i < path_len; ++i) ++path[i]->__head.size; \
+		for (i = path_len - 1; i >= 0; --i) { \
+			krmq_update_min_##suf(path[i], path[i]->__head.p[0], path[i]->__head.p[1]); \
+			if (path[i]->__head.s != x) break; \
+		} \
+		for (p = bp, top = 0; p != x; p = p->__head.p[stack[top]], ++top) /* update balance factors */ \
+			if (stack[top] == 0) --p->__head.balance; \
+			else ++p->__head.balance; \
+		if (bp->__head.balance > -2 && bp->__head.balance < 2) return x; /* no re-balance needed */ \
+		/* re-balance */ \
+		which = (bp->__head.balance < 0); \
+		b1 = which == 0? +1 : -1; \
+		q = bp->__head.p[1 - which]; \
+		if (q->__head.balance == b1) { \
+			r = krmq_rotate1_##suf(bp, which); \
+			q->__head.balance = bp->__head.balance = 0; \
+		} else r = krmq_rotate2_##suf(bp, which); \
+		if (bq == 0) *root_ = r; \
+		else bq->__head.p[bp != bq->__head.p[0]] = r; \
+		return x; \
+	}
+
+#define __KRMQ_ERASE(suf, __scope, __type, __head, __cmp, __lt2) \
+	__scope __type *krmq_erase_##suf(__type **root_, const __type *x, unsigned *cnt_) { \
+		__type *p, *path[KRMQ_MAX_DEPTH], fake; \
+		unsigned char dir[KRMQ_MAX_DEPTH]; \
+		int i, d = 0, cmp; \
+		unsigned cnt = 0; \
+		fake = **root_, fake.__head.p[0] = *root_, fake.__head.p[1] = 0; \
+		if (cnt_) *cnt_ = 0; \
+		if (x) { \
+			for (cmp = -1, p = &fake; cmp; cmp = __cmp(x, p)) { \
+				int which = (cmp > 0); \
+				if (cmp > 0) cnt += krmq_size_child(__head, p, 0) + 1; \
+				dir[d] = which; \
+				path[d++] = p; \
+				p = p->__head.p[which]; \
+				if (p == 0) { \
+					if (cnt_) *cnt_ = 0; \
+					return 0; \
+				} \
+			} \
+			cnt += krmq_size_child(__head, p, 0) + 1; /* because p==x is not counted */ \
+		} else { \
+			for (p = &fake, cnt = 1; p; p = p->__head.p[0]) \
+				dir[d] = 0, path[d++] = p; \
+			p = path[--d]; \
+		} \
+		if (cnt_) *cnt_ = cnt; \
+		for (i = 1; i < d; ++i) --path[i]->__head.size; \
+		if (p->__head.p[1] == 0) { /* ((1,.)2,3)4 => (1,3)4; p=2 */ \
+			path[d-1]->__head.p[dir[d-1]] = p->__head.p[0]; \
+		} else { \
+			__type *q = p->__head.p[1]; \
+			if (q->__head.p[0] == 0) { /* ((1,2)3,4)5 => ((1)2,4)5; p=3,q=2 */ \
+				q->__head.p[0] = p->__head.p[0]; \
+				q->__head.balance = p->__head.balance; \
+				path[d-1]->__head.p[dir[d-1]] = q; \
+				path[d] = q, dir[d++] = 1; \
+				q->__head.size = p->__head.size - 1; \
+			} else { /* ((1,((.,2)3,4)5)6,7)8 => ((1,(2,4)5)3,7)8; p=6 */ \
+				__type *r; \
+				int e = d++; /* backup _d_ */\
+				for (;;) { \
+					dir[d] = 0; \
+					path[d++] = q; \
+					r = q->__head.p[0]; \
+					if (r->__head.p[0] == 0) break; \
+					q = r; \
+				} \
+				r->__head.p[0] = p->__head.p[0]; \
+				q->__head.p[0] = r->__head.p[1]; \
+				r->__head.p[1] = p->__head.p[1]; \
+				r->__head.balance = p->__head.balance; \
+				path[e-1]->__head.p[dir[e-1]] = r; \
+				path[e] = r, dir[e] = 1; \
+				for (i = e + 1; i < d; ++i) --path[i]->__head.size; \
+				r->__head.size = p->__head.size - 1; \
+			} \
+		} \
+		for (i = d - 1; i >= 0; --i) /* not sure why adding condition "path[i]->__head.s==p" doesn't work */ \
+			krmq_update_min_##suf(path[i], path[i]->__head.p[0], path[i]->__head.p[1]); \
+		while (--d > 0) { \
+			__type *q = path[d]; \
+			int which, other, b1 = 1, b2 = 2; \
+			which = dir[d], other = 1 - which; \
+			if (which) b1 = -b1, b2 = -b2; \
+			q->__head.balance += b1; \
+			if (q->__head.balance == b1) break; \
+			else if (q->__head.balance == b2) { \
+				__type *r = q->__head.p[other]; \
+				if (r->__head.balance == -b1) { \
+					path[d-1]->__head.p[dir[d-1]] = krmq_rotate2_##suf(q, which); \
+				} else { \
+					path[d-1]->__head.p[dir[d-1]] = krmq_rotate1_##suf(q, which); \
+					if (r->__head.balance == 0) { \
+						r->__head.balance = -b1; \
+						q->__head.balance = b1; \
+						break; \
+					} else r->__head.balance = q->__head.balance = 0; \
+				} \
+			} \
+		} \
+		*root_ = fake.__head.p[0]; \
+		return p; \
+	}
+
+#define krmq_free(__type, __head, __root, __free) do { \
+		__type *_p, *_q; \
+		for (_p = __root; _p; _p = _q) { \
+			if (_p->__head.p[0] == 0) { \
+				_q = _p->__head.p[1]; \
+				__free(_p); \
+			} else { \
+				_q = _p->__head.p[0]; \
+				_p->__head.p[0] = _q->__head.p[1]; \
+				_q->__head.p[1] = _p; \
+			} \
+		} \
+	} while (0)
+
+#define __KRMQ_ITR(suf, __scope, __type, __head, __cmp) \
+	struct krmq_itr_##suf { \
+		const __type *stack[KRMQ_MAX_DEPTH], **top; \
+	}; \
+	__scope void krmq_itr_first_##suf(const __type *root, struct krmq_itr_##suf *itr) { \
+		const __type *p; \
+		for (itr->top = itr->stack - 1, p = root; p; p = p->__head.p[0]) \
+			*++itr->top = p; \
+	} \
+	__scope int krmq_itr_find_##suf(const __type *root, const __type *x, struct krmq_itr_##suf *itr) { \
+		const __type *p = root; \
+		itr->top = itr->stack - 1; \
+		while (p != 0) { \
+			int cmp; \
+			*++itr->top = p; \
+			cmp = __cmp(x, p); \
+			if (cmp < 0) p = p->__head.p[0]; \
+			else if (cmp > 0) p = p->__head.p[1]; \
+			else break; \
+		} \
+		return p? 1 : 0; \
+	} \
+	__scope int krmq_itr_next_bidir_##suf(struct krmq_itr_##suf *itr, int dir) { \
+		const __type *p; \
+		if (itr->top < itr->stack) return 0; \
+		dir = !!dir; \
+		p = (*itr->top)->__head.p[dir]; \
+		if (p) { /* go down */ \
+			for (; p; p = p->__head.p[!dir]) \
+				*++itr->top = p; \
+			return 1; \
+		} else { /* go up */ \
+			do { \
+				p = *itr->top--; \
+			} while (itr->top >= itr->stack && p == (*itr->top)->__head.p[dir]); \
+			return itr->top < itr->stack? 0 : 1; \
+		} \
+	} \
+
+/**
+ * Insert a node to the tree
+ *
+ * @param suf     name suffix used in KRMQ_INIT()
+ * @param proot   pointer to the root of the tree (in/out: root may change)
+ * @param x       node to insert (in)
+ * @param cnt     number of nodes smaller than or equal to _x_; can be NULL (out)
+ *
+ * @return _x_ if not present in the tree, or the node equal to x.
+ */
+#define krmq_insert(suf, proot, x, cnt) krmq_insert_##suf(proot, x, cnt)
+
+/**
+ * Find a node in the tree
+ *
+ * @param suf     name suffix used in KRMQ_INIT()
+ * @param root    root of the tree
+ * @param x       node value to find (in)
+ * @param cnt     number of nodes smaller than or equal to _x_; can be NULL (out)
+ *
+ * @return node equal to _x_ if present, or NULL if absent
+ */
+#define krmq_find(suf, root, x, cnt) krmq_find_##suf(root, x, cnt)
+#define krmq_interval(suf, root, x, lower, upper) krmq_interval_##suf(root, x, lower, upper)
+#define krmq_rmq(suf, root, lo, up) krmq_rmq_##suf(root, lo, up)
+
+/**
+ * Delete a node from the tree
+ *
+ * @param suf     name suffix used in KRMQ_INIT()
+ * @param proot   pointer to the root of the tree (in/out: root may change)
+ * @param x       node value to delete; if NULL, delete the first node (in)
+ *
+ * @return node removed from the tree if present, or NULL if absent
+ */
+#define krmq_erase(suf, proot, x, cnt) krmq_erase_##suf(proot, x, cnt)
+#define krmq_erase_first(suf, proot) krmq_erase_##suf(proot, 0, 0)
+
+#define krmq_itr_t(suf) struct krmq_itr_##suf
+
+/**
+ * Place the iterator at the smallest object
+ *
+ * @param suf     name suffix used in KRMQ_INIT()
+ * @param root    root of the tree
+ * @param itr     iterator
+ */
+#define krmq_itr_first(suf, root, itr) krmq_itr_first_##suf(root, itr)
+
+/**
+ * Place the iterator at the object equal to or greater than the query
+ *
+ * @param suf     name suffix used in KRMQ_INIT()
+ * @param root    root of the tree
+ * @param x       query (in)
+ * @param itr     iterator (out)
+ *
+ * @return 1 if find; 0 otherwise. krmq_at(itr) is NULL if and only if query is
+ *         larger than all objects in the tree
+ */
+#define krmq_itr_find(suf, root, x, itr) krmq_itr_find_##suf(root, x, itr)
+
+/**
+ * Move to the next object in order
+ *
+ * @param itr     iterator (modified)
+ *
+ * @return 1 if there is a next object; 0 otherwise
+ */
+#define krmq_itr_next(suf, itr) krmq_itr_next_bidir_##suf(itr, 1)
+#define krmq_itr_prev(suf, itr) krmq_itr_next_bidir_##suf(itr, 0)
+
+/**
+ * Return the pointer at the iterator
+ *
+ * @param itr     iterator
+ *
+ * @return pointer if present; NULL otherwise
+ */
+#define krmq_at(itr) ((itr)->top < (itr)->stack? 0 : *(itr)->top)
+
+#define KRMQ_INIT2(suf, __scope, __type, __head, __cmp, __lt2) \
+	__KRMQ_FIND(suf, __scope, __type, __head,  __cmp) \
+	__KRMQ_RMQ(suf, __scope, __type, __head,  __cmp, __lt2) \
+	__KRMQ_ROTATE(suf, __type, __head, __lt2) \
+	__KRMQ_INSERT(suf, __scope, __type, __head, __cmp, __lt2) \
+	__KRMQ_ERASE(suf, __scope, __type, __head, __cmp, __lt2) \
+	__KRMQ_ITR(suf, __scope, __type, __head, __cmp)
+
+#define KRMQ_INIT(suf, __type, __head, __cmp, __lt2) \
+	KRMQ_INIT2(suf,, __type, __head, __cmp, __lt2)
+
+#endif

kseq.h

@@ -37,6 +37,14 @@
 #define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
 #define KS_SEP_MAX   2
 
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
 #define __KS_TYPE(type_t) \
 	typedef struct __kstream_t { \
 		int begin, end; \
@@ -64,7 +72,7 @@
 	}
 
 #define __KS_INLINED(__read) \
-	static inline int ks_getc(kstream_t *ks) \
+	static inline klib_unused int ks_getc(kstream_t *ks) \
 	{ \
 		if (ks->is_eof && ks->begin >= ks->end) return -1; \
 		if (ks->begin >= ks->end) { \
@@ -81,7 +89,7 @@
 #ifndef KSTRING_T
 #define KSTRING_T kstring_t
 typedef struct __kstring_t {
-	unsigned l, m;
+	size_t l, m;
 	char *s;
 } kstring_t;
 #endif

ksort.h

@@ -37,9 +37,26 @@ typedef struct {
 	int depth;
 } ks_isort_stack_t;
 
-#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
+#define KSORT_SWAP(type_t, a, b) { type_t t=(a); (a)=(b); (b)=t; }
 
-#define KSORT_INIT(name, type_t, __sort_lt)								\
+#define KSORT_INIT(name, type_t, __sort_lt) \
+	void ks_heapdown_##name(size_t i, size_t n, type_t l[]) \
+	{ \
+		size_t k = i; \
+		type_t tmp = l[i]; \
+		while ((k = (k << 1) + 1) < n) { \
+			if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k; \
+			if (__sort_lt(l[k], tmp)) break; \
+			l[i] = l[k]; i = k; \
+		} \
+		l[i] = tmp; \
+	} \
+	void ks_heapmake_##name(size_t lsize, type_t l[]) \
+	{ \
+		size_t i; \
+		for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i) \
+			ks_heapdown_##name(i, lsize, l); \
+	} \
 	type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk)			\
 	{																	\
 		type_t *low, *high, *k, *ll, *hh, *mid;							\

ksw2.h

@@ -15,6 +15,17 @@
 #define KSW_EZ_SPLICE_FOR  0x100
 #define KSW_EZ_SPLICE_REV  0x200
 #define KSW_EZ_SPLICE_FLANK 0x400
+#define KSW_EZ_SPLICE_CMPLX 0x800  // use the miniprot splice model
+#define KSW_EZ_SPLICE_SCORE 0x1000 // use splice score
+
+// The subset of CIGAR operators used by ksw code.
+// Use MM_CIGAR_* from minimap.h if you need the full list.
+#define KSW_CIGAR_MATCH  0
+#define KSW_CIGAR_INS    1
+#define KSW_CIGAR_DEL    2
+#define KSW_CIGAR_N_SKIP 3
+
+#define KSW_SPSC_OFFSET  64
 
 #ifdef __cplusplus
 extern "C" {
@@ -61,7 +72,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t gape2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
+				   int8_t gapo, int8_t gape, int8_t gapo2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
 
 void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez);
 
@@ -127,23 +138,23 @@ static inline void ksw_backtrack(void *km, int is_rot, int is_rev, int min_intro
 			r = i + j;
 			if (i < off[r]) force_state = 2;
 			if (off_end && i > off_end[r]) force_state = 1;
-			tmp = force_state < 0? p[r * n_col + i - off[r]] : 0;
+			tmp = force_state < 0? p[(size_t)r * n_col + i - off[r]] : 0;
 		} else {
 			if (j < off[i]) force_state = 2;
 			if (off_end && j > off_end[i]) force_state = 1;
-			tmp = force_state < 0? p[i * n_col + j - off[i]] : 0;
+			tmp = force_state < 0? p[(size_t)i * n_col + j - off[i]] : 0;
 		}
 		if (state == 0) state = tmp & 7; // if requesting the H state, find state one maximizes it.
 		else if (!(tmp >> (state + 2) & 1)) state = 0; // if requesting other states, _state_ stays the same if it is a continuation; otherwise, set to H
 		if (state == 0) state = tmp & 7; // TODO: probably this line can be merged into the "else if" line right above; not 100% sure
 		if (force_state >= 0) state = force_state;
-		if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
-		else if (state == 1 || (state == 3 && min_intron_len <= 0)) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
-		else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 3, 1), --i; // intron
-		else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
+		if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_MATCH, 1), --i, --j;
+		else if (state == 1 || (state == 3 && min_intron_len <= 0)) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_DEL, 1), --i;
+		else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_N_SKIP, 1), --i;
+		else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, 1), --j;
 	}
-	if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, min_intron_len > 0 && i >= min_intron_len? 3 : 2, i + 1); // first deletion
-	if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
+	if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, min_intron_len > 0 && i >= min_intron_len? KSW_CIGAR_N_SKIP : KSW_CIGAR_DEL, i + 1); // first deletion
+	if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, j + 1); // first insertion
 	if (!is_rev)
 		for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
 			tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;

ksw2_dispatch.c

@@ -17,18 +17,20 @@
 void __cpuidex(int cpuid[4], int func_id, int subfunc_id)
 {
 #if defined(__x86_64__)
-	asm volatile ("cpuid"
+	__asm__ volatile ("cpuid"
 			: "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
 			: "0" (func_id), "2" (subfunc_id));
 #else // on 32bit, ebx can NOT be used as PIC code
-	asm volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"
+	__asm__ volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"
 			: "=a" (cpuid[0]), "=r" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
 			: "0" (func_id), "2" (subfunc_id));
 #endif
 }
 #endif
 
-int x86_simd(void)
+static int ksw_simd = -1;
+
+static int x86_simd(void)
 {
 	int flag = 0, cpuid[4], max_id;
 	__cpuidex(cpuid, 0, 0);
@@ -54,11 +56,10 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 {
 	extern void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 	extern void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
 		ksw_extz2_sse41(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, end_bonus, flag, ez);
-	else if (simd & SIMD_SSE2)
+	else if (ksw_simd & SIMD_SSE2)
 		ksw_extz2_sse2(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, end_bonus, flag, ez);
 	else abort();
 }
@@ -70,28 +71,26 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 	extern void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
 				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
 		ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
-	else if (simd & SIMD_SSE2)
+	else if (ksw_simd & SIMD_SSE2)
 		ksw_extd2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
 	else abort();
 }
 
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 {
 	extern void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
 	extern void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
-		ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
-	else if (simd & SIMD_SSE2)
-		ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez);
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
+		ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, end_bonus, junc_bonus, junc_pen, flag, junc, ez);
+	else if (ksw_simd & SIMD_SSE2)
+		ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, end_bonus, junc_bonus, junc_pen, flag, junc, ez);
 	else abort();
 }
 #endif

ksw2_extd2_sse.c

@@ -4,15 +4,23 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
+#ifdef USE_SIMDE
+#include <simde/x86/sse2.h>
+#else
 #include <emmintrin.h>
+#endif
 
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
+#ifdef USE_SIMDE
+#include <simde/x86/sse4.1.h>
+#else
 #include <smmintrin.h>
 #endif
+#endif
 
 #ifdef KSW_CPU_DISPATCH
 #ifdef __SSE4_1__
@@ -76,7 +84,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 	qe2_    = _mm_set1_epi8(q2 + e2);
 	sc_mch_ = _mm_set1_epi8(mat[0]);
 	sc_mis_ = _mm_set1_epi8(mat[1]);
-	sc_N_   = _mm_set1_epi8(-e2);
+	sc_N_   = mat[m*m-1] == 0? _mm_set1_epi8(-e2) : _mm_set1_epi8(mat[m*m-1]);
 	m1_     = _mm_set1_epi8(m - 1); // wildcard
 
 	if (w < 0) w = tlen > qlen? tlen : qlen;
@@ -111,7 +119,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
 	}
 	if (with_cigar) {
-		mem2 = (uint8_t*)kmalloc(km, ((qlen + tlen - 1) * n_col_ + 1) * 16);
+		mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 16);
 		p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
 		off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
 		off_end = off + qlen + tlen - 1;
@@ -218,7 +226,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 #endif
 			}
 		} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
-			__m128i *pr = p + r * n_col_ - st_;
+			__m128i *pr = p + (size_t)r * n_col_ - st_;
 			off[r] = st, off_end[r] = en;
 			for (t = st_; t <= en_; ++t) {
 				__m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
@@ -265,7 +273,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				_mm_store_si128(&pr[t], d);
 			}
 		} else { // gap right-alignment
-			__m128i *pr = p + r * n_col_ - st_;
+			__m128i *pr = p + (size_t)r * n_col_ - st_;
 			off[r] = st, off_end[r] = en;
 			for (t = st_; t <= en_; ++t) {
 				__m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
@@ -350,7 +358,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e2)) break;
@@ -382,7 +390,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
 		if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
 			ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
-		} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > ez->max) {
+		} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
 			ez->reach_end = 1;
 			ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
 		} else if (ez->max_t >= 0 && ez->max_q >= 0) {

ksw2_exts2_sse.c

@@ -4,27 +4,34 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
+#ifdef USE_SIMDE
+#include <simde/x86/sse2.h>
+#else
 #include <emmintrin.h>
-
+#endif
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
+#ifdef USE_SIMDE
+#include <simde/x86/sse4.1.h>
+#else
 #include <smmintrin.h>
 #endif
+#endif
 
 #ifdef KSW_CPU_DISPATCH
 #ifdef __SSE4_1__
 void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #else
 void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #endif
 #else
 void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
-				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)
+				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int end_bonus, int8_t junc_bonus, int8_t junc_pen, int flag, const uint8_t *junc, ksw_extz_t *ez)
 #endif // ~KSW_CPU_DISPATCH
 {
 #define __dp_code_block1 \
@@ -64,6 +71,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 
 	ksw_reset_extz(ez);
 	if (m <= 1 || qlen <= 0 || tlen <= 0 || q2 <= q + e) return;
+	assert((flag & KSW_EZ_SPLICE_FOR) == 0 || (flag & KSW_EZ_SPLICE_REV) == 0); // can't be both set
 
 	zero_   = _mm_set1_epi8(0);
 	q_      = _mm_set1_epi8(q);
@@ -71,7 +79,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 	qe_     = _mm_set1_epi8(q + e);
 	sc_mch_ = _mm_set1_epi8(mat[0]);
 	sc_mis_ = _mm_set1_epi8(mat[1]);
-	sc_N_   = _mm_set1_epi8(-e);
+	sc_N_   = mat[m*m-1] == 0? _mm_set1_epi8(-e) : _mm_set1_epi8(mat[m*m-1]);
 	m1_     = _mm_set1_epi8(m - 1); // wildcard
 
 	tlen_ = (tlen + 15) / 16;
@@ -100,7 +108,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
 	}
 	if (with_cigar) {
-		mem2 = (uint8_t*)kmalloc(km, ((qlen + tlen - 1) * n_col_ + 1) * 16);
+		mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 16);
 		p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
 		off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
 		off_end = off + qlen + tlen - 1;
@@ -111,22 +119,100 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 
 	// set the donor and acceptor arrays. TODO: this assumes 0/1/2/3 encoding!
 	if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) {
-		int semi_cost = flag&KSW_EZ_SPLICE_FLANK? -noncan/2 : 0; // GTr or yAG is worth 0.5 bit; see PMID:18688272
-		memset(donor, -noncan, tlen_ * 16);
-		for (t = 0; t < tlen - 4; ++t) {
-			int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG
-			if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) can_type = 1; // GTr...
-			if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) can_type = 1; // CTr...
-			if (can_type && (target[t+3] == 0 || target[t+3] == 2)) can_type = 2;
-			if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost;
+		const int sp0[4] = { 8, 15, 21, 30 };
+		int sp[4];
+		if (flag & KSW_EZ_SPLICE_CMPLX) {
+			for (t = 0; t < 4; ++t)
+				sp[t] = (int)((double)sp0[t] / 3. + .499);
+		} else {
+			sp[0] = flag&KSW_EZ_SPLICE_FLANK? noncan / 2 : 0;
+			sp[1] = sp[2] = sp[3] = noncan;
 		}
-		memset(acceptor, -noncan, tlen_ * 16);
-		for (t = 2; t < tlen; ++t) {
-			int can_type = 0;
-			if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) can_type = 1; // ...yAG
-			if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) can_type = 1; // ...yAC
-			if (can_type && (target[t-2] == 1 || target[t-2] == 3)) can_type = 2;
-			if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost;
+		memset(donor,    -sp[3], tlen_ * 16);
+		memset(acceptor, -sp[3], tlen_ * 16);
+		if (!(flag & KSW_EZ_REV_CIGAR)) {
+			for (t = 0; t < tlen - 4; ++t) {
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t+1] == 2 && target[t+2] == 3)             // |GT.
+						z = target[t+3] == 0 || target[t+3] == 2? -1 : 0; // |GTr or not
+					else if (target[t+1] == 2 && target[t+2] == 1) z = 1; // |GC.
+					else if (target[t+1] == 0 && target[t+2] == 3) z = 2; // |AT.
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t+1] == 1 && target[t+2] == 3)             // |CT. (revcomp of .AG|)
+						z = target[t+3] == 0 || target[t+3] == 2? -1 : 0;
+					else if (target[t+1] == 2 && target[t+2] == 3) z = 2; // |GT. (revcomp of .AC|)
+				}
+				((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
+			}
+			for (t = 2; t < tlen; ++t) {
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t-1] == 0 && target[t] == 2)               // .AG|
+						z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAG| or not
+					else if (target[t-1] == 0 && target[t] == 1) z = 2;   // .AC|
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t-1] == 0 && target[t] == 1)               // .AC| (revcomp of |GT.)
+						z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAC| or not
+					else if (target[t-1] == 2 && target[t] == 1) z = 1;   // .GC| (revcomp of |GC.)
+					else if (target[t-1] == 0 && target[t] == 3) z = 2;   // .AT| (revcomp of |AT.)
+				}
+				((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
+			}
+		} else {
+			for (t = 0; t < tlen - 4; ++t) {
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t+1] == 2 && target[t+2] == 0)             // |GA. (rev of .AG|)
+						z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
+					else if (target[t+1] == 1 && target[t+2] == 0) z = 2; // |CA. (rev of .AC|)
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t+1] == 1 && target[t+2] == 0)             // |CA. (comp of |GT.)
+						z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
+					else if (target[t+1] == 1 && target[t+2] == 2) z = 1; // |CG. (comp of |GC.)
+					else if (target[t+1] == 3 && target[t+2] == 0) z = 2; // |TA. (comp of |AT.)
+				}
+				((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
+			}
+			for (t = 2; t < tlen; ++t) {
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t-1] == 3 && target[t] == 2)               // .TG| (rev of |GT.)
+						z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
+					else if (target[t-1] == 1 && target[t] == 2) z = 1;   // .CG| (rev of |GC.)
+					else if (target[t-1] == 3 && target[t] == 0) z = 2;   // .TA| (rev of |AT.)
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t-1] == 3 && target[t] == 1)               // .TC| (comp of .AG|)
+						z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
+					else if (target[t-1] == 3 && target[t] == 2) z = 2;   // .TG| (comp of .AC|)
+				}
+				((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
+			}
+		}
+	}
+
+	if (junc && (flag & KSW_EZ_SPLICE_SCORE)) { // junc[] keeps the donor score
+		uint8_t donor_val = !!(flag & KSW_EZ_SPLICE_FOR) == !(flag & KSW_EZ_REV_CIGAR)? 0 : 1;
+		for (t = 0; t < tlen - 1; ++t)
+			((int8_t*)donor)[t]    += junc[t+1] == 0xff || (junc[t+1]&1) !=  donor_val? -junc_pen : (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET;
+		for (t = 0; t < tlen - 1; ++t)
+			((int8_t*)acceptor)[t] += junc[t+1] == 0xff || (junc[t+1]&1) != !donor_val? -junc_pen : (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET;
+		//for (t = 0; t < tlen - 1; ++t) if (junc[t+1] != 0xff) fprintf(stderr, "Y2\t%d\t%d\t%c\t%d\n", ((int8_t*)donor)[t], ((int8_t*)acceptor)[t], "DA"[junc[t+1]&1], (int8_t)(junc[t+1]>>1) - (int8_t)KSW_SPSC_OFFSET);
+	} else if (junc) { // junc[] keeps the splice sites
+		if (!(flag & KSW_EZ_REV_CIGAR)) {
+			for (t = 0; t < tlen - 1; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8)))
+					((int8_t*)donor)[t] += junc_bonus;
+			for (t = 0; t < tlen; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&4)))
+					((int8_t*)acceptor)[t] += junc_bonus;
+		} else {
+			for (t = 0; t < tlen - 1; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&4)))
+					((int8_t*)donor)[t] += junc_bonus;
+			for (t = 0; t < tlen; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
+					((int8_t*)acceptor)[t] += junc_bonus;
 		}
 	}
 
@@ -336,7 +422,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, 0)) break;
@@ -366,10 +452,14 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 	if (!approx_max) kfree(km, H);
 	if (with_cigar) { // backtrack
 		int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
-		if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY))
+		if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
 			ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
-		else if (ez->max_t >= 0 && ez->max_q >= 0)
+		} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
+			ez->reach_end = 1;
+			ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
+		} else if (ez->max_t >= 0 && ez->max_q >= 0) {
 			ksw_backtrack(km, 1, rev_cigar, long_thres, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
+		}
 		kfree(km, mem2); kfree(km, off);
 	}
 }

ksw2_extz2_sse.c

@@ -3,15 +3,23 @@
 #include "ksw2.h"
 
 #ifdef __SSE2__
+#ifdef USE_SIMDE
+#include <simde/x86/sse2.h>
+#else
 #include <emmintrin.h>
+#endif
 
 #ifdef KSW_SSE2_ONLY
 #undef __SSE4_1__
 #endif
 
 #ifdef __SSE4_1__
+#ifdef USE_SIMDE
+#include <simde/x86/sse4.1.h>
+#else
 #include <smmintrin.h>
 #endif
+#endif
 
 #ifdef KSW_CPU_DISPATCH
 #ifdef __SSE4_1__
@@ -65,7 +73,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 	flag16_ = _mm_set1_epi8(0x10);
 	sc_mch_ = _mm_set1_epi8(mat[0]);
 	sc_mis_ = _mm_set1_epi8(mat[1]);
-	sc_N_   = _mm_set1_epi8(-e);
+	sc_N_   = mat[m*m-1] == 0? _mm_set1_epi8(-e) : _mm_set1_epi8(mat[m*m-1]);
 	m1_     = _mm_set1_epi8(m - 1); // wildcard
 	max_sc_ = _mm_set1_epi8(mat[0] + (q + e) * 2);
 
@@ -89,7 +97,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		for (t = 0; t < tlen_ * 16; ++t) H[t] = KSW_NEG_INF;
 	}
 	if (with_cigar) {
-		mem2 = (uint8_t*)kmalloc(km, ((qlen + tlen - 1) * n_col_ + 1) * 16);
+		mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 16);
 		p = (__m128i*)(((size_t)mem2 + 15) >> 4 << 4);
 		off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
 		off_end = off + qlen + tlen - 1;
@@ -169,7 +177,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 #endif
 			}
 		} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
-			__m128i *pr = p + r * n_col_ - st_;
+			__m128i *pr = p + (size_t)r * n_col_ - st_;
 			off[r] = st, off_end[r] = en;
 			for (t = st_; t <= en_; ++t) {
 				__m128i d, z, a, b, xt1, vt1, ut, tmp;
@@ -195,7 +203,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				_mm_store_si128(&pr[t], d);
 			}
 		} else { // gap right-alignment
-			__m128i *pr = p + r * n_col_ - st_;
+			__m128i *pr = p + (size_t)r * n_col_ - st_;
 			off[r] = st, off_end[r] = en;
 			for (t = st_; t <= en_; ++t) {
 				__m128i d, z, a, b, xt1, vt1, ut, tmp;
@@ -261,7 +269,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e)) break;
@@ -293,7 +301,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 		int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
 		if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
 			ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
-		} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > ez->max) {
+		} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
 			ez->reach_end = 1;
 			ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
 		} else if (ez->max_t >= 0 && ez->max_q >= 0) {

ksw2_ll_sse.c

@@ -1,9 +1,14 @@
 #include <stdlib.h>
 #include <stdint.h>
 #include <string.h>
-#include <emmintrin.h>
 #include "ksw2.h"
 
+#ifdef USE_SIMDE
+#include <simde/x86/sse2.h>
+#else
+#include <emmintrin.h>
+#endif
+
 #ifdef __GNUC__
 #define LIKELY(x) __builtin_expect((x),1)
 #define UNLIKELY(x) __builtin_expect((x),0)
@@ -62,7 +67,7 @@ void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, co
 			const int8_t *ma = mat + a * m;
 			for (i = 0; i < slen; ++i)
 				for (k = i; k < nlen; k += slen) // p iterations
-					*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
+					*t++ = (k >= qlen? -1 : ma[query[k]]) + q->shift;
 		}
 	} else {
 		int16_t *t = (int16_t*)q->qp;
@@ -71,7 +76,7 @@ void *ksw_ll_qinit(void *km, int size, int qlen, const uint8_t *query, int m, co
 			const int8_t *ma = mat + a * m;
 			for (i = 0; i < slen; ++i)
 				for (k = i; k < nlen; k += slen) // p iterations
-					*t++ = (k >= qlen? 0 : ma[query[k]]);
+					*t++ = (k >= qlen? -1 : ma[query[k]]);
 		}
 	}
 	return q;

kthread.c

@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <limits.h>
 #include <stdint.h>
+#include "kthread.h"
 
 #if (defined(WIN32) || defined(_WIN32)) && defined(_MSC_VER)
 #define __sync_fetch_and_add(ptr, addend)     _InterlockedExchangeAdd((void*)ptr, addend)

lchain.c

@@ -0,0 +1,368 @@
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <assert.h>
+#include "mmpriv.h"
+#include "kalloc.h"
+#include "krmq.h"
+
+static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
+{
+	int64_t i = z[k].y, end_i = -1, max_i = i;
+	int32_t max_s = 0;
+	if (i < 0 || t[i] != 0) return i;
+	do {
+		int32_t s;
+		t[i] = 2;
+		end_i = i = p[i];
+		s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+		if (s > max_s) max_s = s, max_i = i;
+		else if (max_s - s > max_drop) break;
+	} while (i >= 0 && t[i] == 0);
+	for (i = z[k].y; i >= 0 && i != end_i; i = p[i]) // reset modified t[]
+		t[i] = 0;
+	return max_i;
+}
+
+uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t max_drop, int32_t *n_u_, int32_t *n_v_)
+{
+	mm128_t *z;
+	uint64_t *u;
+	int64_t i, k, n_z, n_v;
+	int32_t n_u;
+
+	*n_u_ = *n_v_ = 0;
+	for (i = 0, n_z = 0; i < n; ++i) // precompute n_z
+		if (f[i] >= min_sc) ++n_z;
+	if (n_z == 0) return 0;
+	z = Kmalloc(km, mm128_t, n_z);
+	for (i = 0, k = 0; i < n; ++i) // populate z[]
+		if (f[i] >= min_sc) z[k].x = f[i], z[k++].y = i;
+	radix_sort_128x(z, z + n_z);
+
+	memset(t, 0, n * 4);
+	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // precompute n_u
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				++n_v, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				++n_u;
+			else n_v = n_v0;
+		}
+	}
+	u = Kmalloc(km, uint64_t, n_u);
+	memset(t, 0, n * 4);
+	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				v[n_v++] = i, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				u[n_u++] = (uint64_t)sc << 32 | (n_v - n_v0);
+			else n_v = n_v0;
+		}
+	}
+	kfree(km, z);
+	assert(n_v < INT32_MAX);
+	*n_u_ = n_u, *n_v_ = n_v;
+	return u;
+}
+
+static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32_t *v, mm128_t *a)
+{
+	mm128_t *b, *w;
+	uint64_t *u2;
+	int64_t i, j, k;
+
+	// write the result to b[]
+	b = Kmalloc(km, mm128_t, n_v);
+	for (i = 0, k = 0; i < n_u; ++i) {
+		int32_t k0 = k, ni = (int32_t)u[i];
+		for (j = 0; j < ni; ++j)
+			b[k++] = a[v[k0 + (ni - j - 1)]];
+	}
+	kfree(km, v);
+
+	// sort u[] and a[] by the target position, such that adjacent chains may be joined
+	w = Kmalloc(km, mm128_t, n_u);
+	for (i = k = 0; i < n_u; ++i) {
+		w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
+		k += (int32_t)u[i];
+	}
+	radix_sort_128x(w, w + n_u);
+	u2 = Kmalloc(km, uint64_t, n_u);
+	for (i = k = 0; i < n_u; ++i) {
+		int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
+		u2[i] = u[j];
+		memcpy(&a[k], &b[w[i].y>>32], n * sizeof(mm128_t));
+		k += n;
+	}
+	memcpy(u, u2, n_u * 8);
+	memcpy(b, a, k * sizeof(mm128_t)); // write _a_ to _b_ and deallocate _a_ because _a_ is oversized, sometimes a lot
+	kfree(km, a); kfree(km, w); kfree(km, u2);
+	return b;
+}
+
+static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t max_dist_x, int32_t max_dist_y, int32_t bw, float chn_pen_gap, float chn_pen_skip, int is_cdna, int n_seg)
+{
+	int32_t dq = (int32_t)ai->y - (int32_t)aj->y, dr, dd, dg, q_span, sc;
+	int32_t sidi = (ai->y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
+	int32_t sidj = (aj->y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
+	if (dq <= 0 || dq > max_dist_x) return INT32_MIN;
+	dr = (int32_t)(ai->x - aj->x);
+	if (sidi == sidj && (dr == 0 || dq > max_dist_y)) return INT32_MIN;
+	dd = dr > dq? dr - dq : dq - dr;
+	if (sidi == sidj && dd > bw) return INT32_MIN;
+	if (n_seg > 1 && !is_cdna && sidi == sidj && dr > max_dist_y) return INT32_MIN;
+	dg = dr < dq? dr : dq;
+	q_span = aj->y>>32&0xff;
+	sc = q_span < dg? q_span : dg;
+	if (dd || dg > q_span) {
+		float lin_pen, log_pen;
+		lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg;
+		log_pen = dd >= 1? mg_log2(dd + 1) : 0.0f; // mg_log2() only works for dd>=2
+		if (is_cdna || sidi != sidj) {
+			if (sidi != sidj && dr == 0) ++sc; // possibly due to overlapping paired ends; give a minor bonus
+			else if (dr > dq || sidi != sidj) sc -= (int)(lin_pen < log_pen? lin_pen : log_pen); // deletion or jump between paired ends
+			else sc -= (int)(lin_pen + .5f * log_pen);
+		} else sc -= (int)(lin_pen + .5f * log_pen);
+	}
+	return sc;
+}
+
+/* Input:
+ *   a[].x: rev<<63 | tid<<32 | tpos
+ *   a[].y: flags<<40 | q_span<<32 | q_pos
+ * Output:
+ *   n_u: #chains
+ *   u[]: score<<32 | #anchors (sum of lower 32 bits of u[] is the returned length of a[])
+ * input a[] is deallocated on return
+ */
+mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
+					  int is_cdna, int n_seg, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
+{ // TODO: make sure this works when n has more than 32 bits
+	int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
+	int64_t *p, i, j, max_ii, st = 0;
+	uint64_t *u;
+
+	if (_u) *_u = 0, *n_u_ = 0;
+	if (n == 0 || a == 0) {
+		kfree(km, a);
+		return 0;
+	}
+	if (max_dist_x < bw) max_dist_x = bw;
+	if (max_dist_y < bw && !is_cdna) max_dist_y = bw;
+	if (is_cdna) max_drop = INT32_MAX;
+	p = Kmalloc(km, int64_t, n);
+	f = Kmalloc(km, int32_t, n);
+	v = Kmalloc(km, int32_t, n);
+	t = Kcalloc(km, int32_t, n);
+
+	// fill the score and backtrack arrays
+	for (i = 0, max_ii = -1; i < n; ++i) {
+		int64_t max_j = -1, end_j;
+		int32_t max_f = a[i].y>>32&0xff, n_skip = 0;
+		while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist_x)) ++st;
+		if (i - st > max_iter) st = i - max_iter;
+		for (j = i - 1; j >= st; --j) {
+			int32_t sc;
+			sc = comput_sc(&a[i], &a[j], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg);
+			if (sc == INT32_MIN) continue;
+			sc += f[j];
+			if (sc > max_f) {
+				max_f = sc, max_j = j;
+				if (n_skip > 0) --n_skip;
+			} else if (t[j] == (int32_t)i) {
+				if (++n_skip > max_skip)
+					break;
+			}
+			if (p[j] >= 0) t[p[j]] = i;
+		}
+		end_j = j;
+		if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) {
+			int32_t max = INT32_MIN;
+			max_ii = -1;
+			for (j = i - 1; j >= st; --j)
+				if (max < f[j]) max = f[j], max_ii = j;
+		}
+		if (max_ii >= 0 && max_ii < end_j) {
+			int32_t tmp;
+			tmp = comput_sc(&a[i], &a[max_ii], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg);
+			if (tmp != INT32_MIN && max_f < tmp + f[max_ii])
+				max_f = tmp + f[max_ii], max_j = max_ii;
+		}
+		f[i] = max_f, p[i] = max_j;
+		v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
+		if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i]))
+			max_ii = i;
+		if (mmax_f < max_f) mmax_f = max_f;
+		//fprintf(stderr, "X1\t%ld\t%ld:%d\t%ld\t%ld:%d\t%ld\t%ld\n", (long)i, (long)(a[i].x>>32), (int32_t)a[i].x, (long)max_j, max_j<0?-1L:(long)(a[max_j].x>>32), max_j<0?-1:(int32_t)a[max_j].x, (long)max_f, (long)v[i]);
+	}
+
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
+	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
+	kfree(km, p); kfree(km, f); kfree(km, t);
+	if (n_u == 0) {
+		kfree(km, a); kfree(km, v);
+		return 0;
+	}
+	return compact_a(km, n_u, u, n_v, v, a);
+}
+
+typedef struct lc_elem_s {
+	int32_t y;
+	int64_t i;
+	double pri;
+	KRMQ_HEAD(struct lc_elem_s) head;
+} lc_elem_t;
+
+#define lc_elem_cmp(a, b) ((a)->y < (b)->y? -1 : (a)->y > (b)->y? 1 : ((a)->i > (b)->i) - ((a)->i < (b)->i))
+#define lc_elem_lt2(a, b) ((a)->pri < (b)->pri)
+KRMQ_INIT(lc_elem, lc_elem_t, head, lc_elem_cmp, lc_elem_lt2)
+
+KALLOC_POOL_INIT(rmq, lc_elem_t)
+
+static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, float chn_pen_gap, float chn_pen_skip, int32_t *exact, int32_t *width)
+{
+	int32_t dq = (int32_t)ai->y - (int32_t)aj->y, dr, dd, dg, q_span, sc;
+	dr = (int32_t)(ai->x - aj->x);
+	*width = dd = dr > dq? dr - dq : dq - dr;
+	dg = dr < dq? dr : dq;
+	q_span = aj->y>>32&0xff;
+	sc = q_span < dg? q_span : dg;
+	if (exact) *exact = (dd == 0 && dg <= q_span);
+	if (dd || dq > q_span) {
+		float lin_pen, log_pen;
+		lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg;
+		log_pen = dd >= 1? mg_log2(dd + 1) : 0.0f; // mg_log2() only works for dd>=2
+		sc -= (int)(lin_pen + .5f * log_pen);
+	}
+	return sc;
+}
+
+mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
+					   int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
+{
+	int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
+	int64_t *p, i, i0, st = 0, st_inner = 0;
+	uint64_t *u;
+	lc_elem_t *root = 0, *root_inner = 0;
+	void *mem_mp = 0;
+	kmp_rmq_t *mp;
+
+	if (_u) *_u = 0, *n_u_ = 0;
+	if (n == 0 || a == 0) {
+		kfree(km, a);
+		return 0;
+	}
+	if (max_dist < bw) max_dist = bw;
+	if (max_dist_inner < 0) max_dist_inner = 0;
+	if (max_dist_inner > max_dist) max_dist_inner = max_dist;
+	p = Kmalloc(km, int64_t, n);
+	f = Kmalloc(km, int32_t, n);
+	t = Kcalloc(km, int32_t, n);
+	v = Kmalloc(km, int32_t, n);
+	mem_mp = km_init2(km, 0x10000);
+	mp = kmp_init_rmq(mem_mp);
+
+	// fill the score and backtrack arrays
+	for (i = i0 = 0; i < n; ++i) {
+		int64_t max_j = -1;
+		int32_t q_span = a[i].y>>32&0xff, max_f = q_span;
+		lc_elem_t s, *q, *r, lo, hi;
+		// add in-range anchors
+		if (i0 < i && a[i0].x != a[i].x) {
+			int64_t j;
+			for (j = i0; j < i; ++j) {
+				q = kmp_alloc_rmq(mp);
+				q->y = (int32_t)a[j].y, q->i = j, q->pri = -(f[j] + 0.5 * chn_pen_gap * ((int32_t)a[j].x + (int32_t)a[j].y));
+				krmq_insert(lc_elem, &root, q, 0);
+				if (max_dist_inner > 0) {
+					r = kmp_alloc_rmq(mp);
+					*r = *q;
+					krmq_insert(lc_elem, &root_inner, r, 0);
+				}
+			}
+			i0 = i;
+		}
+		// get rid of active chains out of range
+		while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) {
+			s.y = (int32_t)a[st].y, s.i = st;
+			if ((q = krmq_find(lc_elem, root, &s, 0)) != 0) {
+				q = krmq_erase(lc_elem, &root, q, 0);
+				kmp_free_rmq(mp, q);
+			}
+			++st;
+		}
+		if (max_dist_inner > 0)  { // similar to the block above, but applied to the inner tree
+			while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) {
+				s.y = (int32_t)a[st_inner].y, s.i = st_inner;
+				if ((q = krmq_find(lc_elem, root_inner, &s, 0)) != 0) {
+					q = krmq_erase(lc_elem, &root_inner, q, 0);
+					kmp_free_rmq(mp, q);
+				}
+				++st_inner;
+			}
+		}
+		// RMQ
+		lo.i = INT32_MAX, lo.y = (int32_t)a[i].y - max_dist;
+		hi.i = 0, hi.y = (int32_t)a[i].y;
+		if ((q = krmq_rmq(lc_elem, root, &lo, &hi)) != 0) {
+			int32_t sc, exact, width, n_skip = 0;
+			int64_t j = q->i;
+			assert(q->y >= lo.y && q->y <= hi.y);
+			sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, &exact, &width);
+			if (width <= bw && sc > max_f) max_f = sc, max_j = j;
+			if (!exact && root_inner && (int32_t)a[i].y > 0) {
+				lc_elem_t *lo, *hi;
+				s.y = (int32_t)a[i].y - 1, s.i = n;
+				krmq_interval(lc_elem, root_inner, &s, &lo, &hi);
+				if (lo) {
+					const lc_elem_t *q;
+					int32_t width;
+					krmq_itr_t(lc_elem) itr;
+					krmq_itr_find(lc_elem, root_inner, lo, &itr);
+					while ((q = krmq_at(&itr)) != 0) {
+						if (q->y < (int32_t)a[i].y - max_dist_inner) break;
+						j = q->i;
+						sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, 0, &width);
+						if (width <= bw) {
+							if (sc > max_f) {
+								max_f = sc, max_j = j;
+								if (n_skip > 0) --n_skip;
+							} else if (t[j] == (int32_t)i) {
+								if (++n_skip > max_chn_skip)
+									break;
+							}
+							if (p[j] >= 0) t[p[j]] = i;
+						}
+						if (!krmq_itr_prev(lc_elem, &itr)) break;
+					}
+				}
+			}
+		}
+		// set max
+		assert(max_j < 0 || (a[max_j].x < a[i].x && (int32_t)a[max_j].y < (int32_t)a[i].y));
+		f[i] = max_f, p[i] = max_j;
+		v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
+		if (mmax_f < max_f) mmax_f = max_f;
+		if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root);
+	}
+	km_destroy(mem_mp);
+
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
+	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
+	kfree(km, p); kfree(km, f); kfree(km, t);
+	if (n_u == 0) {
+		kfree(km, a); kfree(km, v);
+		return 0;
+	}
+	return compact_a(km, n_u, u, n_v, v, a);
+}

main.c

@@ -1,12 +1,11 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
+#include <errno.h>
 #include "bseq.h"
 #include "minimap.h"
 #include "mmpriv.h"
-#include "getopt.h"
-
-#define MM_VERSION "2.7-r654"
+#include "ketopt.h"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -22,58 +21,123 @@ void liftrlimit()
 void liftrlimit() {}
 #endif
 
-static struct option long_options[] = {
-	{ "bucket-bits",    required_argument, 0, 0 },
-	{ "mb-size",        required_argument, 0, 'K' },
-	{ "seed",           required_argument, 0, 0 },
-	{ "no-kalloc",      no_argument,       0, 0 },
-	{ "print-qname",    no_argument,       0, 0 },
-	{ "no-self",        no_argument,       0, 0 },
-	{ "print-seeds",    no_argument,       0, 0 },
-	{ "max-chain-skip", required_argument, 0, 0 },
-	{ "min-dp-len",     required_argument, 0, 0 },
-	{ "print-aln-seq",  no_argument,       0, 0 },
-	{ "splice",         no_argument,       0, 0 },
-	{ "cost-non-gt-ag", required_argument, 0, 'C' },
-	{ "no-long-join",   no_argument,       0, 0 },
-	{ "sr",             no_argument,       0, 0 },
-	{ "frag",           optional_argument, 0, 0 },
-	{ "secondary",      optional_argument, 0, 0 },
-	{ "cs",             optional_argument, 0, 0 },
-	{ "end-bonus",      required_argument, 0, 0 },
-	{ "no-pairing",     no_argument,       0, 0 },
-	{ "splice-flank",   optional_argument, 0, 0 },
-	{ "idx-no-seq",     no_argument,       0, 0 },
-	{ "end-seed-pen",   required_argument, 0, 0 },   // 21
-	{ "help",           no_argument,       0, 'h' },
-	{ "max-intron-len", required_argument, 0, 'G' },
-	{ "version",        no_argument,       0, 'V' },
-	{ "min-count",      required_argument, 0, 'n' },
-	{ "min-chain-score",required_argument, 0, 'm' },
-	{ "mask-level",     required_argument, 0, 'M' },
-	{ "min-dp-score",   required_argument, 0, 's' },
-	{ "sam",            no_argument,       0, 'a' },
-	{ 0, 0, 0, 0}
+static ko_longopt_t long_options[] = {
+	{ "bucket-bits",    ko_required_argument, 300 },
+	{ "mb-size",        ko_required_argument, 'K' },
+	{ "seed",           ko_required_argument, 302 },
+	{ "no-kalloc",      ko_no_argument,       303 },
+	{ "print-qname",    ko_no_argument,       304 },
+	{ "no-self",        ko_no_argument,       'D' },
+	{ "print-seeds",    ko_no_argument,       306 },
+	{ "max-chain-skip", ko_required_argument, 307 },
+	{ "min-dp-len",     ko_required_argument, 308 },
+	{ "print-aln-seq",  ko_no_argument,       309 },
+	{ "splice",         ko_no_argument,       310 },
+	{ "cost-non-gt-ag", ko_required_argument, 'C' },
+	{ "no-long-join",   ko_no_argument,       312 },
+	{ "sr",             ko_optional_argument, 313 },
+	{ "frag",           ko_required_argument, 314 },
+	{ "secondary",      ko_required_argument, 315 },
+	{ "cs",             ko_optional_argument, 316 },
+	{ "end-bonus",      ko_required_argument, 317 },
+	{ "no-pairing",     ko_no_argument,       318 }, // deprecated but reserved for backward compatibility
+	{ "splice-flank",   ko_required_argument, 319 },
+	{ "idx-no-seq",     ko_no_argument,       320 },
+	{ "end-seed-pen",   ko_required_argument, 321 },
+	{ "for-only",       ko_no_argument,       322 },
+	{ "rev-only",       ko_no_argument,       323 },
+	{ "heap-sort",      ko_required_argument, 324 },
+	{ "all-chain",      ko_no_argument,       'P' },
+	{ "dual",           ko_required_argument, 326 },
+	{ "max-clip-ratio", ko_required_argument, 327 },
+	{ "min-occ-floor",  ko_required_argument, 328 },
+	{ "MD",             ko_no_argument,       329 },
+	{ "lj-min-ratio",   ko_required_argument, 330 },
+	{ "score-N",        ko_required_argument, 331 },
+	{ "eqx",            ko_no_argument,       332 },
+	{ "paf-no-hit",     ko_no_argument,       333 },
+	{ "split-prefix",   ko_required_argument, 334 },
+	{ "no-end-flt",     ko_no_argument,       335 },
+	{ "hard-mask-level",ko_no_argument,       336 },
+	{ "cap-sw-mem",     ko_required_argument, 337 },
+	{ "max-qlen",       ko_required_argument, 338 },
+	{ "max-chain-iter", ko_required_argument, 339 },
+	{ "junc-bed",       ko_required_argument, 340 },
+	{ "junc-bonus",     ko_required_argument, 341 },
+	{ "sam-hit-only",   ko_no_argument,       342 },
+	{ "chain-gap-scale",ko_required_argument, 343 },
+	{ "alt",            ko_required_argument, 344 },
+	{ "alt-drop",       ko_required_argument, 345 },
+	{ "mask-len",       ko_required_argument, 346 },
+	{ "rmq",            ko_optional_argument, 347 },
+	{ "qstrand",        ko_no_argument,       348 },
+	{ "cap-kalloc",     ko_required_argument, 349 },
+	{ "q-occ-frac",     ko_required_argument, 350 },
+	{ "chain-skip-scale",ko_required_argument,351 },
+	{ "print-chains",   ko_no_argument,       352 },
+	{ "no-hash-name",   ko_no_argument,       353 },
+	{ "secondary-seq",  ko_no_argument,       354 },
+	{ "ds",             ko_no_argument,       355 },
+	{ "rmq-inner",      ko_required_argument, 356 },
+	{ "spsc",           ko_required_argument, 357 },
+	{ "junc-pen",       ko_required_argument, 358 },
+	{ "pairing",        ko_required_argument, 359 },
+	{ "jump-min-match", ko_required_argument, 360 },
+	{ "write-junc",     ko_no_argument,       361 },
+	{ "pass1",          ko_required_argument, 362 },
+	{ "spsc-scale",     ko_required_argument, 363 },
+	{ "spsc0",          ko_required_argument, 364 },
+	{ "dbg-seed-occ",   ko_no_argument,       501 },
+	{ "help",           ko_no_argument,       'h' },
+	{ "max-intron-len", ko_required_argument, 'G' },
+	{ "version",        ko_no_argument,       'V' },
+	{ "min-count",      ko_required_argument, 'n' },
+	{ "min-chain-score",ko_required_argument, 'm' },
+	{ "mask-level",     ko_required_argument, 'M' },
+	{ "min-dp-score",   ko_required_argument, 's' },
+	{ "sam",            ko_no_argument,       'a' },
+	{ 0, 0, 0 }
 };
 
-static inline int64_t mm_parse_num(const char *str)
+static inline int64_t mm_parse_num2(const char *str, char **q)
 {
 	double x;
 	char *p;
-	x = strtod(optarg, &p);
-	if (*p == 'G' || *p == 'g') x *= 1e9;
-	else if (*p == 'M' || *p == 'm') x *= 1e6;
-	else if (*p == 'K' || *p == 'k') x *= 1e3;
+	x = strtod(str, &p);
+	if (*p == 'G' || *p == 'g') x *= 1e9, ++p;
+	else if (*p == 'M' || *p == 'm') x *= 1e6, ++p;
+	else if (*p == 'K' || *p == 'k') x *= 1e3, ++p;
+	if (q) *q = p;
 	return (int64_t)(x + .499);
 }
 
+static inline int64_t mm_parse_num(const char *str)
+{
+	return mm_parse_num2(str, 0);
+}
+
+static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const char *arg, int yes_to_set)
+{
+	if (yes_to_set) {
+		if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag |= flag;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag &= ~flag;
+		else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
+	} else {
+		if (strcmp(arg, "yes") == 0 || strcmp(arg, "y") == 0) opt->flag &= ~flag;
+		else if (strcmp(arg, "no") == 0 || strcmp(arg, "n") == 0) opt->flag |= flag;
+		else fprintf(stderr, "[WARNING]\033[1;31m option '--%s' only accepts 'yes' or 'no'.\033[0m\n", long_options[long_idx].name);
+	}
+}
+
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:";
+	const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:b:O:E:m:N:Qu:R:hF:LC:yYPo:e:U:J:j:";
+	ketopt_t o = KETOPT_INIT;
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
-	int i, c, n_threads = 3, long_idx;
-	char *fnw = 0, *rg = 0, *s;
+	int i, c, n_threads = 3, n_parts, old_best_n = -1;
+	float spsc_scale = 0.7f;
+	char *fnw = 0, *rg = 0, *fn_bed_junc = 0, *fn_bed_jump = 0, *fn_bed_pass1 = 0, *fn_spsc = 0, *s, *alt_list = 0;
 	FILE *fp_help = stderr;
 	mm_idx_reader_t *idx_rdr;
 	mm_idx_t *mi;
@@ -83,88 +147,168 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_set_opt(0, &ipt, &opt);
 
-	while ((c = getopt_long(argc, argv, opt_str, long_options, &long_idx)) >= 0) // apply option -x/preset first
+	while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) { // test command line options and apply option -x/preset first
 		if (c == 'x') {
-			if (mm_set_opt(optarg, &ipt, &opt) < 0) {
-				fprintf(stderr, "[ERROR] unknown preset '%s'\n", optarg);
+			if (mm_set_opt(o.arg, &ipt, &opt) < 0) {
+				fprintf(stderr, "[ERROR] unknown preset '%s'\n", o.arg);
 				return 1;
 			}
-			break;
+		} else if (c == ':') {
+			fprintf(stderr, "[ERROR] missing option argument\n");
+			return 1;
+		} else if (c == '?') {
+			fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i - 1]);
+			return 1;
 		}
-	optreset = 1;
+	}
+	o = KETOPT_INIT;
 
-	while ((c = getopt_long(argc, argv, opt_str, long_options, &long_idx)) >= 0) {
-		if (c == 'w') ipt.w = atoi(optarg);
-		else if (c == 'k') ipt.k = atoi(optarg);
+	while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
+		if (c == 'w') ipt.w = atoi(o.arg);
+		else if (c == 'k') ipt.k = atoi(o.arg);
 		else if (c == 'H') ipt.flag |= MM_I_HPC;
-		else if (c == 'd') fnw = optarg; // the above are indexing related options, except -I
-		else if (c == 'r') opt.bw = (int)mm_parse_num(optarg);
-		else if (c == 't') n_threads = atoi(optarg);
-		else if (c == 'v') mm_verbose = atoi(optarg);
-		else if (c == 'g') opt.max_gap = (int)mm_parse_num(optarg);
-		else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(optarg));
-		else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(optarg);
-		else if (c == 'N') opt.best_n = atoi(optarg);
-		else if (c == 'p') opt.pri_ratio = atof(optarg);
-		else if (c == 'M') opt.mask_level = atof(optarg);
+		else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
+		else if (c == 't') n_threads = atoi(o.arg);
+		else if (c == 'v') mm_verbose = atoi(o.arg);
+		else if (c == 'g') opt.max_gap = (int)mm_parse_num(o.arg);
+		else if (c == 'G') mm_mapopt_max_intron_len(&opt, (int)mm_parse_num(o.arg));
+		else if (c == 'F') opt.max_frag_len = (int)mm_parse_num(o.arg);
+		else if (c == 'N') old_best_n = opt.best_n, opt.best_n = atoi(o.arg);
+		else if (c == 'p') opt.pri_ratio = atof(o.arg);
+		else if (c == 'M') opt.mask_level = atof(o.arg);
 		else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
-		else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
+		else if (c == 'D') opt.flag |= MM_F_NO_DIAG;
+		else if (c == 'P') opt.flag |= MM_F_ALL_CHAINS;
+		else if (c == 'X') opt.flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN; // -D -P --no-long-join --dual=no
 		else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
 		else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
 		else if (c == 'Y') opt.flag |= MM_F_SOFTCLIP;
 		else if (c == 'L') opt.flag |= MM_F_LONG_CIGAR;
-		else if (c == 'T') opt.sdust_thres = atoi(optarg);
-		else if (c == 'n') opt.min_cnt = atoi(optarg);
-		else if (c == 'm') opt.min_chain_score = atoi(optarg);
-		else if (c == 'A') opt.a = atoi(optarg);
-		else if (c == 'B') opt.b = atoi(optarg);
-		else if (c == 'z') opt.zdrop = atoi(optarg);
-		else if (c == 's') opt.min_dp_max = atoi(optarg);
-		else if (c == 'C') opt.noncan = atoi(optarg);
-		else if (c == 'I') ipt.batch_size = mm_parse_num(optarg);
-		else if (c == 'K') opt.mini_batch_size = (int)mm_parse_num(optarg);
-		else if (c == 'R') rg = optarg;
+		else if (c == 'y') opt.flag |= MM_F_COPY_COMMENT;
+		else if (c == 'T') opt.sdust_thres = atoi(o.arg);
+		else if (c == 'n') opt.min_cnt = atoi(o.arg);
+		else if (c == 'm') opt.min_chain_score = atoi(o.arg);
+		else if (c == 'A') opt.a = atoi(o.arg);
+		else if (c == 'B') opt.b = atoi(o.arg);
+		else if (c == 'b') opt.transition = atoi(o.arg);
+		else if (c == 's') opt.min_dp_max = atoi(o.arg);
+		else if (c == 'C') opt.noncan = atoi(o.arg);
+		else if (c == 'I') ipt.batch_size = mm_parse_num(o.arg);
+		else if (c == 'K') opt.mini_batch_size = mm_parse_num(o.arg);
+		else if (c == 'e') opt.occ_dist = mm_parse_num(o.arg);
+		else if (c == 'R') rg = o.arg;
 		else if (c == 'h') fp_help = stdout;
 		else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
-		else if (c == 0 && long_idx == 0) ipt.bucket_bits = atoi(optarg); // --bucket-bits
-		else if (c == 0 && long_idx == 2) opt.seed = atoi(optarg); // --seed
-		else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
-		else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
-		else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF; // --no-self
-		else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
-		else if (c == 0 && long_idx == 7) opt.max_chain_skip = atoi(optarg); // --max-chain-skip
-		else if (c == 0 && long_idx == 8) opt.min_ksw_len = atoi(optarg); // --min-dp-len
-		else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
-		else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
-		else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
-		else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
-		else if (c == 0 && long_idx ==17) opt.end_bonus = atoi(optarg); // --end-bonus
-		else if (c == 0 && long_idx ==18) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing
-		else if (c == 0 && long_idx ==20) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
-		else if (c == 0 && long_idx ==21) opt.anchor_ext_shift = atoi(optarg); // --end-seed-pen
-		else if (c == 0 && long_idx == 14) { // --frag
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_FRAG_MODE;
-			else opt.flag &= ~MM_F_FRAG_MODE;
-		} else if (c == 0 && long_idx == 15) { // --secondary
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag &= ~MM_F_NO_PRINT_2ND;
-			else opt.flag |= MM_F_NO_PRINT_2ND;
-		} else if (c == 0 && long_idx == 16) { // --cs
+		else if (c == 'j') fn_bed_jump = o.arg;
+		else if (c == 'J') {
+			int t;
+			t = atoi(o.arg);
+			if (t == 0) opt.flag |= MM_F_SPLICE_OLD;
+			else if (t == 1) opt.flag &= ~MM_F_SPLICE_OLD;
+		} else if (c == 'o') {
+			if (strcmp(o.arg, "-") != 0) {
+				if (freopen(o.arg, "wb", stdout) == NULL) {
+					fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", o.arg, strerror(errno));
+					exit(1);
+				}
+			}
+		}
+		else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
+		else if (c == 302) opt.seed = atoi(o.arg); // --seed
+		else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
+		else if (c == 304) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
+		else if (c == 306) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED, n_threads = 1; // --print-seed
+		else if (c == 307) opt.max_chain_skip = atoi(o.arg); // --max-chain-skip
+		else if (c == 339) opt.max_chain_iter = atoi(o.arg); // --max-chain-iter
+		else if (c == 308) opt.min_ksw_len = atoi(o.arg); // --min-dp-len
+		else if (c == 309) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ, n_threads = 1; // --print-aln-seq
+		else if (c == 310) opt.flag |= MM_F_SPLICE; // --splice
+		else if (c == 312) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
+		else if (c == 317) opt.end_bonus = atoi(o.arg); // --end-bonus
+		else if (c == 318) opt.flag |= MM_F_INDEPEND_SEG; // --no-pairing (deprecated)
+		else if (c == 320) ipt.flag |= MM_I_NO_SEQ; // --idx-no-seq
+		else if (c == 321) opt.anchor_ext_shift = atoi(o.arg); // --end-seed-pen
+		else if (c == 322) opt.flag |= MM_F_FOR_ONLY; // --for-only
+		else if (c == 323) opt.flag |= MM_F_REV_ONLY; // --rev-only
+		else if (c == 327) opt.max_clip_ratio = atof(o.arg); // --max-clip-ratio
+		else if (c == 328) opt.min_mid_occ = atoi(o.arg); // --min-occ-floor
+		else if (c == 329) opt.flag |= MM_F_OUT_MD; // --MD
+		else if (c == 331) opt.sc_ambi = atoi(o.arg); // --score-N
+		else if (c == 332) opt.flag |= MM_F_EQX; // --eqx
+		else if (c == 333) opt.flag |= MM_F_PAF_NO_HIT; // --paf-no-hit
+		else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
+		else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
+		else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
+		else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
+		else if (c == 338) opt.max_qlen = mm_parse_num(o.arg); // --max-qlen
+		else if (c == 340) fn_bed_junc = o.arg; // --junc-bed
+		else if (c == 341) opt.junc_bonus = atoi(o.arg); // --junc-bonus
+		else if (c == 342) opt.flag |= MM_F_SAM_HIT_ONLY; // --sam-hit-only
+		else if (c == 343) opt.chain_gap_scale = atof(o.arg); // --chain-gap-scale
+		else if (c == 351) opt.chain_skip_scale = atof(o.arg); // --chain-skip-scale
+		else if (c == 344) alt_list = o.arg; // --alt
+		else if (c == 345) opt.alt_drop = atof(o.arg); // --alt-drop
+		else if (c == 346) opt.mask_len = mm_parse_num(o.arg); // --mask-len
+		else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
+		else if (c == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
+		else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
+		else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
+		else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
+		else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
+		else if (c == 355) opt.flag |= MM_F_OUT_DS; // --ds
+		else if (c == 356) opt.rmq_inner_dist = mm_parse_num(o.arg); // --rmq-inner
+		else if (c == 357) fn_spsc = o.arg; // --spsc
+		else if (c == 360) opt.jump_min_match = mm_parse_num(o.arg); // --jump-min-match
+		else if (c == 361) opt.flag |= MM_F_OUT_JUNC | MM_F_CIGAR; // --write-junc
+		else if (c == 362) fn_bed_pass1 = o.arg; // --jump-pass1
+		else if (c == 501) mm_dbg_flag |= MM_DBG_SEED_FREQ; // --dbg-seed-occ
+		else if (c == 363) spsc_scale = atof(o.arg); // --spsc-scale
+		else if (c == 358 || c == 364) opt.junc_pen = atoi(o.arg); // --junc-pen or --spsc0
+		else if (c == 330) {
+			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
+		} else if (c == 313) { // --sr
+			if (o.arg == 0 || strcmp(o.arg, "dna") == 0) {
+				opt.flag |= MM_F_SR;
+			} else if (strcmp(o.arg, "rna") == 0) {
+				opt.flag |= MM_F_SR_RNA;
+			} else if (strcmp(o.arg, "no") == 0) {
+				opt.flag &= ~(uint64_t)(MM_F_SR|MM_F_SR_RNA);
+			} else if (mm_verbose >= 2) {
+				opt.flag |= MM_F_SR;
+				fprintf(stderr, "[WARNING]\033[1;31m --sr only takes 'dna' or 'rna'. Invalid values are assumed to be 'dna'.\033[0m\n");
+			}
+		} else if (c == 314) { // --frag
+			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
+		} else if (c == 315) { // --secondary
+			yes_or_no(&opt, MM_F_NO_PRINT_2ND, o.longidx, o.arg, 0);
+		} else if (c == 316) { // --cs
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
-			if (optarg == 0 || strcmp(optarg, "short") == 0) {
+			if (o.arg == 0 || strcmp(o.arg, "short") == 0) {
 				opt.flag &= ~MM_F_OUT_CS_LONG;
-			} else if (strcmp(optarg, "long") == 0) {
+			} else if (strcmp(o.arg, "long") == 0) {
 				opt.flag |= MM_F_OUT_CS_LONG;
-			} else if (strcmp(optarg, "none") == 0) {
+			} else if (strcmp(o.arg, "none") == 0) {
 				opt.flag &= ~MM_F_OUT_CS;
 			} else if (mm_verbose >= 2) {
 				fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
 			}
-		} else if (c == 0 && long_idx == 19) { // --splice-flank
-			if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
-				opt.flag |= MM_F_SPLICE_FLANK;
-			else opt.flag &= ~MM_F_SPLICE_FLANK;
+		} else if (c == 319) { // --splice-flank
+			yes_or_no(&opt, MM_F_SPLICE_FLANK, o.longidx, o.arg, 1);
+		} else if (c == 324) { // --heap-sort
+			yes_or_no(&opt, MM_F_HEAP_SORT, o.longidx, o.arg, 1);
+		} else if (c == 326) { // --dual
+			yes_or_no(&opt, MM_F_NO_DUAL, o.longidx, o.arg, 0);
+		} else if (c == 347) { // --rmq
+			if (o.arg) yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
+			else opt.flag |= MM_F_RMQ;
+		} else if (c == 359) { // --pairing
+			if (strcmp(o.arg, "no") == 0) opt.flag |= MM_F_INDEPEND_SEG;
+			else if (strcmp(o.arg, "weak") == 0) opt.flag |= MM_F_WEAK_PAIRING, opt.flag &= ~(uint64_t)MM_F_INDEPEND_SEG;
+			else {
+				if (strcmp(o.arg, "strong") != 0 && mm_verbose >= 2)
+					fprintf(stderr, "[WARNING]\033[1;31m unrecognized argument for --pairing; assuming 'strong'.\033[0m\n");
+				opt.flag &= ~(uint64_t)(MM_F_INDEPEND_SEG|MM_F_WEAK_PAIRING);
+			}
 		} else if (c == 'S') {
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
 			if (mm_verbose >= 2)
@@ -172,54 +316,63 @@ int main(int argc, char *argv[])
 		} else if (c == 'V') {
 			puts(MM_VERSION);
 			return 0;
+		} else if (c == 'r') {
+			opt.bw = (int)mm_parse_num2(o.arg, &s);
+			if (*s == ',') opt.bw_long = (int)mm_parse_num2(s + 1, &s);
+		} else if (c == 'U') {
+			opt.min_mid_occ = strtol(o.arg, &s, 10);
+			if (*s == ',') opt.max_mid_occ = strtol(s + 1, &s, 10);
 		} else if (c == 'f') {
 			double x;
 			char *p;
-			x = strtod(optarg, &p);
+			x = strtod(o.arg, &p);
 			if (x < 1.0) opt.mid_occ_frac = x, opt.mid_occ = 0;
 			else opt.mid_occ = (int)(x + .499);
 			if (*p == ',') opt.max_occ = (int)(strtod(p+1, &p) + .499);
 		} else if (c == 'u') {
-			if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
-			else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
-			else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
-			else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
+			if (*o.arg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV; // both strands
+			else if (*o.arg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV; // match GT-AG
+			else if (*o.arg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR; // match CT-AC (reverse complement of GT-AG)
+			else if (*o.arg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV); // don't try to match the GT-AG signal
 			else {
 				fprintf(stderr, "[ERROR]\033[1;31m unrecognized cDNA direction\033[0m\n");
 				return 1;
 			}
+		} else if (c == 'z') {
+			opt.zdrop = opt.zdrop_inv = strtol(o.arg, &s, 10);
+			if (*s == ',') opt.zdrop_inv = strtol(s + 1, &s, 10);
 		} else if (c == 'O') {
-			opt.q = opt.q2 = strtol(optarg, &s, 10);
+			opt.q = opt.q2 = strtol(o.arg, &s, 10);
 			if (*s == ',') opt.q2 = strtol(s + 1, &s, 10);
 		} else if (c == 'E') {
-			opt.e = opt.e2 = strtol(optarg, &s, 10);
+			opt.e = opt.e2 = strtol(o.arg, &s, 10);
 			if (*s == ',') opt.e2 = strtol(s + 1, &s, 10);
 		}
 	}
-	if ((opt.flag & MM_F_SPLICE) && (opt.flag & MM_F_FRAG_MODE)) {
-		fprintf(stderr, "[ERROR]\033[1;31m --splice and --frag should not be specified at the same time.\033[0m\n");
-		return 1;
-	}
 	if (!fnw && !(opt.flag&MM_F_CIGAR))
 		ipt.flag |= MM_I_NO_SEQ;
 	if (mm_check_opt(&ipt, &opt) < 0)
 		return 1;
+	if (opt.best_n == 0) {
+		fprintf(stderr, "[WARNING]\033[1;31m changed '-N 0' to '-N %d --secondary=no'.\033[0m\n", old_best_n);
+		opt.best_n = old_best_n, opt.flag |= MM_F_NO_PRINT_2ND;
+	}
 
-	if (argc == optind || fp_help == stdout) {
+	if (argc == o.ind || fp_help == stdout) {
 		fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
 		fprintf(fp_help, "Options:\n");
 		fprintf(fp_help, "  Indexing:\n");
-		fprintf(fp_help, "    -H           use homopolymer-compressed k-mer\n");
+		fprintf(fp_help, "    -H           use homopolymer-compressed k-mer (preferrable for PacBio)\n");
 		fprintf(fp_help, "    -k INT       k-mer size (no larger than 28) [%d]\n", ipt.k);
-		fprintf(fp_help, "    -w INT       minizer window size [%d]\n", ipt.w);
-		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [4G]\n");
+		fprintf(fp_help, "    -w INT       minimizer window size [%d]\n", ipt.w);
+		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [8G]\n");
 		fprintf(fp_help, "    -d FILE      dump index to FILE []\n");
 		fprintf(fp_help, "  Mapping:\n");
 		fprintf(fp_help, "    -f FLOAT     filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
 		fprintf(fp_help, "    -g NUM       stop chain enlongation if there are no minimizers in INT-bp [%d]\n", opt.max_gap);
 		fprintf(fp_help, "    -G NUM       max intron length (effective with -xsplice; changing -r) [200k]\n");
 		fprintf(fp_help, "    -F NUM       max fragment length (effective with -xsr or in the fragment mode) [800]\n");
-		fprintf(fp_help, "    -r NUM       bandwidth used in chaining and DP-based alignment [%d]\n", opt.bw);
+		fprintf(fp_help, "    -r NUM[,NUM] chaining/alignment bandwidth and long-join bandwidth [%d,%d]\n", opt.bw, opt.bw_long);
 		fprintf(fp_help, "    -n INT       minimal number of minimizers on a chain [%d]\n", opt.min_cnt);
 		fprintf(fp_help, "    -m INT       minimal chaining score (matching bases minus log gap penalty) [%d]\n", opt.min_chain_score);
 //		fprintf(fp_help, "    -T INT       SDUST threshold; 0 to disable SDUST [%d]\n", opt.sdust_thres); // TODO: this option is never used; might be buggy
@@ -228,44 +381,53 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -N INT       retain at most INT secondary alignments [%d]\n", opt.best_n);
 		fprintf(fp_help, "  Alignment:\n");
 		fprintf(fp_help, "    -A INT       matching score [%d]\n", opt.a);
-		fprintf(fp_help, "    -B INT       mismatch penalty [%d]\n", opt.b);
+		fprintf(fp_help, "    -B INT       mismatch penalty (larger value for lower divergence) [%d]\n", opt.b);
 		fprintf(fp_help, "    -O INT[,INT] gap open penalty [%d,%d]\n", opt.q, opt.q2);
 		fprintf(fp_help, "    -E INT[,INT] gap extension penalty; a k-long gap costs min{O1+k*E1,O2+k*E2} [%d,%d]\n", opt.e, opt.e2);
-		fprintf(fp_help, "    -z INT       Z-drop score [%d]\n", opt.zdrop);
+		fprintf(fp_help, "    -z INT[,INT] Z-drop score and inversion Z-drop score [%d,%d]\n", opt.zdrop, opt.zdrop_inv);
 		fprintf(fp_help, "    -s INT       minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(fp_help, "    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
+		fprintf(fp_help, "    -J INT       splice mode. 0: original minimap2 model; 1: miniprot model [1]\n");
+		fprintf(fp_help, "    -j FILE      junctions in BED12 to extend *short* RNA-seq alignment []\n");
 		fprintf(fp_help, "  Input/Output:\n");
 		fprintf(fp_help, "    -a           output in the SAM format (PAF by default)\n");
-		fprintf(fp_help, "    -Q           don't output base quality in SAM\n");
+		fprintf(fp_help, "    -o FILE      output alignments to FILE [stdout]\n");
 		fprintf(fp_help, "    -L           write CIGAR with >65535 ops at the CG tag\n");
 		fprintf(fp_help, "    -R STR       SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
 		fprintf(fp_help, "    -c           output CIGAR in PAF\n");
 		fprintf(fp_help, "    --cs[=STR]   output the cs tag; STR is 'short' (if absent) or 'long' [none]\n");
+		fprintf(fp_help, "    --ds         output the ds tag, which is an extension to cs\n");
+		fprintf(fp_help, "    --MD         output the MD tag\n");
+		fprintf(fp_help, "    --eqx        write =/X CIGAR operators\n");
 		fprintf(fp_help, "    -Y           use soft clipping for supplementary alignments\n");
+		fprintf(fp_help, "    -y           copy FASTA/Q comments to output SAM\n");
 		fprintf(fp_help, "    -t INT       number of threads [%d]\n", n_threads);
 		fprintf(fp_help, "    -K NUM       minibatch size for mapping [500M]\n");
 //		fprintf(fp_help, "    -v INT       verbose level [%d]\n", mm_verbose);
 		fprintf(fp_help, "    --version    show version number\n");
 		fprintf(fp_help, "  Preset:\n");
-		fprintf(fp_help, "    -x STR       preset (always applied before other options) []\n");
-		fprintf(fp_help, "                 map-pb: -Hk19 (PacBio vs reference mapping)\n");
-		fprintf(fp_help, "                 map-ont: -k15 (Oxford Nanopore vs reference mapping)\n");
-		fprintf(fp_help, "                 asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
-		fprintf(fp_help, "                 asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
-		fprintf(fp_help, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (PacBio read overlap)\n");
-		fprintf(fp_help, "                 ava-ont: -k15 -w5 -Xp0 -m100 -g10000 --max-chain-skip 25 (ONT read overlap)\n");
-		fprintf(fp_help, "                 splice: long-read spliced alignment (see minimap2.1 for details)\n");
-		fprintf(fp_help, "                 sr: short single-end reads without splicing (see minimap2.1 for details)\n");
-		fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of command-line options.\n");
+		fprintf(fp_help, "    -x STR       preset (always applied before other options; see minimap2.1 for details) []\n");
+		fprintf(fp_help, "                 - lr:hq - accurate long reads (error rate <1%%) against a reference genome\n");
+		fprintf(fp_help, "                 - splice/splice:hq - spliced alignment for long reads/accurate long reads\n");
+		fprintf(fp_help, "                 - splice:sr - spliced alignment for short RNA-seq reads\n");
+		fprintf(fp_help, "                 - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
+		fprintf(fp_help, "                 - sr - short reads against a reference\n");
+		fprintf(fp_help, "                 - map-pb/map-hifi/map-ont/map-iclr - CLR/HiFi/Nanopore/ICLR vs reference mapping\n");
+		fprintf(fp_help, "                 - ava-pb/ava-ont - PacBio CLR/Nanopore read overlap\n");
+		fprintf(fp_help, "\nSee `man ./minimap2.1' for detailed description of these and other advanced command-line options.\n");
 		return fp_help == stdout? 0 : 1;
 	}
 
-	idx_rdr = mm_idx_reader_open(argv[optind], &ipt, fnw);
-	if (idx_rdr == 0) {
-		fprintf(stderr, "[ERROR] failed to open file '%s'\n", argv[optind]);
+	if ((opt.flag & MM_F_SR) && argc - o.ind > 3) {
+		fprintf(stderr, "[ERROR] incorrect input: in the sr mode, please specify no more than two query files.\n");
 		return 1;
 	}
-	if (!idx_rdr->is_idx && fnw == 0 && argc - optind < 2) {
+	idx_rdr = mm_idx_reader_open(argv[o.ind], &ipt, fnw);
+	if (idx_rdr == 0) {
+		fprintf(stderr, "[ERROR] failed to open file '%s': %s\n", argv[o.ind], strerror(errno));
+		return 1;
+	}
+	if (!idx_rdr->is_idx && fnw == 0 && argc - o.ind < 2) {
 		fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
 		mm_idx_reader_close(idx_rdr);
 		return 1;
@@ -273,6 +435,7 @@ int main(int argc, char *argv[])
 	if (opt.best_n == 0 && (opt.flag&MM_F_CIGAR) && mm_verbose >= 2)
 		fprintf(stderr, "[WARNING]\033[1;31m `-N 0' reduces alignment accuracy. Please use --secondary=no to suppress secondary alignments.\033[0m\n");
 	while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
+		int ret;
 		if ((opt.flag & MM_F_CIGAR) && (mi->flag & MM_I_NO_SEQ)) {
 			fprintf(stderr, "[ERROR] the prebuilt index doesn't contain sequences.\n");
 			mm_idx_destroy(mi);
@@ -281,32 +444,83 @@ int main(int argc, char *argv[])
 		}
 		if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
 			if (mm_idx_reader_eof(idx_rdr)) {
-				mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
+				if (opt.split_prefix == 0)
+					ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
+				else
+					ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
 			} else {
-				mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
-				if (mm_verbose >= 2)
-					fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
+				ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
+				if (opt.split_prefix == 0 && mm_verbose >= 2)
+					fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
+			}
+			if (ret != 0) {
+				mm_idx_destroy(mi);
+				mm_idx_reader_close(idx_rdr);
+				return 1;
 			}
 		}
 		if (mm_verbose >= 3)
 			fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
 					__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
-		if (argc != optind + 1) mm_mapopt_update(&opt, mi);
+		if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
 		if (mm_verbose >= 3) mm_idx_stat(mi);
+		if (fn_bed_junc) {
+			mm_idx_bed_read(mi, fn_bed_junc, 1);
+			if (mi->I == 0 && mm_verbose >= 2)
+				fprintf(stderr, "[WARNING] failed to load the junction BED file\n");
+		}
+		if (fn_bed_jump) {
+			mm_idx_jjump_read(mi, fn_bed_jump, MM_JUNC_ANNO, -1);
+			if (mi->J == 0 && mm_verbose >= 2)
+				fprintf(stderr, "[WARNING] failed to load the jump BED file\n");
+		}
+		if (fn_bed_pass1) {
+			mm_idx_jjump_read(mi, fn_bed_pass1, MM_JUNC_MISC, 5);
+			if (mi->J == 0 && mm_verbose >= 2)
+				fprintf(stderr, "[WARNING] failed to load the pass-1 jump BED file\n");
+		}
+		if (fn_spsc) {
+			mm_idx_spsc_read2(mi, fn_spsc, mm_max_spsc_bonus(&opt), spsc_scale);
+			if (mi->spsc == 0 && mm_verbose >= 2)
+				fprintf(stderr, "[WARNING] failed to load the splice score file\n");
+		}
+		if (alt_list) mm_idx_alt_read(mi, alt_list);
+		if (argc - (o.ind + 1) == 0) {
+			mm_idx_destroy(mi);
+			continue; // no query files
+		}
+		ret = 0;
 		if (!(opt.flag & MM_F_FRAG_MODE)) {
-			for (i = optind + 1; i < argc; ++i)
-				mm_map_file(mi, argv[i], &opt, n_threads);
+			for (i = o.ind + 1; i < argc; ++i) {
+				ret = mm_map_file(mi, argv[i], &opt, n_threads);
+				if (ret < 0) break;
+			}
 		} else {
-			mm_map_file_frag(mi, argc - (optind + 1), (const char**)&argv[optind + 1], &opt, n_threads);
+			ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
 		}
 		mm_idx_destroy(mi);
+		if (ret < 0) {
+			fprintf(stderr, "ERROR: failed to map the query file\n");
+			exit(EXIT_FAILURE);
+		}
 	}
+	n_parts = idx_rdr->n_parts;
 	mm_idx_reader_close(idx_rdr);
 
-	fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
-	fprintf(stderr, "[M::%s] CMD:", __func__);
-	for (i = 0; i < argc; ++i)
-		fprintf(stderr, " %s", argv[i]);
-	fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - mm_realtime0, cputime());
+	if (opt.split_prefix)
+		mm_split_merge(argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_parts);
+
+	if (fflush(stdout) == EOF) {
+		perror("[ERROR] failed to write the results");
+		exit(EXIT_FAILURE);
+	}
+
+	if (mm_verbose >= 3) {
+		fprintf(stderr, "[M::%s] Version: %s\n", __func__, MM_VERSION);
+		fprintf(stderr, "[M::%s] CMD:", __func__);
+		for (i = 0; i < argc; ++i)
+			fprintf(stderr, " %s", argv[i]);
+		fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, realtime() - mm_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
+	}
 	return 0;
 }

map.c

@@ -1,6 +1,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <assert.h>
+#include <errno.h>
 #include "kthread.h"
 #include "kvec.h"
 #include "kalloc.h"
@@ -9,138 +10,6 @@
 #include "bseq.h"
 #include "khash.h"
 
-void mm_mapopt_init(mm_mapopt_t *opt)
-{
-	memset(opt, 0, sizeof(mm_mapopt_t));
-	opt->seed = 11;
-	opt->mid_occ_frac = 2e-4f;
-	opt->sdust_thres = 0; // no SDUST masking
-
-	opt->min_cnt = 3;
-	opt->min_chain_score = 40;
-	opt->bw = 500;
-	opt->max_gap = 5000;
-	opt->max_gap_ref = -1;
-	opt->max_chain_skip = 25;
-
-	opt->mask_level = 0.5f;
-	opt->pri_ratio = 0.8f;
-	opt->best_n = 5;
-
-	opt->max_join_long = 20000;
-	opt->max_join_short = 2000;
-	opt->min_join_flank_sc = 1000;
-
-	opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
-	opt->zdrop = 400;
-	opt->end_bonus = -1;
-	opt->min_dp_max = opt->min_chain_score * opt->a;
-	opt->min_ksw_len = 200;
-	opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
-	opt->mini_batch_size = 500000000;
-
-	opt->pe_ori = 0; // FF
-	opt->pe_bonus = 33;
-}
-
-void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
-{
-	if ((opt->flag & MM_F_SPLICE_FOR) && (opt->flag & MM_F_SPLICE_REV))
-		opt->flag |= MM_F_SPLICE;
-	if (opt->mid_occ <= 0)
-		opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
-	if (mm_verbose >= 3)
-		fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
-}
-
-void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len)
-{
-	if ((opt->flag & MM_F_SPLICE) && max_intron_len > 0)
-		opt->max_gap_ref = opt->bw = max_intron_len;
-}
-
-int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
-{
-	if (preset == 0) {
-		mm_idxopt_init(io);
-		mm_mapopt_init(mo);
-	} else if (strcmp(preset, "ava-ont") == 0) {
-		io->flag = 0, io->k = 15, io->w = 5;
-		mo->flag |= MM_F_AVA | MM_F_NO_SELF;
-		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
-	} else if (strcmp(preset, "ava-pb") == 0) {
-		io->flag |= MM_I_HPC, io->k = 19, io->w = 5;
-		mo->flag |= MM_F_AVA | MM_F_NO_SELF;
-		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_gap = 10000, mo->max_chain_skip = 25;
-	} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
-		io->flag |= MM_I_HPC, io->k = 19;
-	} else if (strcmp(preset, "map-ont") == 0) {
-		io->flag = 0, io->k = 15;
-	} else if (strcmp(preset, "asm5") == 0) {
-		io->flag = 0, io->k = 19, io->w = 19;
-		mo->a = 1, mo->b = 19, mo->q = 39, mo->q2 = 81, mo->e = 3, mo->e2 = 1, mo->zdrop = 200;
-		mo->min_dp_max = 200;
-		mo->best_n = 50;
-	} else if (strcmp(preset, "asm10") == 0) {
-		io->flag = 0, io->k = 19, io->w = 19;
-		mo->a = 1, mo->b = 9, mo->q = 16, mo->q2 = 41, mo->e = 2, mo->e2 = 1, mo->zdrop = 200;
-		mo->min_dp_max = 200;
-		mo->best_n = 50;
-	} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
-		io->flag = 0, io->k = 21, io->w = 11;
-		mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS;
-		mo->pe_ori = 0<<1|1; // FR
-		mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
-		mo->zdrop = 100;
-		mo->end_bonus = 10;
-		mo->max_frag_len = 800;
-		mo->max_gap = 100;
-		mo->bw = 100;
-		mo->pri_ratio = 0.5f;
-		mo->min_cnt = 2;
-		mo->min_chain_score = 25;
-		mo->min_dp_max = 40;
-		mo->best_n = 20;
-		mo->mid_occ = 1000;
-		mo->max_occ = 5000;
-		mo->mini_batch_size = 50000000;
-	} else if (strcmp(preset, "splice") == 0 || strcmp(preset, "cdna") == 0) {
-		io->flag = 0, io->k = 15, io->w = 5;
-		mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
-		mo->max_gap = 2000, mo->max_gap_ref = mo->bw = 200000;
-		mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
-		mo->noncan = 9;
-		mo->zdrop = 200;
-	} else return -1;
-	return 0;
-}
-
-int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
-{
-	if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
-		if (mm_verbose >= 1)
-			fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");
-		return -2;
-	}
-	if ((mo->q + mo->e) + (mo->q2 + mo->e2) > 127) {
-		if (mm_verbose >= 1)
-			fprintf(stderr, "[ERROR]\033[1;31m scoring system violating ({-O}+{-E})+({-O2}+{-E2}) <= 127\033[0m\n");
-		return -1;
-	}
-	return 0;
-}
-
-typedef struct {
-	uint32_t n;
-	uint32_t qpos;
-	uint32_t seg_id;
-	const uint64_t *cr;
-} mm_match_t;
-
-struct mm_tbuf_s {
-	void *km;
-};
-
 mm_tbuf_t *mm_tbuf_init(void)
 {
 	mm_tbuf_t *b;
@@ -156,6 +25,11 @@ void mm_tbuf_destroy(mm_tbuf_t *b)
 	free(b);
 }
 
+void *mm_tbuf_get_km(mm_tbuf_t *b)
+{
+	return b->km;
+}
+
 static int mm_dust_minier(void *km, int n, mm128_t *a, int l_seq, const char *seq, int sdust_thres)
 {
 	int n_dreg, j, k, u = 0;
@@ -167,12 +41,12 @@ static int mm_dust_minier(void *km, int n, mm128_t *a, int l_seq, const char *se
 	for (j = k = 0; j < n; ++j) { // squeeze out minimizers that significantly overlap with LCRs
 		int32_t qpos = (uint32_t)a[j].y>>1, span = a[j].x&0xff;
 		int32_t s = qpos - (span - 1), e = s + span;
-		while (u < n_dreg && (uint32_t)dreg[u] <= s) ++u;
-		if (u < n_dreg && dreg[u]>>32 < e) {
+		while (u < n_dreg && (int32_t)dreg[u] <= s) ++u;
+		if (u < n_dreg && (int32_t)(dreg[u]>>32) < e) {
 			int v, l = 0;
-			for (v = u; v < n_dreg && dreg[v]>>32 < e; ++v) { // iterate over LCRs overlapping this minimizer
-				int ss = s > dreg[v]>>32? s : dreg[v]>>32;
-				int ee = e < (uint32_t)dreg[v]? e : (uint32_t)dreg[v];
+			for (v = u; v < n_dreg && (int32_t)(dreg[v]>>32) < e; ++v) { // iterate over LCRs overlapping this minimizer
+				int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32;
+				int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v];
 				l += ee - ss;
 			}
 			if (l <= span>>1) a[k++] = a[j]; // keep the minimizer if less than half of it falls in masked region
@@ -184,9 +58,10 @@ static int mm_dust_minier(void *km, int n, mm128_t *a, int l_seq, const char *se
 
 static void collect_minimizers(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, mm128_v *mv)
 {
-	int i, j, n, sum = 0;
+	int i, n, sum = 0;
 	mv->n = 0;
 	for (i = n = 0; i < n_segs; ++i) {
+		size_t j;
 		mm_sketch(km, seqs[i], qlens[i], mi->w, mi->k, i, mi->flag&MM_I_HPC, mv);
 		for (j = n; j < mv->n; ++j)
 			mv->a[j].y += sum << 1;
@@ -196,99 +71,163 @@ static void collect_minimizers(void *km, const mm_mapopt_t *opt, const mm_idx_t
 	}
 }
 
+#include "ksort.h"
+#define heap_lt(a, b) ((a).x > (b).x)
+KSORT_INIT(heap, mm128_t, heap_lt)
+
+static inline int skip_seed(int flag, uint64_t r, const mm_seed_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
+{
+	*is_self = 0;
+	if (qname && (flag & (MM_F_NO_DIAG|MM_F_NO_DUAL))) {
+		const mm_idx_seq_t *s = &mi->seq[r>>32];
+		int cmp;
+		cmp = strcmp(qname, s->name);
+		if ((flag&MM_F_NO_DIAG) && cmp == 0 && (int)s->len == qlen) {
+			if ((uint32_t)r>>1 == (q->q_pos>>1)) return 1; // avoid the diagnonal anchors
+			if ((r&1) == (q->q_pos&1)) *is_self = 1; // this flag is used to avoid spurious extension on self chain
+		}
+		if ((flag&MM_F_NO_DUAL) && cmp > 0) // all-vs-all mode: map once
+			return 1;
+	}
+	if (flag & (MM_F_FOR_ONLY|MM_F_REV_ONLY)) {
+		if ((r&1) == (q->q_pos&1)) { // forward strand
+			if (flag & MM_F_REV_ONLY) return 1;
+		} else {
+			if (flag & MM_F_FOR_ONLY) return 1;
+		}
+	}
+	return 0;
+}
+
+static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len,
+								  int *n_mini_pos, uint64_t **mini_pos)
+{
+	int i, n_m, heap_size = 0;
+	int64_t j, n_for = 0, n_rev = 0;
+	mm_seed_t *m;
+	mm128_t *a, *heap;
+
+	m = mm_collect_matches(km, &n_m, qlen, max_occ, opt->max_max_occ, opt->occ_dist, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
+
+	heap = (mm128_t*)kmalloc(km, n_m * sizeof(mm128_t));
+	a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
+
+	for (i = 0, heap_size = 0; i < n_m; ++i) {
+		if (m[i].n > 0) {
+			heap[heap_size].x = m[i].cr[0];
+			heap[heap_size].y = (uint64_t)i<<32;
+			++heap_size;
+		}
+	}
+	ks_heapmake_heap(heap_size, heap);
+	while (heap_size > 0) {
+		mm_seed_t *q = &m[heap->y>>32];
+		mm128_t *p;
+		uint64_t r = heap->x;
+		int32_t is_self, rpos = (uint32_t)r >> 1;
+		if (!skip_seed(opt->flag, r, q, qname, qlen, mi, &is_self)) {
+			if ((r&1) == (q->q_pos&1)) { // forward strand
+				p = &a[n_for++];
+				p->x = (r&0xffffffff00000000ULL) | rpos;
+				p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
+			} else { // reverse strand
+				p = &a[(*n_a) - (++n_rev)];
+				p->x = 1ULL<<63 | (r&0xffffffff00000000ULL) | rpos;
+				p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
+			}
+			p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
+			if (q->is_tandem) p->y |= MM_SEED_TANDEM;
+			if (is_self) p->y |= MM_SEED_SELF;
+		}
+		// update the heap
+		if ((uint32_t)heap->y < q->n - 1) {
+			++heap[0].y;
+			heap[0].x = m[heap[0].y>>32].cr[(uint32_t)heap[0].y];
+		} else {
+			heap[0] = heap[heap_size - 1];
+			--heap_size;
+		}
+		ks_heapdown_heap(0, heap_size, heap);
+	}
+	kfree(km, m);
+	kfree(km, heap);
+
+	// reverse anchors on the reverse strand, as they are in the descending order
+	for (j = 0; j < n_rev>>1; ++j) {
+		mm128_t t = a[(*n_a) - 1 - j];
+		a[(*n_a) - 1 - j] = a[(*n_a) - (n_rev - j)];
+		a[(*n_a) - (n_rev - j)] = t;
+	}
+	if (*n_a > n_for + n_rev) {
+		memmove(a + n_for, a + (*n_a) - n_rev, n_rev * sizeof(mm128_t));
+		*n_a = n_for + n_rev;
+	}
+	return a;
+}
+
 static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len,
 								  int *n_mini_pos, uint64_t **mini_pos)
 {
-	int rep_st = 0, rep_en = 0, i;
-	mm_match_t *m;
+	int i, n_m;
+	mm_seed_t *m;
 	mm128_t *a;
-
-	*n_mini_pos = 0;
-	*mini_pos = (uint64_t*)kmalloc(km, mv->n * sizeof(uint64_t));
-	m = (mm_match_t*)kmalloc(km, mv->n * sizeof(mm_match_t));
-	for (i = 0; i < mv->n; ++i) {
-		int t;
-		mm128_t *p = &mv->a[i];
-		m[i].qpos = (uint32_t)p->y;
-		m[i].cr = mm_idx_get(mi, p->x>>8, &t);
-		m[i].n = t;
-		m[i].seg_id = p->y >> 32;
-	}
-	for (i = 0, *n_a = 0; i < mv->n; ++i) // find the length of a[]
-		if (m[i].n < max_occ) *n_a += m[i].n;
+	m = mm_collect_matches(km, &n_m, qlen, max_occ, opt->max_max_occ, opt->occ_dist, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
 	a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
-	for (i = *rep_len = 0, *n_a = 0; i < mv->n; ++i) {
-		mm128_t *p = &mv->a[i];
-		mm_match_t *q = &m[i];
+	for (i = 0, *n_a = 0; i < n_m; ++i) {
+		mm_seed_t *q = &m[i];
 		const uint64_t *r = q->cr;
-		int k, q_span = p->x & 0xff, is_tandem = 0;
-		if (q->n >= max_occ) {
-			int en = (q->qpos>>1) + 1, st = en - q_span;
-			if (st > rep_en) {
-				*rep_len += rep_en - rep_st;
-				rep_st = st, rep_en = en;
-			} else rep_en = en;
-			continue;
-		}
-		(*mini_pos)[(*n_mini_pos)++] = (uint64_t)q_span<<32 | q->qpos>>1;
-		if (i > 0 && p->x>>8 == mv->a[i - 1].x>>8) is_tandem = 1;
-		if (i < mv->n - 1 && p->x>>8 == mv->a[i + 1].x>>8) is_tandem = 1;
+		uint32_t k;
 		for (k = 0; k < q->n; ++k) {
-			int32_t rpos = (uint32_t)r[k] >> 1;
+			int32_t is_self, rpos = (uint32_t)r[k] >> 1;
 			mm128_t *p;
-			if (qname && (opt->flag&(MM_F_NO_SELF|MM_F_AVA))) {
-				const char *tname = mi->seq[r[k]>>32].name;
-				int cmp;
-				cmp = strcmp(qname, tname);
-				if ((opt->flag&MM_F_NO_SELF) && cmp == 0 && rpos == (q->qpos>>1)) // avoid the diagonal
-					continue;
-				if ((opt->flag&MM_F_AVA) && cmp > 0) // all-vs-all mode: map once
-					continue;
-			}
+			if (skip_seed(opt->flag, r[k], q, qname, qlen, mi, &is_self)) continue;
 			p = &a[(*n_a)++];
-			if ((r[k]&1) == (q->qpos&1)) { // forward strand
+			if ((r[k]&1) == (q->q_pos&1)) { // forward strand
 				p->x = (r[k]&0xffffffff00000000ULL) | rpos;
-				p->y = (uint64_t)q_span << 32 | q->qpos >> 1;
-			} else { // reverse strand
+				p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
+			} else if (!(opt->flag & MM_F_QSTRAND)) { // reverse strand and not in the query-strand mode
 				p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | rpos;
-				p->y = (uint64_t)q_span << 32 | (qlen - ((q->qpos>>1) + 1 - q_span) - 1);
+				p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
+			} else { // reverse strand; query-strand
+				int32_t len = mi->seq[r[k]>>32].len;
+				p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (len - (rpos + 1 - q->q_span) - 1); // coordinate only accurate for non-HPC seeds
+				p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
 			}
 			p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
-			if (is_tandem) p->y |= MM_SEED_TANDEM;
+			if (q->is_tandem) p->y |= MM_SEED_TANDEM;
+			if (is_self) p->y |= MM_SEED_SELF;
 		}
 	}
-	*rep_len += rep_en - rep_st;
 	kfree(km, m);
+	radix_sort_128x(a, a + (*n_a));
 	return a;
 }
 
 static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
 {
-	if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
-		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
-		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
+	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
+		mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
+		if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 1, opt->max_gap * 0.8, n_regs, regs);
 		else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
-		if (!(opt->flag & MM_F_SPLICE) && !(opt->flag & MM_F_SR) && !(opt->flag & MM_F_NO_LJOIN))
-			mm_join_long(km, opt, qlen, n_regs, regs, a);
 	}
 }
 
-static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int qlen, const char *seq, const char *qual, int *n_regs, mm_reg1_t *regs, mm128_t *a)
+static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int qlen, const char *seq, int *n_regs, mm_reg1_t *regs, mm128_t *a)
 {
 	if (!(opt->flag & MM_F_CIGAR)) return regs;
 	regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
-	if (!(opt->flag & MM_F_AVA)) {
-		mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
-		mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
+	if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
+		mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
+		mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 0, opt->max_gap * 0.8, n_regs, regs);
 		mm_set_sam_pri(*n_regs, regs);
 	}
 	return regs;
 }
 
-void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, const char **quals, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
+void mm_map_frag_core(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
 {
 	int i, j, rep_len, qlen_sum, n_regs0, n_mini_pos;
-	int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
+	int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR), is_sr_rna = !!(opt->flag & MM_F_SR_RNA);
 	uint32_t hash;
 	int64_t n_a;
 	uint64_t *u, *mini_pos;
@@ -296,19 +235,22 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	mm128_v mv = {0,0,0};
 	mm_reg1_t *regs0;
 	km_stat_t kmst;
+	float chn_pen_gap, chn_pen_skip;
 
 	for (i = 0, qlen_sum = 0; i < n_segs; ++i)
 		qlen_sum += qlens[i], n_regs[i] = 0, regs[i] = 0;
 
 	if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
+	if (opt->max_qlen > 0 && qlen_sum > opt->max_qlen) return;
 
-	hash  = qname? __ac_X31_hash_string(qname) : 0;
+	hash  = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
 	hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
 	hash  = __ac_Wang_hash(hash);
 
 	collect_minimizers(b->km, opt, mi, n_segs, qlens, seqs, &mv);
-	a = collect_seed_hits(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
-	radix_sort_128x(a, a + n_a);
+	if (opt->q_occ_frac > 0.0f) mm_seed_mz_flt(b->km, &mv, opt->mid_occ, opt->q_occ_frac);
+	if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
+	else a = collect_seed_hits(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
 
 	if (mm_dbg_flag & MM_DBG_PRINT_SEED) {
 		fprintf(stderr, "RS\t%d\n", rep_len);
@@ -328,17 +270,35 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
 	} else max_chain_gap_ref = opt->max_gap;
 
-	a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
+	chn_pen_gap  = opt->chain_gap_scale * 0.01 * mi->k;
+	chn_pen_skip = opt->chain_skip_scale * 0.01 * mi->k;
+	if (opt->flag & MM_F_RMQ) {
+		a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
+						  chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
+	} else {
+		a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
+						 chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
+	}
 
-	if (opt->max_occ > opt->mid_occ && rep_len > 0) {
+	if (opt->bw_long > opt->bw && (opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
+		int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
+		if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
+			int32_t i;
+			for (i = 0, n_a = 0; i < n_regs0; ++i) n_a += (int32_t)u[i];
+			kfree(b->km, u);
+			radix_sort_128x(a, a + n_a);
+			a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
+							  chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
+		}
+	} else if (opt->max_occ > opt->mid_occ && rep_len > 0 && !(opt->flag & MM_F_RMQ)) { // re-chain, mostly for short reads
 		int rechain = 0;
 		if (n_regs0 > 0) { // test if the best chain has all the segments
 			int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
 			for (i = 0; i < n_regs0; ++i) { // find the best chain
-				if (max < u[i]>>32) max = u[i]>>32, max_i = i, max_off = off;
+				if (max < (int)(u[i]>>32)) max = u[i]>>32, max_i = i, max_off = off;
 				off += (uint32_t)u[i];
 			}
-			for (i = 1; i < (uint32_t)u[max_i]; ++i) // count the number of segments in the best chain
+			for (i = 1; i < (int32_t)u[max_i]; ++i) // count the number of segments in the best chain
 				if ((a[max_off+i].y&MM_SEED_SEG_MASK) != (a[max_off+i-1].y&MM_SEED_SEG_MASK))
 					++n_chained_segs;
 			if (n_chained_segs < n_segs)
@@ -348,35 +308,46 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 			kfree(b->km, a);
 			kfree(b->km, u);
 			kfree(b->km, mini_pos);
-			a = collect_seed_hits(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
-			radix_sort_128x(a, a + n_a);
-			a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
+			if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
+			else a = collect_seed_hits(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
+			a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
+							 chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
 		}
 	}
+	b->frag_gap = max_chain_gap_ref;
+	b->rep_len = rep_len;
 
-	regs0 = mm_gen_regs(b->km, hash, qlen_sum, n_regs0, u, a);
+	regs0 = mm_gen_regs(b->km, hash, qlen_sum, n_regs0, u, a, !!(opt->flag&MM_F_QSTRAND));
+	if (mi->n_alt) {
+		mm_mark_alt(mi, n_regs0, regs0);
+		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
+	}
 
-	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
+	if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
 		for (j = 0; j < n_regs0; ++j)
 			for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
 				fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
 						i == regs0[j].as? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
 
 	chain_post(opt, max_chain_gap_ref, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
-	if (!is_sr) mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
+	if (!is_sr && !(opt->flag&MM_F_QSTRAND)) {
+		mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
+		n_regs0 = mm_filter_strand_retained(n_regs0, regs0);
+	}
 
 	if (n_segs == 1) { // uni-segment
-		regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], quals? quals[0] : 0, &n_regs0, regs0, a);
-		mm_set_mapq(n_regs0, regs0, opt->min_chain_score, opt->a, rep_len, is_sr);
+		regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);
+		regs0 = (mm_reg1_t*)realloc(regs0, sizeof(*regs0) * n_regs0);
+		mm_set_mapq2(b->km, n_regs0, regs0, opt->min_chain_score, opt->a, rep_len, is_sr || is_sr_rna, is_splice);
 		n_regs[0] = n_regs0, regs[0] = regs0;
 	} else { // multi-segment
 		mm_seg_t *seg;
 		seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
 		free(regs0);
 		for (i = 0; i < n_segs; ++i) {
-			mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b); // update mm_reg1_t::parent
-			regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], quals? quals[i] : 0, &n_regs[i], regs[i], seg[i].a);
-			mm_set_mapq(n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr);
+			mm_set_parent(b->km, opt->mask_level, opt->mask_len, n_regs[i], regs[i], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); // update mm_reg1_t::parent
+			regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
+			mm_set_mapq2(b->km, n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr || is_sr_rna, is_splice);
 		}
 		mm_seg_free(b->km, n_segs, seg);
 		if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
@@ -388,22 +359,40 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	kfree(b->km, u);
 	kfree(b->km, mini_pos);
 
+	if (mi->J && n_segs == 1 && is_splice)
+		for (i = 0; i < n_regs0; ++i)
+			mm_jump_split(b->km, mi, opt, qlens[0], (const uint8_t*)seqs[0], &regs0[i], 0);
+
 	if (b->km) {
 		km_stat(b->km, &kmst);
 		if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
 			fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
 		assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak
-		if (kmst.largest > 1U<<28) {
+		if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) {
+			if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
+				fprintf(stderr, "[W::%s] reset thread-local memory after read %s\n", __func__, qname);
 			km_destroy(b->km);
 			b->km = km_init();
 		}
 	}
 }
 
+void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
+{
+	if ((opt->flag & MM_F_WEAK_PAIRING) && n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR)) {
+		int i;
+		for (i = 0; i < n_segs; ++i)
+			mm_map_frag_core(mi, 1, &qlens[i], &seqs[i], &n_regs[i], &regs[i], b, opt, qname);
+		mm_pair(b->km, opt->max_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs);
+	} else {
+		mm_map_frag_core(mi, n_segs, qlens, seqs, n_regs, regs, b, opt, qname);
+	}
+}
+
 mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
 {
 	mm_reg1_t *regs;
-	mm_map_frag(mi, 1, &qlen, &seq, 0, n_regs, &regs, b, opt, qname);
+	mm_map_frag(mi, 1, &qlen, &seq, n_regs, &regs, b, opt, qname);
 	return regs;
 }
 
@@ -412,18 +401,23 @@ mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm
  **************************/
 
 typedef struct {
-	int mini_batch_size, n_processed, n_threads, n_fp;
+	int n_processed, n_threads, n_fp;
+	int64_t mini_batch_size;
 	const mm_mapopt_t *opt;
 	mm_bseq_file_t **fp;
 	const mm_idx_t *mi;
 	kstring_t str;
+
+	int n_parts;
+	uint32_t *rid_shift;
+	FILE *fp_split, **fp_parts;
 } pipeline_t;
 
 typedef struct {
 	const pipeline_t *p;
     int n_seq, n_frag;
 	mm_bseq1_t *seq;
-	int *n_reg, *seg_off, *n_seg;
+	int *n_reg, *seg_off, *n_seg, *rep_len, *frag_gap;
 	mm_reg1_t **reg;
 	mm_tbuf_t **buf;
 } step_t;
@@ -431,25 +425,33 @@ typedef struct {
 static void worker_for(void *_data, long i, int tid) // kt_for() callback
 {
     step_t *s = (step_t*)_data;
-	int qlens[MM_MAX_SEG], j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori, is_sr = !!(s->p->opt->flag & MM_F_SR);
-	const char *qseqs[MM_MAX_SEG], *quals[MM_MAX_SEG];
+	int qlens[MM_MAX_SEG], j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori;
+	const char *qseqs[MM_MAX_SEG];
+	double t = 0.0;
 	mm_tbuf_t *b = s->buf[tid];
 	assert(s->n_seg[i] <= MM_MAX_SEG);
-	memset(quals, 0, sizeof(char*) * MM_MAX_SEG);
-	if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
+	if (mm_dbg_flag & MM_DBG_PRINT_QNAME) {
 		fprintf(stderr, "QR\t%s\t%d\t%d\n", s->seq[off].name, tid, s->seq[off].l_seq);
+		t = realtime();
+	}
 	for (j = 0; j < s->n_seg[i]; ++j) {
 		if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
 			mm_revcomp_bseq(&s->seq[off + j]);
 		qlens[j] = s->seq[off + j].l_seq;
 		qseqs[j] = s->seq[off + j].seq;
-		quals[j] = is_sr? s->seq[off + j].qual : 0;
 	}
 	if (s->p->opt->flag & MM_F_INDEPEND_SEG) {
-		for (j = 0; j < s->n_seg[i]; ++j)
-			mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &quals[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
+		for (j = 0; j < s->n_seg[i]; ++j) {
+			mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
+			s->rep_len[off + j] = b->rep_len;
+			s->frag_gap[off + j] = b->frag_gap;
+		}
 	} else {
-		mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, quals, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
+		mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
+		for (j = 0; j < s->n_seg[i]; ++j) {
+			s->rep_len[off + j] = b->rep_len;
+			s->frag_gap[off + j] = b->frag_gap;
+		}
 	}
 	for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
 		if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
@@ -461,8 +463,79 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
 				r->qs = qlens[j] - r->qe;
 				r->qe = qlens[j] - t;
 				r->rev = !r->rev;
+				if (r->p) {
+					if (r->p->trans_strand == 1) r->p->trans_strand = 2;
+					else if (r->p->trans_strand == 2) r->p->trans_strand = 1;
+				}
 			}
 		}
+	if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
+		fprintf(stderr, "QT\t%s\t%d\t%.6f\n", s->seq[off].name, tid, realtime() - t);
+}
+
+static void merge_hits(step_t *s)
+{
+	int f, i, k0, k, max_seg = 0, *n_reg_part, *rep_len_part, *frag_gap_part, *qlens;
+	void *km;
+	FILE **fp = s->p->fp_parts;
+	const mm_mapopt_t *opt = s->p->opt;
+
+	km = km_init();
+	for (f = 0; f < s->n_frag; ++f)
+		max_seg = max_seg > s->n_seg[f]? max_seg : s->n_seg[f];
+	qlens = CALLOC(int, max_seg + s->p->n_parts * 3);
+	n_reg_part = qlens + max_seg;
+	rep_len_part = n_reg_part + s->p->n_parts;
+	frag_gap_part = rep_len_part + s->p->n_parts;
+	for (f = 0, k = k0 = 0; f < s->n_frag; ++f) {
+		k0 = k;
+		for (i = 0; i < s->n_seg[f]; ++i, ++k) {
+			int j, l, t, rep_len = 0;
+			qlens[i] = s->seq[k].l_seq;
+			for (j = 0, s->n_reg[k] = 0; j < s->p->n_parts; ++j) {
+				mm_err_fread(&n_reg_part[j],    sizeof(int), 1, fp[j]);
+				mm_err_fread(&rep_len_part[j],  sizeof(int), 1, fp[j]);
+				mm_err_fread(&frag_gap_part[j], sizeof(int), 1, fp[j]);
+				s->n_reg[k] += n_reg_part[j];
+				if (rep_len < rep_len_part[j])
+					rep_len = rep_len_part[j];
+			}
+			s->reg[k] = CALLOC(mm_reg1_t, s->n_reg[k]);
+			for (j = 0, l = 0; j < s->p->n_parts; ++j) {
+				for (t = 0; t < n_reg_part[j]; ++t, ++l) {
+					mm_reg1_t *r = &s->reg[k][l];
+					uint32_t capacity;
+					mm_err_fread(r, sizeof(mm_reg1_t), 1, fp[j]);
+					r->rid += s->p->rid_shift[j];
+					if (opt->flag & MM_F_CIGAR) {
+						mm_err_fread(&capacity, 4, 1, fp[j]);
+						r->p = (mm_extra_t*)calloc(capacity, 4);
+						r->p->capacity = capacity;
+						mm_err_fread(r->p, r->p->capacity, 4, fp[j]);
+					}
+				}
+			}
+			if (!(opt->flag&MM_F_SR) && s->seq[k].l_seq >= opt->rank_min_len)
+				mm_update_dp_max(s->seq[k].l_seq, s->n_reg[k], s->reg[k], opt->rank_frac, opt->a, opt->b);
+			for (j = 0; j < s->n_reg[k]; ++j) {
+				mm_reg1_t *r = &s->reg[k][j];
+				if (r->p) r->p->dp_max2 = 0; // reset ->dp_max2 as mm_set_parent() doesn't clear it; necessary with mm_update_dp_max()
+				r->subsc = 0; // this may not be necessary
+				r->n_sub = 0; // n_sub will be an underestimate as we don't see all the chains now, but it can't be accurate anyway
+			}
+			mm_hit_sort(km, &s->n_reg[k], s->reg[k], opt->alt_drop);
+			mm_set_parent(km, opt->mask_level, opt->mask_len, s->n_reg[k], s->reg[k], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
+			if (!(opt->flag & MM_F_ALL_CHAINS)) {
+				mm_select_sub(km, opt->pri_ratio, s->p->mi->k*2, opt->best_n, 0, opt->max_gap * 0.8, &s->n_reg[k], s->reg[k]);
+				mm_set_sam_pri(s->n_reg[k], s->reg[k]);
+			}
+			mm_set_mapq2(km, s->n_reg[k], s->reg[k], opt->min_chain_score, opt->a, rep_len, !!(opt->flag & (MM_F_SR|MM_F_SR_RNA)), !!(opt->flag & MM_F_SPLICE));
+		}
+		if (s->n_seg[f] == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
+			mm_pair(km, frag_gap_part[0], opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, &s->n_reg[k0], &s->reg[k0]);
+	}
+	free(qlens);
+	km_destroy(km);
 }
 
 static void *worker_pipeline(void *shared, int step, void *in)
@@ -471,11 +544,12 @@ static void *worker_pipeline(void *shared, int step, void *in)
     pipeline_t *p = (pipeline_t*)shared;
     if (step == 0) { // step 0: read sequences
 		int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
+		int with_comment = !!(p->opt->flag & MM_F_COPY_COMMENT);
 		int frag_mode = (p->n_fp > 1 || !!(p->opt->flag & MM_F_FRAG_MODE));
         step_t *s;
         s = (step_t*)calloc(1, sizeof(step_t));
-		if (p->n_fp > 1) s->seq = mm_bseq_read_frag(p->n_fp, p->fp, p->mini_batch_size, with_qual, &s->n_seq);
-		else s->seq = mm_bseq_read2(p->fp[0], p->mini_batch_size, with_qual, frag_mode, &s->n_seq);
+		if (p->n_fp > 1) s->seq = mm_bseq_read_frag2(p->n_fp, p->fp, p->mini_batch_size, with_qual, with_comment, &s->n_seq);
+		else s->seq = mm_bseq_read3(p->fp[0], p->mini_batch_size, with_qual, with_comment, frag_mode, &s->n_seq);
 		if (s->seq) {
 			s->p = p;
 			for (i = 0; i < s->n_seq; ++i)
@@ -483,9 +557,11 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			s->buf = (mm_tbuf_t**)calloc(p->n_threads, sizeof(mm_tbuf_t*));
 			for (i = 0; i < p->n_threads; ++i)
 				s->buf[i] = mm_tbuf_init();
-			s->n_reg = (int*)calloc(3 * s->n_seq, sizeof(int));
-			s->seg_off = s->n_reg + s->n_seq; // seg_off and n_seg are allocated together with n_reg
+			s->n_reg = (int*)calloc(5 * s->n_seq, sizeof(int));
+			s->seg_off = s->n_reg + s->n_seq; // seg_off, n_seg, rep_len and frag_gap are allocated together with n_reg
 			s->n_seg = s->seg_off + s->n_seq;
+			s->rep_len = s->n_seg + s->n_seq;
+			s->frag_gap = s->rep_len + s->n_seq;
 			s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*));
 			for (i = 1, j = 0; i <= s->n_seq; ++i)
 				if (i == s->n_seq || !frag_mode || !mm_qname_same(s->seq[i-1].name, s->seq[i].name)) {
@@ -496,7 +572,8 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			return s;
 		} else free(s);
     } else if (step == 1) { // step 1: map
-		kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_frag);
+		if (p->n_parts > 0) merge_hits((step_t*)in);
+		else kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_frag);
 		return in;
     } else if (step == 2) { // step 2: output
 		void *km = 0;
@@ -509,20 +586,43 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			int seg_st = s->seg_off[k], seg_en = s->seg_off[k] + s->n_seg[k];
 			for (i = seg_st; i < seg_en; ++i) {
 				mm_bseq1_t *t = &s->seq[i];
-				for (j = 0; j < s->n_reg[i]; ++j) {
-					mm_reg1_t *r = &s->reg[i][j];
-					assert(!r->sam_pri || r->id == r->parent);
-					if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
-						continue;
+				if (p->opt->split_prefix && p->n_parts == 0) { // then write to temporary files
+					mm_err_fwrite(&s->n_reg[i],    sizeof(int), 1, p->fp_split);
+					mm_err_fwrite(&s->rep_len[i],  sizeof(int), 1, p->fp_split);
+					mm_err_fwrite(&s->frag_gap[i], sizeof(int), 1, p->fp_split);
+					for (j = 0; j < s->n_reg[i]; ++j) {
+						mm_reg1_t *r = &s->reg[i][j];
+						mm_err_fwrite(r, sizeof(mm_reg1_t), 1, p->fp_split);
+						if (p->opt->flag & MM_F_CIGAR) {
+							mm_err_fwrite(&r->p->capacity, 4, 1, p->fp_split);
+							mm_err_fwrite(r->p, r->p->capacity, 4, p->fp_split);
+						}
+					}
+				} else if (p->opt->flag & MM_F_OUT_JUNC) { // extra logic for --write-junc
+					for (j = 0; j < s->n_reg[i]; ++j) {
+						const mm_reg1_t *r = &s->reg[i][j];
+						if (r->id != r->parent || r->mapq < 10) continue;
+						mm_write_junc(&p->str, mi, t, r);
+						if (p->str.l > 0) mm_err_puts(p->str.s);
+					}
+				} else if (s->n_reg[i] > 0) { // the query has at least one hit
+					for (j = 0; j < s->n_reg[i]; ++j) {
+						const mm_reg1_t *r = &s->reg[i][j];
+						assert(!r->sam_pri || r->id == r->parent);
+						if ((p->opt->flag & MM_F_NO_PRINT_2ND) && r->id != r->parent)
+							continue;
+						if (p->opt->flag & MM_F_OUT_SAM)
+							mm_write_sam3(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag, s->rep_len[i]);
+						else
+							mm_write_paf4(&p->str, mi, t, r, km, p->opt->flag, s->rep_len[i], s->n_seg[k], i - seg_st);
+						mm_err_puts(p->str.s);
+					}
+				} else if ((p->opt->flag & MM_F_PAF_NO_HIT) || ((p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_SAM_HIT_ONLY))) { // output an empty hit, if requested
 					if (p->opt->flag & MM_F_OUT_SAM)
-						mm_write_sam2(&p->str, mi, t, i - seg_st, j, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
+						mm_write_sam3(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag, s->rep_len[i]);
 					else
-						mm_write_paf(&p->str, mi, t, r, km, p->opt->flag);
-					puts(p->str.s);
-				}
-				if (s->n_reg[i] == 0 && (p->opt->flag & MM_F_OUT_SAM)) {
-					mm_write_sam2(&p->str, mi, t, i - seg_st, -1, s->n_seg[k], &s->n_reg[seg_st], (const mm_reg1_t*const*)&s->reg[seg_st], km, p->opt->flag);
-					puts(p->str.s);
+						mm_write_paf4(&p->str, mi, t, 0, 0, p->opt->flag, s->rep_len[i], s->n_seg[k], i - seg_st);
+					mm_err_puts(p->str.s);
 				}
 			}
 			for (i = seg_st; i < seg_en; ++i) {
@@ -530,9 +630,10 @@ static void *worker_pipeline(void *shared, int step, void *in)
 				free(s->reg[i]);
 				free(s->seq[i].seq); free(s->seq[i].name);
 				if (s->seq[i].qual) free(s->seq[i].qual);
+				if (s->seq[i].comment) free(s->seq[i].comment);
 			}
 		}
-		free(s->reg); free(s->n_reg); free(s->seq); // seg_off and n_seg were allocated with reg; no memory leak here
+		free(s->reg); free(s->n_reg); free(s->seq); // seg_off, n_seg, rep_len and frag_gap were allocated with reg; no memory leak here
 		km_destroy(km);
 		if (mm_verbose >= 3)
 			fprintf(stderr, "[M::%s::%.3f*%.2f] mapped %d sequences\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), s->n_seq);
@@ -541,32 +642,44 @@ static void *worker_pipeline(void *shared, int step, void *in)
     return 0;
 }
 
+static mm_bseq_file_t **open_bseqs(int n, const char **fn)
+{
+	mm_bseq_file_t **fp;
+	int i, j;
+	fp = (mm_bseq_file_t**)calloc(n, sizeof(mm_bseq_file_t*));
+	for (i = 0; i < n; ++i) {
+		if ((fp[i] = mm_bseq_open(fn[i])) == 0) {
+			if (mm_verbose >= 1)
+				fprintf(stderr, "ERROR: failed to open file '%s': %s\n", fn[i], strerror(errno));
+			for (j = 0; j < i; ++j)
+				mm_bseq_close(fp[j]);
+			free(fp);
+			return 0;
+		}
+	}
+	return fp;
+}
+
 int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads)
 {
-	int i, j, pl_threads;
+	int i, pl_threads;
 	pipeline_t pl;
 	if (n_segs < 1) return -1;
 	memset(&pl, 0, sizeof(pipeline_t));
 	pl.n_fp = n_segs;
-	pl.fp = (mm_bseq_file_t**)calloc(n_segs, sizeof(mm_bseq_file_t*));
-	for (i = 0; i < n_segs; ++i) {
-		pl.fp[i] = mm_bseq_open(fn[i]);
-		if (pl.fp[i] == 0) {
-			if (mm_verbose >= 1)
-				fprintf(stderr, "ERROR: failed to open file '%s'\n", fn[i]);
-			for (j = 0; j < i; ++j)
-				mm_bseq_close(pl.fp[j]);
-			free(pl.fp);
-			return -1;
-		}
-	}
+	pl.fp = open_bseqs(pl.n_fp, fn);
+	if (pl.fp == 0) return -1;
 	pl.opt = opt, pl.mi = idx;
 	pl.n_threads = n_threads > 1? n_threads : 1;
 	pl.mini_batch_size = opt->mini_batch_size;
+	if (opt->split_prefix)
+		pl.fp_split = mm_split_init(opt->split_prefix, idx);
 	pl_threads = n_threads == 1? 1 : (opt->flag&MM_F_2_IO_THREADS)? 3 : 2;
 	kt_pipeline(pl_threads, worker_pipeline, &pl, 3);
+
 	free(pl.str.s);
-	for (i = 0; i < n_segs; ++i)
+	if (pl.fp_split) fclose(pl.fp_split);
+	for (i = 0; i < pl.n_fp; ++i)
 		mm_bseq_close(pl.fp[i]);
 	free(pl.fp);
 	return 0;
@@ -576,3 +689,48 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
 {
 	return mm_map_file_frag(idx, 1, &fn, opt, n_threads);
 }
+
+int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx)
+{
+	int i;
+	pipeline_t pl;
+	mm_idx_t *mi;
+	if (n_segs < 1 || n_split_idx < 1) return -1;
+	memset(&pl, 0, sizeof(pipeline_t));
+	pl.n_fp = n_segs;
+	pl.fp = open_bseqs(pl.n_fp, fn);
+	if (pl.fp == 0) return -1;
+	pl.opt = opt;
+	pl.mini_batch_size = opt->mini_batch_size;
+
+	pl.n_parts = n_split_idx;
+	pl.fp_parts  = CALLOC(FILE*, pl.n_parts);
+	pl.rid_shift = CALLOC(uint32_t, pl.n_parts);
+	pl.mi = mi = mm_split_merge_prep(opt->split_prefix, n_split_idx, pl.fp_parts, pl.rid_shift);
+	if (pl.mi == 0) {
+		free(pl.fp_parts);
+		free(pl.rid_shift);
+		return -1;
+	}
+	for (i = n_split_idx - 1; i > 0; --i)
+		pl.rid_shift[i] = pl.rid_shift[i - 1];
+	for (pl.rid_shift[0] = 0, i = 1; i < n_split_idx; ++i)
+		pl.rid_shift[i] += pl.rid_shift[i - 1];
+	if (opt->flag & MM_F_OUT_SAM)
+		for (i = 0; i < (int32_t)pl.mi->n_seq; ++i)
+			printf("@SQ\tSN:%s\tLN:%d\n", pl.mi->seq[i].name, pl.mi->seq[i].len);
+
+	kt_pipeline(2, worker_pipeline, &pl, 3);
+
+	free(pl.str.s);
+	mm_idx_destroy(mi);
+	free(pl.rid_shift);
+	for (i = 0; i < n_split_idx; ++i)
+		fclose(pl.fp_parts[i]);
+	free(pl.fp_parts);
+	for (i = 0; i < pl.n_fp; ++i)
+		mm_bseq_close(pl.fp[i]);
+	free(pl.fp);
+	mm_split_rm_tmp(opt->split_prefix, n_split_idx);
+	return 0;
+}

minimap.h

@@ -5,26 +5,49 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_F_NO_SELF     0x001
-#define MM_F_AVA         0x002
-#define MM_F_CIGAR       0x004
-#define MM_F_OUT_SAM     0x008
-#define MM_F_NO_QUAL     0x010
-#define MM_F_OUT_CG      0x020
-#define MM_F_OUT_CS      0x040
-#define MM_F_SPLICE      0x080 // splice mode
-#define MM_F_SPLICE_FOR  0x100 // match GT-AG
-#define MM_F_SPLICE_REV  0x200 // match CT-AC, the reverse complement of GT-AG
-#define MM_F_NO_LJOIN    0x400
-#define MM_F_OUT_CS_LONG 0x800
-#define MM_F_SR          0x1000
-#define MM_F_FRAG_MODE   0x2000
-#define MM_F_NO_PRINT_2ND  0x4000
-#define MM_F_2_IO_THREADS  0x8000
-#define MM_F_LONG_CIGAR    0x10000
-#define MM_F_INDEPEND_SEG  0x20000
-#define MM_F_SPLICE_FLANK  0x40000
-#define MM_F_SOFTCLIP      0x80000
+#define MM_VERSION "2.31-r1302"
+
+#define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
+#define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name
+#define MM_F_CIGAR         (0x004LL)
+#define MM_F_OUT_SAM       (0x008LL)
+#define MM_F_NO_QUAL       (0x010LL)
+#define MM_F_OUT_CG        (0x020LL)
+#define MM_F_OUT_CS        (0x040LL)
+#define MM_F_SPLICE        (0x080LL) // splice mode
+#define MM_F_SPLICE_FOR    (0x100LL) // match GT-AG
+#define MM_F_SPLICE_REV    (0x200LL) // match CT-AC, the reverse complement of GT-AG
+#define MM_F_NO_LJOIN      (0x400LL)
+#define MM_F_OUT_CS_LONG   (0x800LL)
+#define MM_F_SR            (0x1000LL)
+#define MM_F_FRAG_MODE     (0x2000LL)
+#define MM_F_NO_PRINT_2ND  (0x4000LL)
+#define MM_F_2_IO_THREADS  (0x8000LL)
+#define MM_F_LONG_CIGAR    (0x10000LL)
+#define MM_F_INDEPEND_SEG  (0x20000LL)
+#define MM_F_SPLICE_FLANK  (0x40000LL)
+#define MM_F_SOFTCLIP      (0x80000LL)
+#define MM_F_FOR_ONLY      (0x100000LL)
+#define MM_F_REV_ONLY      (0x200000LL)
+#define MM_F_HEAP_SORT     (0x400000LL)
+#define MM_F_ALL_CHAINS    (0x800000LL)
+#define MM_F_OUT_MD        (0x1000000LL)
+#define MM_F_COPY_COMMENT  (0x2000000LL)
+#define MM_F_EQX           (0x4000000LL) // use =/X instead of M
+#define MM_F_PAF_NO_HIT    (0x8000000LL) // output unmapped reads to PAF
+#define MM_F_NO_END_FLT    (0x10000000LL)
+#define MM_F_HARD_MLEVEL   (0x20000000LL)
+#define MM_F_SAM_HIT_ONLY  (0x40000000LL)
+#define MM_F_RMQ           (0x80000000LL)
+#define MM_F_QSTRAND       (0x100000000LL)
+#define MM_F_NO_INV        (0x200000000LL)
+#define MM_F_NO_HASH_NAME  (0x400000000LL)
+#define MM_F_SPLICE_OLD    (0x800000000LL)
+#define MM_F_SECONDARY_SEQ (0x1000000000LL)	//output SEQ field for seqondary alignments using hard clipping
+#define MM_F_OUT_DS        (0x2000000000LL)
+#define MM_F_WEAK_PAIRING  (0x4000000000LL)
+#define MM_F_SR_RNA        (0x8000000000LL)
+#define MM_F_OUT_JUNC      (0x10000000000LL)
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
@@ -34,6 +57,18 @@
 
 #define MM_MAX_SEG       255
 
+#define MM_CIGAR_MATCH      0
+#define MM_CIGAR_INS        1
+#define MM_CIGAR_DEL        2
+#define MM_CIGAR_N_SKIP     3
+#define MM_CIGAR_SOFTCLIP   4
+#define MM_CIGAR_HARDCLIP   5
+#define MM_CIGAR_PADDING    6
+#define MM_CIGAR_EQ_MATCH   7
+#define MM_CIGAR_X_MISMATCH 8
+
+#define MM_CIGAR_STR  "MIDNSHP=XB"
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -47,21 +82,28 @@ typedef struct {
 	char *name;      // name of the db sequence
 	uint64_t offset; // offset in mm_idx_t::S
 	uint32_t len;    // length
+	uint32_t is_alt;
 } mm_idx_seq_t;
 
 typedef struct {
 	int32_t b, w, k, flag;
 	uint32_t n_seq;            // number of reference sequences
+	int32_t index;
+	int32_t n_alt;
 	mm_idx_seq_t *seq;         // sequence name, length and offset
 	uint32_t *S;               // 4-bit packed sequence
 	struct mm_idx_bucket_s *B; // index (hidden)
-	void *km;
+	struct mm_idx_intv_s *I;   // intervals (hidden)
+	struct mm_idx_spsc_s *spsc;// splice score (hidden)
+	struct mm_idx_jjump_s *J;  // junctions to create jumps (hidden)
+	void *km, *h;
 } mm_idx_t;
 
 // minimap2 alignment
 typedef struct {
 	uint32_t capacity;                  // the capacity of cigar[]
 	int32_t dp_score, dp_max, dp_max2;  // DP score; score of the max-scoring segment; score of the best alternate mappings
+	int32_t dp_max0;                    // DP score before mm_update_dp_max() adjustment
 	uint32_t n_ambi:30, trans_strand:2; // number of ambiguous bases; transcript strand: 0 for unknown, 1 for +, 2 for -
 	uint32_t n_cigar;                   // number of cigar operations in cigar[]
 	uint32_t cigar[];
@@ -78,7 +120,7 @@ typedef struct {
 	int32_t mlen, blen;     // seeded exact match length; seeded alignment block length
 	int32_t n_sub;          // number of suboptimal mappings
 	int32_t score0;         // initial chaining score (before chain merging/spliting)
-	uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, dummy:16;
+	uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, split_inv:1, is_alt:1, strand_retained:1, is_spliced:1, dummy:4;
 	uint32_t hash;
 	float div;
 	mm_extra_t *p;
@@ -87,43 +129,66 @@ typedef struct {
 // indexing and mapping options
 typedef struct {
 	short k, w, flag, bucket_bits;
-	int mini_batch_size;
+	int64_t mini_batch_size;
 	uint64_t batch_size;
 } mm_idxopt_t;
 
 typedef struct {
+	int64_t flag;    // see MM_F_* macros
 	int seed;
 	int sdust_thres; // score threshold for SDUST; 0 to disable
-	int flag;        // see MM_F_* macros
 
-	int bw;          // bandwidth
+	int max_qlen;    // max query length
+
+	int bw, bw_long; // bandwidth
 	int max_gap, max_gap_ref; // break a chain if there are no minimizers in a max_gap window
 	int max_frag_len;
-	int max_chain_skip;
+	int max_chain_skip, max_chain_iter;
 	int min_cnt;         // min number of minimizers on each chain
 	int min_chain_score; // min chaining score
+	float chain_gap_scale;
+	float chain_skip_scale;
+	int rmq_size_cap, rmq_inner_dist;
+	int rmq_rescue_size;
+	float rmq_rescue_ratio;
 
 	float mask_level;
+	int mask_len;
 	float pri_ratio;
 	int best_n;      // top best_n chains are subjected to DP alignment
 
-	int max_join_long, max_join_short;
-	int min_join_flank_sc;
+	float alt_drop;
 
 	int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
+	int transition; // transition mismatch score (A:G, C:T)
+	int sc_ambi; // score when one or both bases are "N"
 	int noncan;      // cost of non-canonical splicing sites
-	int zdrop;       // break alignment if alignment score drops too fast along the diagonal
+	int junc_bonus;  // bonus for a splice site in annotation
+	int junc_pen;    // penalty for GT- or -AG not scored in --spsc
+	int zdrop, zdrop_inv;   // break alignment if alignment score drops too fast along the diagonal
 	int end_bonus;
 	int min_dp_max;  // drop an alignment if the score of the max scoring segment is below this threshold
 	int min_ksw_len;
 	int anchor_ext_len, anchor_ext_shift;
+	float max_clip_ratio; // drop an alignment if BOTH ends are clipped above this ratio
+
+	int rank_min_len;
+	float rank_frac;
 
 	int pe_ori, pe_bonus;
 
+	int32_t jump_min_match;
+
 	float mid_occ_frac;  // only used by mm_mapopt_update(); see below
+	float q_occ_frac;
+	int32_t min_mid_occ, max_mid_occ;
 	int32_t mid_occ;     // ignore seeds with occurrences above this threshold
-	int32_t max_occ;
-	int mini_batch_size; // size of a batch of query bases to process in parallel
+	int32_t max_occ, max_max_occ, occ_dist;
+	int64_t mini_batch_size; // size of a batch of query bases to process in parallel
+	int64_t max_sw_mat;
+	int64_t cap_kalloc;
+
+	const char *split_prefix;
 } mm_mapopt_t;
 
 // index reader
@@ -139,6 +204,11 @@ typedef struct {
 } mm_idx_reader_t;
 
 // memory buffer for thread-local storage during mapping
+struct mm_tbuf_s {
+	void *km;
+	int rep_len, frag_gap;
+};
+
 typedef struct mm_tbuf_s mm_tbuf_t;
 
 // global variables
@@ -208,6 +278,36 @@ void mm_idx_reader_close(mm_idx_reader_t *r);
 
 int mm_idx_reader_eof(const mm_idx_reader_t *r);
 
+/**
+ * Check whether the file contains a minimap2 index
+ *
+ * @param fn         file name
+ *
+ * @return the file size if fn is an index file; 0 if fn is not.
+ */
+int64_t mm_idx_is_idx(const char *fn);
+
+/**
+ * Load a part of an index
+ *
+ * Given a uni-part index, this function loads the entire index into memory.
+ * Given a multi-part index, it loads one part only and places the file pointer
+ * at the end of that part.
+ *
+ * @param fp         pointer to FILE object
+ *
+ * @return minimap2 index read from fp
+ */
+mm_idx_t *mm_idx_load(FILE *fp);
+
+/**
+ * Append an index (or one part of a full index) to file
+ *
+ * @param fp         pointer to FILE object
+ * @param mi         minimap2 index
+ */
+void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
+
 /**
  * Create an index from strings in memory
  *
@@ -256,6 +356,8 @@ mm_tbuf_t *mm_tbuf_init(void);
  */
 void mm_tbuf_destroy(mm_tbuf_t *b);
 
+void *mm_tbuf_get_km(mm_tbuf_t *b);
+
 /**
  * Align a query sequence against an index
  *
@@ -276,6 +378,8 @@ void mm_tbuf_destroy(mm_tbuf_t *b);
  */
 mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
 
+void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname);
+
 /**
  * Align a fasta/fastq file and print alignments to stdout
  *
@@ -290,6 +394,37 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
 
 int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads);
 
+/**
+ * Generate the cs tag (new in 2.12)
+ *
+ * @param km         memory blocks; set to NULL if unsure
+ * @param buf        buffer to write the cs/MD tag; typicall NULL on the first call
+ * @param max_len    max length of the buffer; typically set to 0 on the first call
+ * @param mi         index
+ * @param r          alignment
+ * @param seq        query sequence
+ * @param no_iden    true to use : instead of =
+ *
+ * @return the length of cs
+ */
+int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden);
+int mm_gen_ds(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden);
+int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq);
+
+// query sequence name and sequence in the minimap2 index
+int mm_idx_index_name(mm_idx_t *mi);
+int mm_idx_name2id(const mm_idx_t *mi, const char *name);
+int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
+
+int mm_idx_alt_read(mm_idx_t *mi, const char *fn);
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
+int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);
+
+int mm_max_spsc_bonus(const mm_mapopt_t *mo);
+int32_t mm_idx_spsc_read(mm_idx_t *idx, const char *fn, int32_t max_sc);
+int32_t mm_idx_spsc_read2(mm_idx_t *idx, const char *fn, int32_t max_sc, float scale);
+int64_t mm_idx_spsc_get(const mm_idx_t *db, int32_t cid, int64_t st0, int64_t en0, int32_t rev, uint8_t *sc);
+
 // deprecated APIs for backward compatibility
 void mm_mapopt_init(mm_mapopt_t *opt);
 mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads);

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "9 January 2018" "minimap2-2.7 (r654)" "Bioinformatics tools"
+.TH minimap2 1 "19 May 2026" "minimap2-2.31 (r1302)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -77,7 +77,7 @@ SAM format.
 Minimizer k-mer length [15]
 .TP
 .BI -w \ INT
-Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
+Minimizer window size [10]. A minimizer is the smallest k-mer
 in a window of w consecutive k-mers.
 .TP
 .B -H
@@ -88,16 +88,17 @@ on the HPC sequence.
 .BI -I \ NUM
 Load at most
 .I NUM
-target bases into RAM for indexing [4G]. If there are more than
+target bases into RAM for indexing [8G]. If there are more than
 .I NUM
 bases in
 .IR target.fa ,
 minimap2 needs to read
 .I query.fa
-multiple times to map it against each batch of target sequences.
+multiple times to map it against each batch of target sequences. This would create a multi-part index.
 .I NUM
 may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
-multi-part index.
+multi-part index. See also option
+.BR --split-prefix .
 .TP
 .B --idx-no-seq
 Don't store target sequences in the index. It saves disk space and memory but
@@ -121,21 +122,62 @@ provided as the target sequences, options
 .BR -w ,
 .B -I
 will be effectively overridden by the options stored in the index file.
+.TP
+.BI --alt \ FILE
+List of ALT contigs [null]
+.TP
+.BI --alt-drop \ FLOAT
+Drop ALT hits by
+.I FLOAT
+fraction when ranking and computing mapping quality [0.15]
 .SS Mapping options
 .TP 10
-.BI -f \ FLOAT
-Ignore top
+.BI -f \ FLOAT | INT1 [, INT2 ]
+If fraction, ignore top
 .I FLOAT
-fraction of most frequent minimizers [0.0002]
+fraction of most frequent minimizers [0.0002]. If integer,
+ignore minimizers occuring more than
+.I INT1
+times.
+.I INT2
+is only effective in the
+.B --sr
+or
+.B -xsr
+mode, which sets the threshold for a second round of seeding.
 .TP
-.BI -g \ INT
-Stop chain enlongation if there are no minimizers in
-.IR INT -bp
-[10000].
+.BI -U \ INT1 [, INT2 ]
+Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
+.RI max{ INT1 ,\ min{ INT2 ,
+.BR -f }}.
+This option prevents excessively small or large
+.B -f
+estimated from the input reference. Available since r1034 and deprecating
+.B --min-occ-floor
+in earlier versions of minimap2.
 .TP
-.BI -r \ INT
-Bandwidth used in chaining and DP-based alignment [500]. This option
-approximately controls the maximum gap size.
+.BI --q-occ-frac \ FLOAT
+Discard a query minimizer if its occurrence is higher than
+.I FLOAT
+fraction of query minimizers and than the reference occurrence threshold
+[0.01]. Set 0 to disable. Available since r1105.
+.TP
+.BI -e \ INT
+Sample a high-frequency minimizer every
+.I INT
+basepairs [500].
+.TP
+.BI -g \ NUM
+Stop chain enlongation if there are no minimizers within
+.IR NUM -bp
+[10k].
+.TP
+.BI -r \ NUM1 [, NUM2 ]
+Bandwidth for chaining and base alignment [500,20k].
+.I NUM1
+is used for initial chaining and alignment extension;
+.I NUM2
+for RMQ-based re-chaining and closing gaps in alignments.
 .TP
 .BI -n \ INT
 Discard chains consisting of
@@ -148,20 +190,42 @@ Discard chains with chaining score
 [40]. Chaining score equals the approximate number of matching bases minus a
 concave gap penalty. It is computed with dynamic programming.
 .TP
+.B -D
+If query sequence name/length are identical to the target name/length, ignore
+diagonal anchors. This option also reduces DP-based extension along the
+diagonal.
+.TP
+.B -P
+Retain all chains and don't attempt to set primary chains. Options
+.B -p
+and
+.B -N
+have no effect when this option is in use.
+.TP
+.BR --dual = yes | no
+If
+.BR no ,
+skip query-target pairs wherein the query name is lexicographically greater
+than the target name [yes]
+.TP
 .B -X
-Perform all-vs-all mapping. In this mode, if the query sequence name is
-lexicographically larger than the target sequence name, the hits between them
-will be suppressed; if the query sequence name is the same as the target name,
-diagonal minimizer hits will also be suppressed.
+Equivalent to
+.RB ' -DP
+.BR --dual = no
+.BR --no-long-join '.
+Primarily used for all-vs-all read overlapping.
 .TP
 .BI -p \ FLOAT
 Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
 Between two chains overlaping over half of the shorter chain (controlled by
-.BR --mask-level ),
+.BR -M ),
 the chain with a lower score is secondary to the chain with a higher score.
 If the ratio of the scores is below
 .IR FLOAT ,
 the secondary chain will not be outputted or extended with DP alignment later.
+This option has no effect when
+.B -X
+is applied.
 .TP
 .BI -N \ INT
 Output at most
@@ -179,17 +243,52 @@ Increasing this option slows down spliced alignment. [200k]
 .TP
 .BI -F \ NUM
 Maximum fragment length (aka insert size; effective with
-.BR -xsr / --frag)
+.BR -xsr / --frag = yes )
 [800]
 .TP
+.BI -M \ FLOAT
+Mark as secondary a chain that overlaps with a better chain by
+.I FLOAT
+or more of the shorter chain [0.5]
+.TP
+.BR --rmq = no | yes
+Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
+for aligning contigs through long INDELs.
+.TP
+.BI --rmq-inner \ NUM
+Apply full dynamic programming for anchors within distance
+.I NUM
+[1000].
+.TP
+.B --hard-mask-level
+Honor option
+.B -M
+and disable a heurstic to save unmapped subsequences and disables
+.BR --mask-len .
+.TP
+.BI --mask-len \ NUM
+Keep an alignment if dropping it leaves an unaligned region on query longer than
+.IR INT
+[inf]. Effective without
+.BR --hard-mask-level .
+.TP
 .BI --max-chain-skip \ INT
-A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
+A heuristics that stops chaining early [25]. Minimap2 uses dynamic programming
 for chaining. The time complexity is quadratic in the number of seeds. This
 option makes minimap2 exits the inner loop if it repeatedly sees seeds already
 on chains. Set
 .I INT
 to a large number to switch off this heurstics.
 .TP
+.BI --max-chain-iter \ INT
+Check up to
+.I INT
+partial chains during chaining [5000]. This is a heuristic to avoid quadratic
+time complexity in the worst case.
+.TP
+.BI --chain-gap-scale \ FLOAT
+Scale of gap cost during chaining [1.0]
+.TP
 .B --no-long-join
 Disable the long gap patching heuristic. When this option is applied, the
 maximum alignment gap is mostly controlled by
@@ -198,14 +297,34 @@ maximum alignment gap is mostly controlled by
 .B --splice
 Enable the splice alignment mode.
 .TP
-.B --sr
-Enable short-read alignment heuristics. In the short-read mode, minimap2
-applies a second round of chaining with a higher minimizer occurrence threshold
-if no good chain is found. In addition, minimap2 attempts to patch gaps between
-seeds with ungapped alignment.
+.BR --sr [= no | dna | rna ]
+Enable short-read alignment heuristics [no]. If this option is used with no argument,
+.RB ` dna '
+is set. In the DNA short-read mode, minimap2 applies a second round of chaining
+with a higher minimizer occurrence threshold if no good chain is found. In
+addition, minimap2 attempts to patch gaps between seeds with ungapped
+alignment.
 .TP
-.BR --frag [= no | yes ]
+.BI --split-prefix \ STR
+Prefix to create temporary files. Typically used for a multi-part index.
+.TP
+.BR --frag = no | yes
 Whether to enable the fragment mode [no]
+.TP
+.B --for-only
+Only map to the forward strand of the reference sequences. For paired-end
+reads in the forward-reverse orientation, the first read is mapped to forward
+strand of the reference and the second read to the reverse stand.
+.TP
+.B --rev-only
+Only map to the reverse complement strand of the reference sequences.
+.TP
+.BR --heap-sort = no | yes
+If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
+faster for short reads, but slower for long reads. [no]
+.TP
+.B --no-hash-name
+Produce the same alignment for identical sequences regardless of their sequence names.
 .SS Alignment options
 .TP 10
 .BI -A \ INT
@@ -214,6 +333,10 @@ Matching score [2]
 .BI -B \ INT
 Mismatching penalty [4]
 .TP
+.BI -b \ INT
+Mismatching penalty for transitions [same as
+.BR -B ].
+.TP
 .BI -O \ INT1[,INT2]
 Gap open penalty [4,24]. If
 .I INT2
@@ -227,16 +350,45 @@ costs
 .RI min{ O1 + k * E1 , O2 + k * E2 }.
 In the splice mode, the second gap penalties are not used.
 .TP
+.BI -J \ INT
+Splice model [1]. 0 for the original minimap2 splice model that always penalizes non-GT-AG splicing;
+1 for the miniprot model that considers non-GT-AG. Option
+.B -C
+has no effect with the default
+.BR -J1 .
+.TP
+.BR -j \ FILE
+Junctions used to extend alignment towards ends of reads [].
+.I FILE
+can be gene annotations in the BED12 format (aka 12-column BED), or intron
+positions in 5-column BED with the strand column required. BED12 file can be
+converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'. This option is
+intended for short RNA-seq reads, while
+.B --junc-bed
+for long noisy RNA-seq reads.
+.TP
 .BI -C \ INT
 Cost for a non-canonical GT-AG splicing (effective with
-.BR --splice )
-[0]
+.B --splice
+.BR -J0 )
+[0].
 .TP
-.BI -z \ INT
-Break an alignment if the running score drops too quickly along the diagonal of
-the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves
-the contiguity of the alignment at the cost of poor alignment in the middle
-(e.g. caused by a long inversion).
+.BI -z \ INT1[,INT2]
+Truncate an alignment if the running alignment score drops too quickly along
+the diagonal of the DP matrix (diagonal X-drop, or Z-drop) [400,200]. If the
+drop of score is above
+.IR INT2 ,
+minimap2 will reverse complement the query in the related region and align
+again to test small inversions. Minimap2 truncates alignment if there is an
+inversion or the drop of score is greater than
+.IR INT1 .
+Decrease
+.I INT2
+to find small inversions at the cost of performance and false positives.
+Increase
+.I INT1
+to improves the contiguity of alignment at the cost of poor alignment in the
+middle.
 .TP
 .BI -s \ INT
 Minimal peak DP alignment score to output [40]. The peak score is computed from
@@ -255,14 +407,25 @@ no attempt to match GT-AG [n]
 .BI --end-bonus \ INT
 Score bonus when alignment extends to the end of the query sequence [0].
 .TP
-.BR --splice-flank [= yes | no ]
+.BI --score-N \ INT
+Penalty of a mismatch involving ambiguous bases [1].
+.TP
+.BR --pairing = strong | weak | no
+How to pair paired-end reads [strong].
+.RB ` no '
+for aligning the two ends in a pair independently with no `properly paired' set.
+.RB ` weak '
+for aligning the two ends independently and then pairing the hits.
+.RB ` strong '
+for jointly aligning and pairing the two ends.
+.TP
+.BR --splice-flank = yes | no
 Assume the next base to a
 .B GT
 donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
 base to a
 .B AG
-acceptor tends to be C/T [yes with
-.BR --splice ].
+acceptor tends to be C/T [no].
 This trend is evolutionarily conservative, all the way to S. cerevisiae
 (PMID:18688272). Specifying this option generally leads to higher junction
 accuracy by several percents, so it is applied by default with
@@ -273,6 +436,50 @@ on SIRV data, please add
 .B --splice-flank=no
 to the command line.
 .TP
+.BR --spsc \ FILE
+Splice scores []. Each line consists of five fields: 1) contig, 2) offset, 3) `+' or `-', 4) `D' or `A', and 5) score,
+where offset is the number of bases before a splice junction, `D' indicates the
+line corresponds to a donor site and `A' for an acceptor site.
+A positive score suggests the junction is preferred and a negative score
+suggests the junction is not preferred.
+.TP
+.BR --spsc0 \ INT
+Penalty for positions not in
+.I FILE
+specified by
+.B --spsc
+[5]. Effective with
+.B --spsc
+but not
+.BR --junc-bed .
+.TP
+.BR --spsc-scale \ FLOAT
+Scale splice scores in
+.B --spsc
+by
+.IR FLOAT
+rounded to the nearest integer [0.7].
+.TP
+.BR --junc-bed \ FILE
+Junctions to prefer during base alignment [].
+Same format as
+.BR -j .
+It is
+.I NOT
+recommended to apply this option to short RNA-seq reads. This would increase
+run time with little improvement to junction accuracy.
+.TP
+.BR --junc-bonus \ INT
+Score bonus for a splice donor or acceptor found in annotation [9]. Effective with
+.B --junc-bed
+but not
+.BR --spsc .
+.TP
+.BR --jump-min-match \ INT
+Minimum matching length to create a jump [3]. Equivalent to
+.B STAR
+.BR --alignSJDBoverhangMin .
+.TP
 .BI --end-seed-pen \ INT
 Drop a terminal anchor if
 .IR s <log( g )+ INT ,
@@ -284,12 +491,31 @@ the length of the terminal gap in the chain. This option is only effective
 with
 .BR --splice .
 It helps to avoid tiny terminal exons. [6]
+.TP
+.B --no-end-flt
+Don't filter seeds towards the ends of chains before performing base-level
+alignment.
+.TP
+.BI --cap-sw-mem \ NUM
+Skip alignment if the DP matrix size is above
+.IR NUM .
+Set 0 to disable [100m].
+.TP
+.BI --cap-kalloc \ NUM
+Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
+.IR NUM .
+Set 0 to disable [500m].
 .SS Input/output options
 .TP 10
 .B -a
 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
 by default.
 .TP
+.BI -o \ FILE
+Output alignments to
+.I FILE
+[stdout].
+.TP
 .B -Q
 Ignore base quality in the input file.
 .TP
@@ -304,27 +530,52 @@ SAM read group line in a format like
 .B @RG\\\\tID:foo\\\\tSM:bar
 [].
 .TP
+.B -y
+Copy input FASTA/Q comments to output.
+.TP
 .B -c
 Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
 .TP
-.BI --cs[= STR ]
+.BR --cs [= short | long ]
 Output the
 .B cs
 tag.
-.I STR
-can be either
-.I short
-or
-.IR long .
-If no
-.I STR
-is given,
-.I short
-is assumed. [none]
+If no argument is given,
+.RB ` short '
+is set. [none]
+.TP
+.B --MD
+Output the MD tag (see the SAM spec).
+.TP
+.B --eqx
+Output =/X CIGAR operators for sequence match/mismatch.
 .TP
 .B -Y
 In SAM output, use soft clipping for supplementary alignments.
 .TP
+.B --secondary-seq
+In SAM output, show query sequences for secondary alignments.
+.TP
+.B --write-junc
+Output splice junctions in 6-column BED: contig name, start, end,
+read name, score and strand. Score is the sum of donor and acceptor scores,
+where GT gets 3, GC gets 2 and AT gets 1 at donor sites,
+while AG gets 3 and AC gets 1 at acceptor sites.
+Alignments with mapping quality below 10 are ignored.
+.TP
+.BI --pass1 \ FILE
+Junctions BED file outputted by
+.B --write-junc
+[]. Rows with scores lower than 5 are ignored. When both
+.B -j
+and
+.B --pass1
+are present, junctions in
+.B -j
+are preferred over in
+.BR --pass1
+when there is ambiguity.
+.TP
 .BI --seed \ INT
 Integer seed for randomizing equally best hits. Minimap2 hashes
 .I INT
@@ -352,9 +603,21 @@ K/M/G/k/m/g suffix is accepted. A large
 helps load balancing in the multi-threading mode, at the cost of increased
 memory.
 .TP
-.BR --secondary [= yes | no ]
+.BR --secondary = yes | no
 Whether to output secondary alignments [yes]
 .TP
+.BI --max-qlen \ NUM
+Filter out query sequences longer than
+.IR NUM .
+.TP
+.B --paf-no-hit
+In PAF, output unmapped queries; the strand and the reference name fields are
+set to `*'. Warning: some paftools.js commands may not work with such output
+for the moment.
+.TP
+.B --sam-hit-only
+In SAM, don't output unmapped reads.
+.TP
 .B --version
 Print version number to stdout
 .SS Preset options
@@ -368,53 +631,75 @@ Available
 .I STR
 are:
 .RS
-.TP 8
-.B map-pb
-PacBio/Oxford Nanopore read to reference mapping
-.RB ( -Hk19 )
-.TP
+.TP 10
 .B map-ont
-Slightly more sensitive for Oxford Nanopore to reference mapping
-.RB ( -k15 ).
-For PacBio reads, HPC minimizers consistently leads to faster performance and
-more sensitive results in comparison to normal minimizers. For Oxford Nanopore
-data, normal minimizers are better, though not much. The effectiveness of HPC
-is determined by the sequencing error mode.
+Align noisy long reads of ~10% error rate to a reference genome. This is the
+default mode.
+.TP
+.B lr:hq
+Align accurate long reads (error rate <1%) to a reference genome
+.RB ( -k19
+.B -w19 -U50,500
+.BR -g10k ).
+This was recommended by ONT developers for recent Nanopore reads
+produced with chemistry v14 that can reach ~99% in accuracy.
+It was shown to work better for accurate Nanopore reads
+than
+.BR map-hifi .
+.TP
+.B map-hifi
+Align PacBio high-fidelity (HiFi) reads to a reference genome
+.RB ( -xlr:hq
+.B -A1 -B4 -O6,26 -E2,1
+.BR -s200 ).
+It differs from
+.B lr:hq
+only in scoring. It has not been tested whether
+.B lr:hq
+would work better for PacBio HiFi reads.
+.TP
+.B map-pb
+Align older PacBio continuous long (CLR) reads to a reference genome
+.RB ( -Hk19 ).
+Note that this data type is effectively deprecated by HiFi.
+Unless you work on very old data, you probably want to use
+.B map-hifi
+or
+.BR lr:hq .
+.TP
+.B map-iclr
+Align Illumina Complete Long Reads (ICLR) to a reference genome
+.RB ( -k19
+.B -B6 -b4
+.BR -O10,50 ).
+This was recommended by Illumina developers.
 .TP
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -A1 -B19 -O39,81 -E3,1 -s200
-.BR -z200 ).
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
+.BR -N50 ).
 Typically, the alignment will not extend to regions with 5% or higher sequence
-divergence. Only use this preset if the average divergence is far below 5%.
+divergence. Use this preset if the average divergence is not much higher than 0.1%.
 .TP
 .B asm10
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -A1 -B9 -O16,41 -E2,1 -s200
-.BR -z200 ).
-Up to 10% sequence divergence.
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
+.BR -N50 ).
+Use this if the average divergence is around 1%.
 .TP
-.B ava-pb
-PacBio all-vs-all overlap mapping
-.RB ( -Hk19
-.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
-.BR 25 ).
-.TP
-.B ava-ont
-Oxford Nanopore all-vs-all overlap mapping
-.RB ( -k15
-.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
-.BR 25 ).
-Similarly, the major difference from
-.B ava-pb
-is that this preset is not using HPC minimizers.
+.B asm20
+Long assembly to reference mapping
+.RB ( -k19
+.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
+.BR -N50 ).
+Use this if the average divergence is around several percent.
 .TP
 .B splice
 Long-read spliced alignment
 .RB ( -k15
-.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub
+.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
 .BR --splice-flank=yes ).
 In the splice mode, 1) long deletions are taken as introns and represented as
 the
@@ -424,12 +709,36 @@ costs are different during chaining; 4) the computation of the
 .RB ` ms '
 tag ignores introns to demote hits to pseudogenes.
 .TP
-.B sr
-Short single-end reads without splicing
-.RB ( -k21
-.B -w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
-.B -s40 -g200 -2K50m
+.B splice:hq
+Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
+.RB ( -xsplice
+.B -C5 -O6,24
+.BR -B4 ).
+.TP
+.B splice:sr
+Spliced alignment for short RNA-seq reads
+.RB ( -xsplice:hq
+.B --frag=yes -m25 -s40 -2K100m --heap-sort=yes --pairing=weak --sr=rna --min-dp-len=20
 .BR --secondary=no ).
+.TP
+.B sr
+Short-read alignment without splicing
+.RB ( -k21
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m25
+.B -s40 -g100 -2K50m --heap-sort=yes
+.BR --secondary=no ).
+.TP
+.B ava-pb
+PacBio CLR all-vs-all overlap mapping
+.RB ( -Hk19
+.B -Xw5 -e0
+.BR -m100 ).
+.TP
+.B ava-ont
+Oxford Nanopore all-vs-all overlap mapping
+.RB ( -k15
+.B -Xw5 -e0 -m100
+.BR -r2k ).
 .RE
 .SS Miscellaneous options
 .TP 10
@@ -486,12 +795,18 @@ cm	i	Number of minimizers on the chain
 s1	i	Chaining score
 s2	i	Chaining score of the best secondary chain
 NM	i	Total number of mismatches and gaps in the alignment
+MD	Z	To generate the ref sequence in the alignment
 AS	i	DP alignment score
+SA	Z	List of other supplementary alignments (with approximate CIGAR strings)
 ms	i	DP score of the max scoring segment in the alignment
 nn	i	Number of ambiguous bases in the alignment
 ts	A	Transcript strand (splice mode only)
 cg	Z	CIGAR string (only in PAF)
 cs	Z	Difference string
+dv	f	Approximate per-base sequence divergence
+de	f	Gap-compressed per-base sequence divergence
+rl	i	Length of query regions harboring repetitive seeds
+zd	i	Alignment broken due to Z-drop; bit 1: left broken; bit 2: right broken
 .TE
 
 .PP
@@ -522,8 +837,8 @@ where seed positions may be suboptimal. This should not be a big concern
 because even the optimal alignment may be wrong in such regions.
 .TP
 *
-Minimap2 requires SSE2 instructions to compile. It is possible to add
-non-SSE2 support, but it would make minimap2 slower by several times.
+Minimap2 requires SSE2 or NEON instructions to compile. It is possible to add
+non-SSE2/NEON support, but it would make minimap2 slower by several times.
 .SH SEE ALSO
 .PP
 miniasm(1), minimap(1), bwa(1).

misc.c

@@ -1,4 +1,5 @@
-#include "minimap.h"
+#include <stdlib.h>
+#include "mmpriv.h"
 
 int mm_verbose = 1;
 int mm_dbg_flag = 0;
@@ -86,6 +87,8 @@ double cputime()
 
 	return kernelModeTime + userModeTime;
 }
+
+long peakrss(void) { return 0; }
 #else
 #include <sys/resource.h>
 #include <sys/time.h>
@@ -96,16 +99,57 @@ double cputime(void)
 	getrusage(RUSAGE_SELF, &r);
 	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
 }
+
+long peakrss(void)
+{
+	struct rusage r;
+	getrusage(RUSAGE_SELF, &r);
+#ifdef __linux__
+	return r.ru_maxrss * 1024;
+#else
+	return r.ru_maxrss;
+#endif
+}
+
 #endif /* WIN32 || _WIN32 */
 
 double realtime(void)
 {
 	struct timeval tp;
-	struct timezone tzp;
-	gettimeofday(&tp, &tzp);
+	gettimeofday(&tp, NULL);
 	return tp.tv_sec + tp.tv_usec * 1e-6;
 }
 
+void mm_err_puts(const char *str)
+{
+	int ret;
+	ret = puts(str);
+	if (ret == EOF) {
+		perror("[ERROR] failed to write the results");
+		exit(EXIT_FAILURE);
+	}
+}
+
+void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp)
+{
+	int ret;
+	ret = fwrite(p, size, nitems, fp);
+	if (ret == EOF) {
+		perror("[ERROR] failed to write data");
+		exit(EXIT_FAILURE);
+	}
+}
+
+void mm_err_fread(void *p, size_t size, size_t nitems, FILE *fp)
+{
+	int ret;
+	ret = fread(p, size, nitems, fp);
+	if (ret == EOF) {
+		perror("[ERROR] failed to read data");
+		exit(EXIT_FAILURE);
+	}
+}
+
 #include "ksort.h"
 
 #define sort_key_128x(a) ((a).x)
@@ -115,3 +159,4 @@ KRADIX_SORT_INIT(128x, mm128_t, sort_key_128x, 8)
 KRADIX_SORT_INIT(64, uint64_t, sort_key_64, 8)
 
 KSORT_INIT_GENERIC(uint32_t)
+KSORT_INIT_GENERIC(uint64_t)

misc/README.md

@@ -1,28 +1,180 @@
-The [K8 Javascript shell][k8] is needed to run Javascripts in this directory.
-Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
-page][k8bin].
+## <a name="started"></a>Getting Started
 
-* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for
-  eyeballing. PAF has to be generated with minimap2 option `-S`, which writes
-  the aligned sequences to the `cs` tag. An example:
-  ```sh
-  ../minimap2 -S ../test/MT-*.fa | k8 paf2aln.js /dev/stdin
-  ```
+```sh
+# install minimap2
+git clone https://github.com/lh3/minimap2
+cd minimap2 && make
+# install the k8 javascript shell
+curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
+cp k8-0.2.4/k8-`uname -s` k8              # or copy it to a directory on your $PATH
+# export PATH="$PATH:`pwd`:`pwd`/misc"    # run this if k8, minimap2 or paftools.js not on your $PATH
+minimap2 --cs test/MT-human.fa test/MT-orang.fa | paftools.js view -     # view alignment
+minimap2 -c test/MT-human.fa test/MT-orang.fa | paftools.js stat -       # basic alignment statistics
+minimap2 -c --cs test/MT-human.fa test/MT-orang.fa \
+  | sort -k6,6 -k8,8n | paftools.js call -L15000 -     # calling variants from asm-to-ref alignment
+minimap2 -c test/MT-human.fa test/MT-orang.fa \
+  | paftools.js liftover -l10000 - <(echo -e "MT_orang\t2000\t5000")     # liftOver
+# no test data for the following examples
+paftools.js junceval -e anno.gtf splice.sam > out.txt  # compare splice junctions to annotations
+paftools.js splice2bed splice.sam > splice.bed             # convert PAF/SAM to BED12
+paftools.js gff2bed anno.gtf > anno.bed             # convert GTF/GFF3 to BED12
+```
 
-* [mapstat.js](mapstat.js): output basic statistics such as the number of
-  non-redundant mapped bases, number of split and secondary alignments and
-  number of long gaps. This scripts seamlessly works with both SAM and PAF.
+## Table of Contents
 
-* [sim-pbsim.js](sim-pbsim.js): convert reads simulated with [PBSIM][pbsim] to
-  FASTA and encode the true mapping positions to read names in a format like
-  `S1_33!chr1!225258409!225267761!-`.
+- [Getting Started](#started)
+- [Introduction](#intro)
+- [Evaluation](#eval)
+  - [Evaluating mapping accuracy with simulated reads](#mapeval)
+  - [Evaluating read overlap sensitivity](#oveval)
+- [Calling Variants from Assemblies](#asmvar)
 
-* [sim-eval.js](sim-eval.js): evaluate mapping accuracy for FASTA generated
-  with [sim-pbsim.js](sim-pbsim.js) or [sim-mason2.js](sim-mason2.js).
+## <a name="intro"></a>Introduction
 
-* [sam2paf.js](sam2paf.js): convert SAM to PAF.
+paftools.js is a script that processes alignments in the [PAF format][paf],
+such as converting between formats, evaluating mapping accuracy, lifting over
+BED files based on alignment, and calling variants from assembly-to-assembly
+alignment. This script *requires* the [k8 Javascript shell][k8] to run. On
+Linux or Mac, you can download the precompiled k8 binary with:
 
+```sh
+curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
+cp k8-0.2.4/k8-`uname -s` $HOME/bin/k8  # assuming $HOME/bin in your $PATH
+```
+
+It is highly recommended to copy the executable `k8` to a directory on your
+`$PATH` such as `/usr/bin/env` can find it. Like python scripts, once you
+install `k8`, you can launch paftools.js in one of the two ways:
+
+```sh
+path/to/paftools.js             # only if k8 is on your $PATH
+k8 path/to/paftools.js
+```
+
+In a nutshell, paftools.js has the following commands:
+
+```
+Usage: paftools.js <command> [arguments]
+Commands:
+  view       convert PAF to BLAST-like (for eyeballing) or MAF
+  splice2bed convert spliced alignment in PAF/SAM to BED12
+  sam2paf    convert SAM to PAF
+  delta2paf  convert MUMmer's delta to PAF
+  gff2bed    convert GTF/GFF3 to BED12
+
+  stat       collect basic mapping information in PAF/SAM
+  liftover   simplistic liftOver
+  call       call variants from asm-to-ref alignment with the cs tag
+  bedcov     compute the number of bases covered
+
+  mapeval    evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ
+  mason2fq   convert mason2-simulated SAM to FASTQ
+  pbsim2fq   convert PBSIM-simulated MAF to FASTQ
+  junceval   evaluate splice junction consistency with known annotations
+  ov-eval    evaluate read overlap sensitivity using read-to-ref mapping
+```
+
+paftools.js seamlessly reads both plain text files and gzip'd text files.
+
+## <a name="eval"></a>Evaluation
+
+### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads
+
+The **pbsim2fq** command of paftools.js converts the MAF output of [pbsim][pbsim]
+to FASTQ and encodes the true mapping position in the read name in a format like
+`S1_33!chr1!225258409!225267761!-`. Similarly, the **mason2fq** command
+converts [mason2][mason2] simulated SAM to FASTQ.
+
+Command **mapeval** evaluates mapped SAM/PAF. Here is example output:
+
+```
+Q       60      32478   0       0.000000000     32478
+Q       22      16      1       0.000030775     32494
+Q       21      43      1       0.000061468     32537
+Q       19      73      1       0.000091996     32610
+Q       14      66      1       0.000122414     32676
+Q       10      27      3       0.000214048     32703
+Q       8       14      1       0.000244521     32717
+Q       7       13      2       0.000305530     32730
+Q       6       46      1       0.000335611     32776
+Q       3       10      1       0.000366010     32786
+Q       2       20      2       0.000426751     32806
+Q       1       248     94      0.003267381     33054
+Q       0       31      17      0.003778147     33085
+U       3
+```
+
+where each Q-line gives the quality threshold, the number of reads mapped with
+mapping quality equal to or greater than the threshold, number of wrong
+mappings, accumulative mapping error rate and the accumulative number of
+mapped reads. The U-line, if present, gives the number of unmapped reads if
+they are present in the SAM file.
+
+Suppose the reported mapping coordinate overlap with the true coordinate like
+the following:
+
+```
+truth:   --------------------
+mapper:           ----------------------
+         |<- l1 ->|<-- o -->|<-- l2 -->|
+```
+
+Let `r=o/(l1+o+l2)`. The reported mapping is considered correct if `r>0.1` by
+default.
+
+### <a name="oveval"></a>Evaluating read overlap sensitivity
+
+Command **ov-eval** takes *sorted* read-to-reference alignment and read
+overlaps in PAF as input, and evaluates the sensitivity. For example:
+
+```sh
+minimap2 -cx map-pb ref.fa reads.fq.gz | sort -k6,6 -k8,8n > reads-to-ref.paf
+minimap2 -x ava-pb reads.fq.gz reads.fq.gz > ovlp.paf
+k8 ov-eval.js reads-to-ref.paf ovlp.paf
+```
+
+## <a name="asmvar"></a>Calling Variants from Haploid Assemblies
+
+The **call** command of paftools.js calls variants from coordinate-sorted
+assembly-to-reference alignment. It calls variants from the [cs tag][cs] and
+identifies confident/callable regions as those covered by exactly one contig.
+Here are example command lines:
+
+```sh
+minimap2 -cx asm5 -t8 --cs ref.fa asm.fa > asm.paf  # keeping this file is recommended; --cs required!
+sort -k6,6 -k8,8n asm.paf > asm.srt.paf             # sort by reference start coordinate
+k8 paftools.js call asm.srt.paf > asm.var.txt
+```
+
+Here is sample output:
+
+```
+V   chr1    2276040 2276041 1   60  c   g   LJII01000171.1  1217409 1217410 +
+V   chr1    2280409 2280410 1   60  a   g   LJII01000171.1  1221778 1221779 +
+V   chr1    2280504 2280505 1   60  a   g   LJII01000171.1  1221873 1221874 +
+R   chr1    2325140 2436340
+V   chr1    2325287 2325287 1   60  -   ct  LJII01000171.1  1272894 1272896 +
+V   chr1    2325642 2325644 1   60  tt  -   LJII01000171.1  1273251 1273251 +
+V   chr1    2326051 2326052 1   60  c   t   LJII01000171.1  1273658 1273659 +
+V   chr1    2326287 2326288 1   60  c   t   LJII01000171.1  1273894 1273895 +
+```
+
+where a line starting with `R` gives regions covered by one query contig, and a
+V-line encodes a variant in the following format: chr, start, end, query depth,
+mapping quality, REF allele, ALT allele, query name, query start, end and the
+query orientation. Generally, you should only look at variants where column 5
+is one.
+
+By default, when calling variants, "paftools.js call" ignores alignments 50kb
+or shorter; when deriving callable regions, it ignores alignments 10kb or
+shorter.  It uses two thresholds to avoid edge effects. These defaults are
+designed for long-read assemblies. For short reads, both should be reduced.
+
+
+
+[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
+[cs]: https://github.com/lh3/minimap2#cs
 [k8]: https://github.com/attractivechaos/k8
-[k8bin]: https://github.com/attractivechaos/k8/releases
 [maf]: https://genome.ucsc.edu/FAQ/FAQformat#format5
 [pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
+[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2

misc/cnt-feat.js

@@ -1,258 +0,0 @@
-/*******************************
- * Command line option parsing *
- *******************************/
-
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-/***********************
- * Interval operations *
- ***********************/
-
-Interval = {};
-
-Interval.sort = function(a)
-{
-	if (typeof a[0] == 'number')
-		a.sort(function(x, y) { return x - y });
-	else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
-}
-
-Interval.merge = function(a, sorted)
-{
-	if (typeof sorted == 'undefined') sorted = true;
-	if (!sorted) Interval.sort(a);
-	var k = 0;
-	for (var i = 1; i < a.length; ++i) {
-		if (a[k][1] >= a[i][0])
-			a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
-		else a[++k] = a[i].slice(0);
-	}
-	a.length = k + 1;
-}
-
-Interval.dedup = function(a, sorted)
-{
-	if (typeof sorted == 'undefined') sorted = true;
-	if (!sorted) Interval.sort(a);
-	var k = 0;
-	for (var i = 1; i < a.length; ++i)
-		if (a[k][0] != a[i][0] || a[k][1] != a[i][1])
-			a[++k] = a[i].slice(0);
-	a.length = k + 1;
-}
-
-Interval.index_end = function(a, sorted)
-{
-	if (a.length == 0) return;
-	if (typeof sorted == 'undefined') sorted = true;
-	if (!sorted) Interval.sort(a);
-	a[0].push(0);
-	var k = 0, k_en = a[0][1];
-	for (var i = 1; i < a.length; ++i) {
-		if (k_en <= a[i][0]) {
-			for (++k; k < i; ++k)
-				if (a[k][1] > a[i][0])
-					break;
-			k_en = a[k][1];
-		}
-		a[i].push(k);
-	}
-}
-
-Interval.find_intv = function(a, x)
-{
-	var left = -1, right = a.length;
-	if (typeof a[0] == 'number') {
-		while (right - left > 1) {
-			var mid = left + ((right - left) >> 1);
-			if (a[mid] > x) right = mid;
-			else if (a[mid] < x) left = mid;
-			else return mid;
-		}
-	} else {
-		while (right - left > 1) {
-			var mid = left + ((right - left) >> 1);
-			if (a[mid][0] > x) right = mid;
-			else if (a[mid][0] < x) left = mid;
-			else return mid;
-		}
-	}
-	return left;
-}
-
-Interval.find_ovlp = function(a, st, en)
-{
-	if (a.length == 0 || st >= en) return [];
-	var l = Interval.find_intv(a, st);
-	var k = l < 0? 0 : a[l][a[l].length - 1];
-	var b = [];
-	for (var i = k; i < a.length; ++i) {
-		if (a[i][0] >= en) break;
-		else if (st < a[i][1])
-			b.push(a[i]);
-	}
-	return b;
-}
-
-/*****************
- * Main function *
- *****************/
-
-function read_bed(fn, to_merge, to_dedup)
-{
-	var file = new File(fn);
-	var buf = new Bytes();
-	var h = {};
-	while (file.readline(buf) >= 0) {
-		var t = buf.toString().split("\t");
-		if (h[t[0]] == null)
-			h[t[0]] = [];
-		var bst = parseInt(t[1]);
-		var ben = parseInt(t[2]);
-		if (t.length >= 12 && /^\d+$/.test(t[9])) {
-			t[9] = parseInt(t[9]);
-			var sz = t[10].split(",");
-			var st = t[11].split(",");
-			for (var i = 0; i < t[9]; ++i) {
-				st[i] = parseInt(st[i]);
-				sz[i] = parseInt(sz[i]);
-				h[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
-			}
-		} else {
-			h[t[0]].push([bst, ben, 0, 0, 0]);
-		}
-	}
-	buf.destroy();
-	file.close();
-	for (var chr in h) {
-		if (to_merge) Interval.merge(h[chr], false);
-		else if (to_dedup) Interval.dedup(h[chr], false);
-		else Interval.sort(h[chr]);
-		Interval.index_end(h[chr]);
-	}
-	return h;
-}
-
-function main(args)
-{
-	var c, print_len = false, to_merge = true, to_dedup = false, fn_excl = null;
-	while ((c = getopt(args, "pde:")) != null) {
-		if (c == 'p') print_len = true;
-		else if (c == 'd') to_dedup = true, to_merge = false;
-		else if (c == 'e') fn_excl = getopt.arg;
-	}
-
-	if (args.length - getopt.ind < 2) {
-		print("Usage: k8 cnt-feat.js [options] <target.bed> <feature.bed>");
-		print("Options:");
-		print("  -e FILE    exclude features overlapping regions in BED FILE []");
-		print("  -p         print number of covered bases for each feature");
-		exit(1);
-	}
-
-	var excl = fn_excl != null? read_bed(fn_excl, true, false) : null;
-	var target = read_bed(args[getopt.ind], to_merge, to_dedup);
-
-	var file, buf = new Bytes();
-	var tot_len = 0, hit_len = 0;
-	file = args[getopt.ind+1] != '-'? new File(args[getopt.ind+1]) : new File();
-	while (file.readline(buf) >= 0) {
-		var t = buf.toString().split("\t");
-		var a = [];
-		var bst = parseInt(t[1]);
-		var ben = parseInt(t[2]);
-		if (t.length >= 12 && /^\d+$/.test(t[9])) { // BED12
-			t[9] = parseInt(t[9]);
-			var sz = t[10].split(",");
-			var st = t[11].split(",");
-			for (var i = 0; i < t[9]; ++i) {
-				st[i] = parseInt(st[i]);
-				sz[i] = parseInt(sz[i]);
-				a.push([bst + st[i], bst + st[i] + sz[i], false]);
-			}
-		} else a.push([bst, ben, false]); // 3-column BED
-		var feat_len = 0;
-		for (var i = 0; i < a.length; ++i) {
-			if (excl != null && excl[t[0]] != null) {
-				var oe = Interval.find_ovlp(excl[t[0]], a[i][0], a[i][1]);
-				if (oe.length > 0)
-					continue;
-			}
-			a[i][2] = true;
-			feat_len += a[i][1] - a[i][0];
-		}
-		tot_len += feat_len;
-		if (target[t[0]] == null) continue;
-		var b = [];
-		for (var i = 0; i < a.length; ++i) {
-			if (!a[i][2]) continue;
-			var o = Interval.find_ovlp(target[t[0]], a[i][0], a[i][1]);
-			for (var j = 0; j < o.length; ++j) {
-				var max_st = o[j][0] > a[i][0]? o[j][0] : a[i][0];
-				var min_en = o[j][1] < a[i][1]? o[j][1] : a[i][1];
-				b.push([max_st, min_en]);
-				o[j][2] += min_en - max_st;
-				++o[j][3];
-				if (max_st == o[j][0] && min_en == o[j][1])
-					++o[j][4];
-			}
-		}
-		// find the length covered
-		var feat_hit_len = 0;
-		if (b.length > 0) {
-			b.sort(function(a,b) {return a[0]-b[0]});
-			var st = b[0][0], en = b[0][1];
-			for (var i = 1; i < b.length; ++i) {
-				if (b[i][0] <= en) en = en > b[i][1]? en : b[i][1];
-				else feat_hit_len += en - st, st = b[i][0], en = b[i][1];
-			}
-			feat_hit_len += en - st;
-		}
-		hit_len += feat_hit_len;
-		if (print_len) print('F', t.slice(0, 4).join("\t"), feat_len, feat_hit_len);
-	}
-	file.close();
-
-	buf.destroy();
-
-	warn("# feature bases: " + tot_len);
-	warn("# feature bases overlapping targets: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
-}
-
-main(arguments);

misc/gff2bed.js

@@ -1,150 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, fn_ucsc_fai = null, is_short = false;
-while ((c = getopt(arguments, "u:s")) != null) {
-	if (c == 'u') fn_ucsc_fai = getopt.arg;
-	else if (c == 's') is_short = true;
-}
-
-if (getopt.ind == arguments.length) {
-	print("Usage: k8 gff2bed.js [-u ucsc-genome.fa.fai] <in.gff>");
-	exit(1);
-}
-
-var ens2ucsc = {};
-if (fn_ucsc_fai != null) {
-	var buf = new Bytes();
-	var file = new File(fn_ucsc_fai);
-	while (file.readline(buf) >= 0) {
-		var t = buf.toString().split("\t");
-		var s = t[0];
-		if (/_(random|alt|decoy)$/.test(s)) {
-			s = s.replace(/_(random|alt|decoy)$/, '');
-			s = s.replace(/^chr\S+_/, '');
-		} else {
-			s = s.replace(/^chrUn_/, '');
-		}
-		s = s.replace(/v(\d+)/, ".$1");
-		if (s != t[0]) ens2ucsc[s] = t[0];
-	}
-	file.close();
-	buf.destroy();
-}
-
-var colors = {
-		'protein_coding':'0,128,255',
-		'lincRNA':'0,192,0',
-		'snRNA':'0,192,0',
-		'miRNA':'0,192,0',
-		'misc_RNA':'0,192,0'
-	};
-
-function print_bed12(exons, cds_st, cds_en, is_short)
-{
-	if (exons.length == 0) return;
-	var name = is_short? exons[0][7] + "|" + exons[0][5] : exons[0].slice(4, 7).join("|");
-	var a = exons.sort(function(a,b) {return a[1]-b[1]});
-	var sizes = [], starts = [], st, en;
-	st = a[0][1];
-	en = a[a.length - 1][2];
-	if (cds_st == 1<<30) cds_st = st;
-	if (cds_en == 0) cds_en = en;
-	if (cds_st < st || cds_en > en)
-		throw Error("inconsistent thick start or end for transcript " + a[0][4]);
-	for (var i = 0; i < a.length; ++i) {
-		sizes.push(a[i][2] - a[i][1]);
-		starts.push(a[i][1] - st);
-	}
-	var color = colors[a[0][5]];
-	if (color == null) color = '196,196,196';
-	print(a[0][0], st, en, name, 1000, a[0][3], cds_st, cds_en, color, a.length, sizes.join(",") + ",", starts.join(",") + ",");
-}
-
-var re_gtf = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name) "([^"]+)";/g;
-var re_gff3 = /(transcript_id|transcript_type|transcript_biotype|gene_name|transcript_name)=([^;]+)/g;
-var buf = new Bytes();
-var file = new File(arguments[getopt.ind]);
-
-var exons = [], cds_st = 1<<30, cds_en = 0, last_id = null;
-while (file.readline(buf) >= 0) {
-	var t = buf.toString().split("\t");
-	if (t[0].charAt(0) == '#') continue;
-	if (t[2] != "CDS" && t[2] != "exon") continue;
-	t[3] = parseInt(t[3]) - 1;
-	t[4] = parseInt(t[4]);
-	var id = null, type = "", gname = "N/A", biotype = "", m, tname = "N/A";
-	while ((m = re_gtf.exec(t[8])) != null) {
-		if (m[1] == "transcript_id") id = m[2];
-		else if (m[1] == "transcript_type") type = m[2];
-		else if (m[1] == "transcript_biotype") biotype = m[2];
-		else if (m[1] == "gene_name") name = m[2];
-		else if (m[1] == "transcript_name") tname = m[2];
-	}
-	while ((m = re_gff3.exec(t[8])) != null) {
-		if (m[1] == "transcript_id") id = m[2];
-		else if (m[1] == "transcript_type") type = m[2];
-		else if (m[1] == "transcript_biotype") biotype = m[2];
-		else if (m[1] == "gene_name") name = m[2];
-		else if (m[1] == "transcript_name") tname = m[2];
-	}
-	if (type == "" && biotype != "") type = biotype;
-	if (id == null) throw Error("No transcript_id");
-	if (id != last_id) {
-		print_bed12(exons, cds_st, cds_en, is_short);
-		exons = [], cds_st = 1<<30, cds_en = 0;
-		last_id = id;
-	}
-	if (t[2] == "CDS") {
-		cds_st = cds_st < t[3]? cds_st : t[3];
-		cds_en = cds_en > t[4]? cds_en : t[4];
-	} else if (t[2] == "exon") {
-		if (fn_ucsc_fai != null) {
-			if (ens2ucsc[t[0]] != null)
-				t[0] = ens2ucsc[t[0]];
-			else if (/^[A-Z]+\d+\.\d+$/.test(t[0]))
-				t[0] = t[0].replace(/([A-Z]+\d+)\.(\d+)/, "chrUn_$1v$2");
-		}
-		exons.push([t[0], t[3], t[4], t[6], id, type, name, tname]);
-	}
-}
-if (last_id != null)
-	print_bed12(exons, cds_st, cds_en, is_short);
-
-file.close();
-buf.destroy();

misc/intron-eval.js

@@ -1,267 +0,0 @@
-/*******************************
- * Command line option parsing *
- *******************************/
-
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-/***********************
- * Interval operations *
- ***********************/
-
-Interval = {};
-
-Interval.sort = function(a)
-{
-	if (typeof a[0] == 'number')
-		a.sort(function(x, y) { return x - y });
-	else a.sort(function(x, y) { return x[0] != y[0]? x[0] - y[0] : x[1] - y[1] });
-}
-
-Interval.merge = function(a, sorted)
-{
-	if (typeof sorted == 'undefined') sorted = true;
-	if (!sorted) Interval.sort(a);
-	var k = 0;
-	for (var i = 1; i < a.length; ++i) {
-		if (a[k][1] >= a[i][0])
-			a[k][1] = a[k][1] > a[i][1]? a[k][1] : a[i][1];
-		else a[++k] = a[i].slice(0);
-	}
-	a.length = k + 1;
-}
-
-Interval.index_end = function(a, sorted)
-{
-	if (a.length == 0) return;
-	if (typeof sorted == 'undefined') sorted = true;
-	if (!sorted) Interval.sort(a);
-	a[0].push(0);
-	var k = 0, k_en = a[0][1];
-	for (var i = 1; i < a.length; ++i) {
-		if (k_en <= a[i][0]) {
-			for (++k; k < i; ++k)
-				if (a[k][1] > a[i][0])
-					break;
-			k_en = a[k][1];
-		}
-		a[i].push(k);
-	}
-}
-
-Interval.find_intv = function(a, x)
-{
-	var left = -1, right = a.length;
-	if (typeof a[0] == 'number') {
-		while (right - left > 1) {
-			var mid = left + ((right - left) >> 1);
-			if (a[mid] > x) right = mid;
-			else if (a[mid] < x) left = mid;
-			else return mid;
-		}
-	} else {
-		while (right - left > 1) {
-			var mid = left + ((right - left) >> 1);
-			if (a[mid][0] > x) right = mid;
-			else if (a[mid][0] < x) left = mid;
-			else return mid;
-		}
-	}
-	return left;
-}
-
-Interval.find_ovlp = function(a, st, en)
-{
-	if (a.length == 0 || st >= en) return [];
-	var l = Interval.find_intv(a, st);
-	var k = l < 0? 0 : a[l][a[l].length - 1];
-	var b = [];
-	for (var i = k; i < a.length; ++i) {
-		if (a[i][0] >= en) break;
-		else if (st < a[i][1])
-			b.push(a[i]);
-	}
-	return b;
-}
-
-/*****************
- * Main function *
- *****************/
-
-var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false;
-while ((c = getopt(arguments, "l:ep")) != null) {
-	if (c == 'l') l_fuzzy = parseInt(getopt.arg);
-	else if (c == 'e') print_err_only = print_ovlp = true;
-	else if (c == 'p') print_ovlp = true;
-}
-
-if (arguments.length - getopt.ind < 2) {
-	print("Usage: k8 intron-eval.js [options] <gene.gtf> <aln.sam>");
-	exit(1);
-}
-
-var file, buf = new Bytes();
-
-var tr = {};
-file = new File(arguments[getopt.ind]);
-while (file.readline(buf) >= 0) {
-	var m, t = buf.toString().split("\t");
-	if (t[0].charAt(0) == '#') continue;
-	if (t[2] != 'exon') continue;
-	var st = parseInt(t[3]) - 1;
-	var en = parseInt(t[4]);
-	if ((m = /transcript_id "(\S+)"/.exec(t[8])) == null) continue;
-	var tid = m[1];
-	if (tr[tid] == null) tr[tid] = [t[0], t[6], 0, 0, []];
-	tr[tid][4].push([st, en]);
-}
-file.close();
-
-var anno = {};
-for (var tid in tr) {
-	var t = tr[tid];
-	Interval.sort(t[4]);
-	t[2] = t[4][0][0];
-	t[3] = t[4][t[4].length - 1][1];
-	if (anno[t[0]] == null) anno[t[0]] = [];
-	var s = t[4];
-	for (var i = 0; i < s.length - 1; ++i) {
-		if (s[i][1] >= s[i+1][0])
-			warn("WARNING: incorrect annotation for transcript "+tid+" ("+s[i][1]+" >= "+s[i+1][0]+")")
-		anno[t[0]].push([s[i][1], s[i+1][0]]);
-	}
-}
-tr = null;
-
-for (var chr in anno) {
-	var e = anno[chr];
-	if (e.length == 0) continue;
-	Interval.sort(e);
-	var k = 0;
-	for (var i = 1; i < e.length; ++i) // dedup
-		if (e[i][0] != e[k][0] || e[i][1] != e[k][1])
-			e[++k] = e[i].slice(0);
-	e.length = k + 1;
-	Interval.index_end(e);
-}
-
-var n_pri = 0, n_unmapped = 0, n_mapped = 0;
-var n_sgl = 0, n_splice = 0, n_splice_hit = 0, n_splice_novel = 0;
-
-file = new File(arguments[getopt.ind+1]);
-var last_qname = null;
-var re_cigar = /(\d+)([MIDNSHX=])/g;
-while (file.readline(buf) >= 0) {
-	var m, t = buf.toString().split("\t");
-
-	if (t[0].charAt(0) == '@') continue;
-	var flag = parseInt(t[1]);
-	if (flag&0x100) continue;
-	if (first_only && last_qname == t[0]) continue;
-	if (t[2] == '*') {
-		++n_unmapped;
-		continue;
-	} else {
-		++n_pri;
-		if (last_qname != t[0]) ++n_mapped;
-	}
-
-	var pos = parseInt(t[3]) - 1, intron = [];
-	while ((m = re_cigar.exec(t[5])) != null) {
-		var len = parseInt(m[1]), op = m[2];
-		if (op == 'N') {
-			intron.push([pos, pos + len]);
-			pos += len;
-		} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
-	}
-	if (intron.length == 0) {
-		++n_sgl;
-		continue;
-	}
-	n_splice += intron.length;
-
-	var chr = anno[t[2]];
-	if (chr != null) {
-		for (var i = 0; i < intron.length; ++i) {
-			var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
-			if (o.length > 0) {
-				var hit = false;
-				for (var j = 0; j < o.length; ++j) {
-					var st_diff = intron[i][0] - o[j][0];
-					var en_diff = intron[i][1] - o[j][1];
-					if (st_diff < 0) st_diff = -st_diff;
-					if (en_diff < 0) en_diff = -en_diff;
-					if (st_diff <= l_fuzzy && en_diff <= l_fuzzy)
-						++n_splice_hit, hit = true;
-					if (hit) break;
-				}
-				if (print_ovlp) {
-					var type = hit? 'C' : 'P';
-					if (hit && print_err_only) continue;
-					var x = '[';
-					for (var j = 0; j < o.length; ++j) {
-						if (j) x += ', ';
-						x += '(' + o[j][0] + "," + o[j][1] + ')';
-					}
-					x += ']';
-					print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x);
-				}
-			} else {
-				++n_splice_novel;
-				if (print_ovlp)
-					print('N', t[0], i+1, t[2], intron[i][0], intron[i][1]);
-			}
-		}
-	} else {
-		n_splice_novel += intron.length;
-	}
-	last_qname = t[0];
-}
-file.close();
-
-buf.destroy();
-
-if (!print_ovlp) {
-	print("# unmapped reads: " + n_unmapped);
-	print("# mapped reads: " + n_mapped);
-	print("# primary alignments: " + n_pri);
-	print("# singletons: " + n_sgl);
-	print("# predicted introns: " + n_splice);
-	print("# non-overlapping introns: " + n_splice_novel);
-	print("# correct introns: " + n_splice_hit + " (" + (n_splice_hit / n_splice * 100).toFixed(2) + "%)");
-}

misc/mapstat.js

@@ -1,183 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, gap_out_len = null;
-while ((c = getopt(arguments, "l:")) != null)
-	if (c == 'l') gap_out_len = parseInt(getopt.arg);
-
-if (getopt.ind == arguments.length) {
-	print("Usage: k8 mapstat.js [-l gapOutLen] <in.sam>|<in.paf>");
-	exit(1);
-}
-
-var buf = new Bytes();
-var file = new File(arguments[getopt.ind]);
-var re = /(\d+)([MIDSHNX=])/g;
-
-var lineno = 0, n_pri = 0, n_2nd = 0, n_seq = 0, n_cigar_64k = 0, l_tot = 0, l_cov = 0;
-var n_gap = [[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0]];
-
-function cov_len(regs)
-{
-	regs.sort(function(a,b) {return a[0]-b[0]});
-	var st = regs[0][0], en = regs[0][1], l = 0;
-	for (var i = 1; i < regs.length; ++i) {
-		if (regs[i][0] < en)
-			en = en > regs[i][1]? en : regs[i][1];
-		else l += en - st, st = regs[i][0], en = regs[i][1];
-	}
-	l += en - st;
-	return l;
-}
-
-var last = null, last_qlen = null, regs = [];
-while (file.readline(buf) >= 0) {
-	var line = buf.toString();
-	++lineno;
-	if (line.charAt(0) != '@') {
-		var t = line.split("\t", 12);
-		var m, rs, cigar = null, is_pri = false, is_sam = false, is_rev = false, tname = null;
-		var atlen = null, aqlen, qs, qe, mapq, ori_qlen;
-		if (t[4] == '+' || t[4] == '-') { // PAF
-			if (!/\ts2:i:\d+/.test(line)) {
-				++n_2nd;
-				continue;
-			}
-			if ((m = /\tcg:Z:(\S+)/.exec(line)) != null)
-				cigar = m[1];
-			if (cigar == null) {
-				warn("WARNING: no CIGAR at line " + lineno);
-				continue;
-			}
-			tname = t[5];
-			qs = parseInt(t[2]), qe = parseInt(t[3]);
-			aqlen = qe - qs;
-			is_rev = t[4] == '+'? false : true;
-			rs = parseInt(t[7]);
-			atlen = parseInt(t[8]) - rs;
-			mapq = parseInt(t[11]);
-			ori_qlen = parseInt(t[1]);
-		} else { // SAM
-			var flag = parseInt(t[1]);
-			if ((flag & 4) || t[2] == '*' || t[5] == '*') continue;
-			if (flag & 0x100) {
-				++n_2nd;
-				continue;
-			}
-			cigar = t[5];
-			tname = t[2];
-			rs = parseInt(t[3]) - 1;
-			mapq = parseInt(t[4]);
-			aqlen = t[9].length;
-			is_sam = true;
-			is_rev = !!(flag&0x10);
-		}
-		++n_pri;
-		if (last != t[0]) {
-			if (last != null) {
-				l_tot += last_qlen;
-				l_cov += cov_len(regs);
-			}
-			regs = [];
-			++n_seq, last = t[0];
-		}
-		var M = 0, tl = 0, ql = 0, clip = [0, 0], n_cigar = 0, sclip = 0;
-		while ((m = re.exec(cigar)) != null) {
-			var l = parseInt(m[1]);
-			++n_cigar;
-			if (m[2] == 'M' || m[2] == '=' || m[2] == 'X') {
-				tl += l, ql += l, M += l;
-			} else if (m[2] == 'I' || m[2] == 'D') {
-				var type;
-				if (l < 50) type = 0;
-				else if (l < 100) type = 1;
-				else if (l < 300) type = 2;
-				else if (l < 400) type = 3;
-				else if (l < 1000) type = 4;
-				else type = 5;
-				if (m[2] == 'I') ql += l, ++n_gap[0][type];
-				else tl += l, ++n_gap[1][type];
-				if (gap_out_len != null && l >= gap_out_len)
-					print(t[0], ql, is_rev? '-' : '+', tname, rs + tl, m[2], l);
-			} else if (m[2] == 'N') {
-				tl += l;
-			} else if (m[2] == 'S') {
-				clip[M == 0? 0 : 1] = l, sclip += l;
-			} else if (m[2] == 'H') {
-				clip[M == 0? 0 : 1] = l;
-			}
-		}
-		if (n_cigar > 65535) ++n_cigar_64k;
-		if (ql + sclip != aqlen)
-			warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno + " (" + (ql+sclip) + " != " + aqlen + ")");
-		if (atlen != null && atlen != tl)
-			warn("WARNING: aligned reference length is inconsistent with CIGAR at line " + lineno);
-		if (is_sam) {
-			qs = clip[is_rev? 1 : 0], qe = qs + ql;
-			ori_qlen = clip[0] + ql + clip[1];
-		}
-		regs.push([qs, qe]);
-		last_qlen = ori_qlen;
-	}
-}
-l_tot += last_qlen;
-l_cov += cov_len(regs);
-
-file.close();
-buf.destroy();
-
-if (gap_out_len == null) {
-	print("Number of mapped sequences: " + n_seq);
-	print("Number of primary alignments: " + n_pri);
-	print("Number of secondary alignments: " + n_2nd);
-	print("Number of primary alignments with >65535 CIGAR operations: " + n_cigar_64k);
-	print("Number of bases in mapped sequences: " + l_tot);
-	print("Number of mapped bases: " + l_cov);
-	print("Number of insertions in [0,50): " + n_gap[0][0]);
-	print("Number of insertions in [50,100): " + n_gap[0][1]);
-	print("Number of insertions in [100,300): " + n_gap[0][2]);
-	print("Number of insertions in [300,400): " + n_gap[0][3]);
-	print("Number of insertions in [400,1000): " + n_gap[0][4]);
-	print("Number of insertions in [1000,inf): " + n_gap[0][5]);
-	print("Number of deletions in [0,50): " + n_gap[1][0]);
-	print("Number of deletions in [50,100): " + n_gap[1][1]);
-	print("Number of deletions in [100,300): " + n_gap[1][2]);
-	print("Number of deletions in [300,400): " + n_gap[1][3]);
-	print("Number of deletions in [400,1000): " + n_gap[1][4]);
-	print("Number of deletions in [1000,inf): " + n_gap[1][5]);
-}

misc/ov-eval.js

@@ -1,105 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, min_ovlp = 2000, min_frac = 0.95, min_mapq = 10;
-while ((c = getopt(arguments, "q:l:f:")) != null) {
-	if (c == 'q') min_mapq = parseInt(getopt.arg);
-	else if (c == 'l') min_ovlp = parseInt(getopt.arg);
-	else if (c == 'f') min_frac = parseFloat(getopt.arg);
-}
-if (arguments.length - getopt.ind < 2) {
-	print("Usage: sort -k6,6 -k8,8n to-ref.paf | k8 ov-eval.js [options] - <ovlp.paf>");
-	print("Options:");
-	print("  -l INT     min overlap length [2000]");
-	print("  -q INT     min mapping quality [10]");
-	print("  -f FLOAT   min fraction of mapped length [0.95]");
-	exit(1);
-}
-
-var buf = new Bytes();
-var file = arguments[getopt.ind] == '-'? new File() : new File(arguments[getopt.ind]);
-var a = [], h = {};
-while (file.readline(buf) >= 0) {
-	var t = buf.toString().split("\t");
-	var is_pri = false;
-	if (parseInt(t[11]) < min_mapq) continue;
-	for (var i = 12; i < t.length; ++i)
-		if (t[i] == 'tp:A:P')
-			is_pri = true;
-	if (!is_pri) continue;
-	for (var i = 1; i <= 3; ++i)
-		t[i] = parseInt(t[i]);
-	for (var i = 6; i <= 8; ++i)
-		t[i] = parseInt(t[i]);
-	if (t[3] - t[2] < min_ovlp || t[8] - t[7] < min_ovlp || (t[3] - t[2]) / t[1] < min_frac)
-		continue;
-	var ctg = t[5], st = t[7], en = t[8];
-	while (a.length > 0) {
-		if (a[0][0] == ctg && a[0][2] > st)
-			break;
-		else a.shift();
-	}
-	for (var j = 0; j < a.length; ++j) {
-		if (a[j][3] == t[0]) continue;
-		var len = (en > a[j][2]? a[j][2] : en) - st;
-		if (len >= min_ovlp) {
-			var key = a[j][3] < t[0]? a[j][3] + "\t" + t[0] : t[0] + "\t" + a[j][3];
-			h[key] = len;
-		}
-	}
-	a.push([ctg, st, en, t[0]]);
-}
-file.close();
-
-file = new File(arguments[getopt.ind + 1]);
-while (file.readline(buf) >= 0) {
-	var t = buf.toString().split("\t");
-	var key = t[0] < t[5]? t[0] + "\t" + t[5] : t[5] + "\t" + t[0];
-	if (h[key] > 0) h[key] = -h[key];
-}
-file.close();
-buf.destroy();
-
-var n_ovlp = 0, n_missing = 0;
-for (var key in h) {
-	++n_ovlp;
-	if (h[key] > 0) ++n_missing;
-}
-print(n_ovlp + " overlaps inferred from the reference mapping");
-print(n_missing + " missed by the read overlapper");
-print((100 * (1 - n_missing / n_ovlp)).toFixed(2) + "% sensitivity");

misc/paf2aln.js

@@ -1,196 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, line_len = 80, fmt = "aln";
-while ((c = getopt(arguments, "f:l:")) != null) {
-	if (c == 'f') {
-		fmt = getopt.arg;
-		if (fmt != "aln" && fmt != "lastz-cigar" && fmt != "maf")
-			throw Error("format must be one of aln, lastz-cigar and maf");
-	} else if (c == 'l') line_len = parseInt(getopt.arg);
-}
-if (line_len == 0) line_len = 0x7fffffff;
-
-if (getopt.ind == arguments.length) {
-	print("Usage: k8 paf2aln.js [options] <in.paf>");
-	print("Options:");
-	print("  -f STR    output format: aln (BLAST-like), maf or lastz-cigar [aln]");
-	print("  -l INT    line length in BLAST-like output [80]");
-	exit(1);
-}
-
-function padding_str(x, len, right)
-{
-	var s = x.toString();
-	if (s.length < len) {
-		if (right) s += Array(len - s.length + 1).join(" ");
-		else s = Array(len - s.length + 1).join(" ") + s;
-	}
-	return s;
-}
-
-function update_aln(s_ref, s_qry, s_mid, type, seq, slen)
-{
-	var l = type == '*'? 1 : seq.length;
-	if (type == '=' || type == ':') {
-		s_ref.set(seq);
-		s_qry.set(seq);
-		s_mid.set(Array(l+1).join("|"));
-		slen[0] += l, slen[1] += l;
-	} else if (type == '*') {
-		s_ref.set(seq.charAt(0));
-		s_qry.set(seq.charAt(1));
-		s_mid.set(' ');
-		slen[0] += 1, slen[1] += 1;
-	} else if (type == '+') {
-		s_ref.set(Array(l+1).join("-"));
-		s_qry.set(seq);
-		s_mid.set(Array(l+1).join(" "));
-		slen[1] += l;
-	} else if (type == '-') {
-		s_ref.set(seq);
-		s_qry.set(Array(l+1).join("-"));
-		s_mid.set(Array(l+1).join(" "));
-		slen[0] += l;
-	}
-}
-
-function print_aln(rs, qs, strand, slen, elen, s_ref, s_qry, s_mid)
-{
-	print(["Ref+:", padding_str(rs + slen[0] + 1, 10, false), s_ref.toString(), padding_str(rs + elen[0], 10, true)].join(" "));
-	print("                 " + s_mid.toString());
-	var st, en;
-	if (strand == '+') st = qs + slen[1] + 1, en = qs + elen[1];
-	else st = qs - slen[1], en = qs - elen[1] + 1;
-	print(["Qry" + strand + ":", padding_str(st, 10, false), s_qry.toString(), padding_str(en, 10, true)].join(" "));
-}
-
-var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes(); // these are used to show padded alignment
-var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
-var re_cg = /(\d+)([MIDNSH])/g;
-
-var buf = new Bytes();
-var file = arguments[getopt.ind] == "-"? new File() : new File(arguments[getopt.ind]);
-var lineno = 0;
-if (fmt == "maf") print("##maf version=1\n");
-while (file.readline(buf) >= 0) {
-	var m, line = buf.toString();
-	var t = line.split("\t", 12);
-	++lineno;
-	s_ref.length = s_qry.length = s_mid.length = 0;
-	var slen = [0, 0], elen = [0, 0];
-	if (fmt == "lastz-cigar") { // LASTZ-cigar output
-		var cg = (m = /\tcg:Z:(\S+)/.exec(line)) != null? m[1] : null;
-		if (cg == null) {
-			warn("WARNING: converting to LASTZ-cigar format requires the 'cg' tag, which is absent on line " + lineno);
-			continue;
-		}
-		var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? m[1] : 0;
-		var out = ['cigar:', t[0], t[2], t[3], t[4], t[5], t[7], t[8], '+', score];
-		while ((m = re_cg.exec(cg)) != null)
-			out.push(m[2], m[1]);
-		print(out.join(" "));
-	} else if (fmt == "maf") { // MAF output
-		var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
-		if (cs == null) {
-			warn("WARNING: converting to MAF requires the 'cs' tag, which is absent on line " + lineno);
-			continue;
-		}
-		while ((m = re_cs.exec(cs)) != null) {
-			if (m[1] == ':')
-				throw Error("converting to MAF only works with 'minimap2 --cs=long'");
-			update_aln(s_ref, s_qry, s_mid, m[1], m[2], elen);
-		}
-		var score = (m = /\tAS:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
-		var len = t[0].length > t[5].length? t[0].length : t[5].length;
-		print("a " + score);
-		print(["s", padding_str(t[5], len, true), padding_str(t[7], 10, false), padding_str(parseInt(t[8]) - parseInt(t[7]), 10, false),
-				"+", padding_str(t[6], 10, false), s_ref.toString()].join(" "));
-		var qs, qe, ql = parseInt(t[1]);
-		if (t[4] == '+') {
-			qs = parseInt(t[2]);
-			qe = parseInt(t[3]);
-		} else {
-			qs = ql - parseInt(t[3]);
-			qe = ql - parseInt(t[2]);
-		}
-		print(["s", padding_str(t[0], len, true), padding_str(qs, 10, false), padding_str(qe - qs, 10, false),
-				t[4], padding_str(ql, 10, false), s_qry.toString()].join(" "));
-		print("");
-	} else { // BLAST-like output
-		var cs = (m = /\tcs:Z:(\S+)/.exec(line)) != null? m[1] : null;
-		if (cs == null) {
-			warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
-			continue;
-		}
-		line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
-		print('>' + line);
-		var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
-		var n_blocks = 0;
-		while ((m = re_cs.exec(cs)) != null) {
-			if (m[1] == ':') m[2] = Array(parseInt(m[2]) + 1).join("=");
-			var start = 0, rest = m[1] == '*'? 1 : m[2].length;
-			while (rest > 0) {
-				var l_proc;
-				if (s_ref.length + rest >= line_len) {
-					l_proc = line_len - s_ref.length;
-					update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
-					if (n_blocks > 0) print("");
-					print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
-					++n_blocks;
-					s_ref.length = s_qry.length = s_mid.length = 0;
-					slen[0] = elen[0], slen[1] = elen[1];
-				} else {
-					l_proc = rest;
-					update_aln(s_ref, s_qry, s_mid, m[1], m[1] == '*'? m[2] : m[2].substr(start, l_proc), elen);
-				}
-				rest -= l_proc, start += l_proc;
-			}
-		}
-		if (s_ref.length > 0) {
-			if (n_blocks > 0) print("");
-			print_aln(rs, qs, t[4], slen, elen, s_ref, s_qry, s_mid);
-			++n_blocks;
-		}
-		print("//");
-	}
-}
-file.close();
-buf.destroy();
-
-s_ref.destroy(); s_qry.destroy(); s_mid.destroy();

misc/paf2diff.js

@@ -1,188 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g;
-var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, min_mapq = 5;
-while ((c = getopt(arguments, "l:L:g:q:")) != null) {
-	if (c == 'l') min_cov_len = parseInt(getopt.arg);
-	else if (c == 'L') min_var_len = parseInt(optarg.arg);
-	else if (c == 'g') gap_thres = parseInt(optarg.arg);
-	else if (c == 'q') min_mapq = parseInt(optarg.arg);
-}
-
-if (arguments.length == getopt.ind) {
-	print("Usage: k8 paf2diff.js [options] <with-cs.paf>");
-	print("Options:");
-	print("  -l INT    min alignment length to compute coverage ["+min_cov_len+"]");
-	print("  -L INT    min alignment length to call variants ["+min_var_len+"]");
-	print("  -q INT    min mapping quality ["+min_mapq+"]");
-	print("  -g INT    short/long gap threshold (for statistics only) ["+gap_thres+"]");
-	exit(1);
-}
-
-var file = new File(arguments[getopt.ind]);
-var buf = new Bytes();
-var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0], n_del = [0, 0, 0, 0];
-
-function count_var(o)
-{
-	if (o[3] > 1) return;
-	if (o[5] == '-' && o[6] == '-') return;
-	if (o[5] == '-') { // insertion
-		var l = o[6].length;
-		if (l == 1) ++n_ins[0];
-		else if (l == 2) ++n_ins[1];
-		else if (l < gap_thres) ++n_ins[2];
-		else ++n_ins[3];
-	} else if (o[6] == '-') { // deletion
-		var l = o[5].length;
-		if (l == 1) ++n_del[0];
-		else if (l == 2) ++n_del[1];
-		else if (l < gap_thres) ++n_del[2];
-		else ++n_del[3];
-	} else {
-		++n_sub[0];
-		var s = o[5] + o[6];
-		if (s == 'ag' || s == 'ga' || s == 'ct' || s == 'tc')
-			++n_sub[1];
-		else ++n_sub[2];
-	}
-}
-
-var a = [], out = [];
-var c1_ctg = null, c1_start = 0, c1_end = 0, c1_counted = false, c1_len = 0;
-while (file.readline(buf) >= 0) {
-	var line = buf.toString();
-	if (!/\ts2:i:/.test(line)) continue; // skip secondary alignments
-	var m, t = line.split("\t", 12);
-	for (var i = 6; i <= 11; ++i)
-		t[i] = parseInt(t[i]);
-	if (t[10] < min_cov_len || t[11] < min_mapq) continue;
-	var ctg = t[5], x = t[7], end = t[8];
-	// compute regions covered by 1 contig
-	if (ctg != c1_ctg || x >= c1_end) {
-		if (c1_counted && c1_end > c1_start) {
-			c1_len += c1_end - c1_start;
-			print('R', c1_ctg, c1_start, c1_end);
-		}
-		c1_ctg = ctg, c1_start = x, c1_end = end;
-		c1_counted = (t[10] >= min_var_len);
-	} else if (end > c1_end) { // overlap
-		if (c1_counted && x > c1_start) {
-			c1_len += x - c1_start;
-			print('R', c1_ctg, c1_start, x);
-		}
-		c1_start = c1_end, c1_end = end;
-		c1_counted = (t[10] >= min_var_len);
-	} else { // contained
-		if (c1_counted && x > c1_start) {
-			c1_len += x - c1_start;
-			print('R', c1_ctg, c1_start, x);
-		}
-		c1_start = end;
-	}
-	// output variants ahead of this alignment
-	while (out.length) {
-		if (out[0][0] != ctg || out[0][2] <= x) {
-			count_var(out[0]);
-			print('V', out[0].join("\t"));
-			out.shift();
-		} else break;
-	}
-	// update coverage
-	for (var i = 0; i < out.length; ++i)
-		if (out[i][1] >= x && out[i][2] <= end)
-			++out[i][3];
-	// drop alignments that don't overlap with the current one
-	var k = 0;
-	for (var i = 0; i < a.length; ++i)
-		if (a[0][0] == ctg && a[0][2] > x)
-			a[k++] = a[i];
-	a.length = k;
-	// core loop
-	if (t[10] >= min_var_len) {
-		if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue; // no cs tag
-		var cs = m[1];
-		var blen = 0, n_diff = 0;
-		tot_len += t[10];
-		while ((m = re_cs.exec(cs)) != null) {
-			var cov = 1;
-			if (m[1] == '*' || m[1] == '+' || m[1] == '-')
-				for (var i = 0; i < a.length; ++i)
-					if (a[0][2] > x) ++cov;
-			if (m[1] == '=' || m[1] == ':') {
-				var l = m[1] == '='? m[2].length : parseInt(m[2]);
-				x += l, blen += l;
-			} else if (m[1] == '*') {
-				out.push([t[5], x, x+1, cov, t[11], m[2].charAt(0), m[2].charAt(1)]);
-				++x, ++blen, ++n_diff;
-			} else if (m[1] == '+') {
-				out.push([t[5], x, x, cov, t[11], '-', m[2]]);
-				++blen, ++n_diff;
-			} else if (m[1] == '-') {
-				out.push([t[5], x, x + m[2].length, cov, t[11], m[2], '-']);
-				x += m[2].length, ++blen, ++n_diff;
-			}
-		}
-	}
-	a.push([t[5], t[7], t[8]]);
-}
-if (c1_counted && c1_end > c1_start) {
-	c1_len += c1_end - c1_start;
-	print('R', c1_ctg, c1_start, c1_end);
-}
-while (out.length) {
-	count_var(out[0]);
-	print('V', out[0].join("\t"));
-	out.shift();
-}
-
-//warn(tot_len + " alignment columns considered in calling");
-warn(c1_len + " reference bases covered by exactly one contig");
-warn(n_sub[0] + " substitutions; ts/tv = " + (n_sub[1]/n_sub[2]).toFixed(3));
-warn(n_del[0] + " 1bp deletions");
-warn(n_ins[0] + " 1bp insertions");
-warn(n_del[1] + " 2bp deletions");
-warn(n_ins[1] + " 2bp insertions");
-warn(n_del[2] + " [3,"+gap_thres+") deletions");
-warn(n_ins[2] + " [3,"+gap_thres+") insertions");
-warn(n_del[3] + " >="+gap_thres+" deletions");
-warn(n_ins[3] + " >="+gap_thres+" insertions");
-
-buf.destroy();
-file.close();

misc/pafcluster.js

@@ -0,0 +1,241 @@
+#!/usr/bin/env k8
+
+"use strict";
+
+Array.prototype.delete_at = function(i) {
+	for (let j = i; j < this.length - 1; ++j)
+		this[j] = this[j + 1];
+	--this.length;
+}
+
+function* getopt(argv, ostr, longopts) {
+	if (argv.length == 0) return;
+	let pos = 0, cur = 0;
+	while (cur < argv.length) {
+		let lopt = "", opt = "?", arg = "";
+		while (cur < argv.length) { // skip non-option arguments
+			if (argv[cur][0] == "-" && argv[cur].length > 1) {
+				if (argv[cur] == "--") cur = argv.length;
+				break;
+			} else ++cur;
+		}
+		if (cur == argv.length) break;
+		let a = argv[cur];
+		if (a[0] == "-" && a[1] == "-") { // a long option
+			pos = -1;
+			let c = 0, k = -1, tmp = "", o;
+			const pos_eq = a.indexOf("=");
+			if (pos_eq > 0) {
+				o = a.substring(2, pos_eq);
+				arg = a.substring(pos_eq + 1);
+			} else o = a.substring(2);
+			for (let i = 0; i < longopts.length; ++i) {
+				let y = longopts[i];
+				if (y[y.length - 1] == "=") y = y.substring(0, y.length - 1);
+				if (o.length <= y.length && o == y.substring(0, o.length)) {
+					k = i, tmp = y;
+					++c; // c is the number of matches
+					if (o == y) { // exact match
+						c = 1;
+						break;
+					}
+				}
+			}
+			if (c == 1) { // find a unique match
+				lopt = tmp;
+				if (pos_eq < 0 && longopts[k][longopts[k].length-1] == "=" && cur + 1 < argv.length) {
+					arg = argv[cur+1];
+					argv.delete_at(cur + 1);
+				}
+			}
+		} else { // a short option
+			if (pos == 0) pos = 1;
+			opt = a[pos++];
+			let k = ostr.indexOf(opt);
+			if (k < 0) {
+				opt = "?";
+			} else if (k + 1 < ostr.length && ostr[k+1] == ":") { // requiring an argument
+				if (pos >= a.length) {
+					arg = argv[cur+1];
+					argv.delete_at(cur + 1);
+				} else arg = a.substring(pos);
+				pos = -1;
+			}
+		}
+		if (pos < 0 || pos >= argv[cur].length) {
+			argv.delete_at(cur);
+			pos = 0;
+		}
+		if (lopt != "") yield { opt: `--${lopt}`, arg: arg };
+		else if (opt != "?") yield { opt: `-${opt}`, arg: arg };
+		else yield { opt: "?", arg: "" };
+	}
+}
+
+function* k8_readline(fn) {
+	let buf = new Bytes();
+	let file = new File(fn);
+	while (file.readline(buf) >= 0) {
+		yield buf.toString();
+	}
+	file.close();
+	buf.destroy();
+}
+
+function merge_hits(b) {
+	if (b.length == 1)
+		return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:b[0].min_cov, max_cov:b[0].max_cov, cov1:b[0].cov1, cov2:b[0].cov2, s1:b[0].s1, dv:b[0].dv };
+	b.sort(function(x, y) { return x.st1 - y.st1 });
+	let f = [], bt = [];
+	for (let i = 0; i < b.length; ++i)
+		f[i] = b[i].s1, bt[i] = -1;
+	for (let i = 0; i < b.length; ++i) {
+		for (let j = 0; j < i; ++j) {
+			if (b[j].st2 < b[i].st2) {
+				if (b[j].en1 >= b[i].en1) continue;
+				if (b[j].en2 >= b[i].en2) continue;
+				const ov1 = b[j].en1 <= b[i].st1? 0 : b[i].st1 - b[j].en1;
+				const li1 = b[i].en1 - b[i].st1;
+				const s11 = b[i].s1 / li1 * (li1 - ov1);
+				const ov2 = b[j].en2 <= b[i].st2? 0 : b[i].st2 - b[j].en2;
+				const li2 = b[i].en2 - b[i].st2;
+				const s12 = b[i].s1 / li2 * (li2 - ov2);
+				const s1 = s11 < s12? s11 : s12;
+				if (f[i] < f[j] + s1)
+					f[i] = f[j] + s1, bt[i] = j;
+			}
+		}
+	}
+	let max_i = -1, max_f = 0, d = [];
+	for (let i = 0; i < b.length; ++i)
+		if (max_f < f[i])
+			max_f = f[i], max_i = i;
+	for (let k = max_i; k >= 0; k = bt[k])
+		d.push(k);
+	d = d.reverse();
+	let dv = 0, tot = 0, cov1 = 0, cov2 = 0, st1 = 0, en1 = 0, st2 = 0, en2 = 0;
+	for (let k = 0; k < d.length; ++k) {
+		const i = d[k];
+		tot += b[i].blen;
+		dv += b[i].dv * b[i].blen;
+		if (b[i].st1 > en1) {
+			cov1 += en1 - st1;
+			st1 = b[i].st1, en1 = b[i].en1;
+		} else en1 = en1 > b[i].en1? en1 : b[i].en1;
+		if (b[i].st2 > en2) {
+			cov2 += en2 - st2;
+			st2 = b[i].st2, en2 = b[i].en2;
+		} else en2 = en2 > b[i].en2? en2 : b[i].en2;
+	}
+	dv /= tot;
+	cov1 = (cov1 + (en1 - st1)) / b[0].len1;
+	cov2 = (cov2 + (en2 - st2)) / b[0].len2;
+	const min_cov = cov1 < cov2? cov1 : cov2;
+	const max_cov = cov1 > cov2? cov1 : cov2;
+	//warn(d.length, b[0].name1, b[0].name2, min_cov, max_cov);
+	return { name1:b[0].name1, name2:b[0].name2, len1:b[0].len1, len2:b[0].len2, min_cov:min_cov, max_cov:max_cov, cov1:cov1, cov2:cov2, s1:max_f, dv:dv };
+}
+
+function main(args) {
+	let opt = { min_cov:.9, max_dv:.015, max_diff:20000 };
+	for (const o of getopt(args, "c:d:e:", [])) {
+		if (o.opt == '-c') opt.min_cov = parseFloat(o.arg);
+		else if (o.opt == '-d') opt.max_dv = parseFloat(o.arg);
+		else if (o.opt == '-e') opt.max_diff = parseFloat(o.arg);
+	}
+	if (args.length == 0) {
+		print("Usage: pafcluster.js [options] <ava.paf>");
+		print("Options:");
+		print(`  -c FLOAT     min coverage [${opt.min_cov}]`);
+		print(`  -d FLOAT     max divergence [${opt.max_dv}]`);
+		print(`  -e FLOAT     max difference [${opt.max_diff}]`);
+		return;
+	}
+
+	// read
+	let a = [], len = {}, name2len = {};
+	for (const line of k8_readline(args[0])) {
+		let m, t = line.split("\t");
+		if (t[4] != "+") continue;
+		for (let i = 1; i < 4;  ++i) t[i] = parseInt(t[i]);
+		for (let i = 6; i < 11; ++i) t[i] = parseInt(t[i]);
+		const len1 = t[1], len2 = t[6];
+		let s1 = -1, dv = -1.0;
+		for (let i = 12; i < t.length; ++i) {
+			if ((m = /^(s1|dv):\S:(\S+)/.exec(t[i])) != null) {
+				if (m[1] == "s1") s1 = parseInt(m[2]);
+				else if (m[1] == "dv") dv = parseFloat(m[2]);
+			}
+		}
+		if (s1 < 0 || dv < 0) continue;
+		const cov1 = (parseInt(t[3]) - parseInt(t[2])) / len1;
+		const cov2 = (parseInt(t[8]) - parseInt(t[7])) / len2;
+		const min_cov = cov1 < cov2? cov1 : cov2;
+		const max_cov = cov1 > cov2? cov1 : cov2;
+		name2len[t[0]] = len1;
+		name2len[t[5]] = len2;
+		a.push({ name1:t[0], name2:t[5], len1:len1, len2:len2, min_cov:min_cov, max_cov:max_cov, s1:s1, dv:dv, cov1:cov1, cov2:cov2, st1:t[2], en1:t[3], st2:t[7], en2:t[8], blen:t[10] });
+		len[t[0]] = len1, len[t[5]] = len2;
+	}
+	warn(`Read ${a.length} hits`);
+
+	// merge duplicated hits
+	let h = {};
+	for (let i = 0; i < a.length; ++i) {
+		const key = `${a[i].name1}\t${a[i].name2}`;
+		if (h[key] == null) h[key] = [];
+		h[key].push(a[i]);
+	}
+	a = [];
+	for (const key in h)
+		a.push(merge_hits(h[key]));
+
+	// core loop
+	while (a.length > 1) {
+		// select the sequence with the highest sum of s1
+		let h = {};
+		for (let i = 0; i < a.length; ++i) {
+			if (h[a[i].name1] == null) h[a[i].name1] = 0;
+			h[a[i].name1] += a[i].s1;
+		}
+		let max_s1 = 0, max_name = "";
+		for (const name in h)
+			if (max_s1 < h[name])
+				max_s1 = h[name], max_name = name;
+		// find contigs in the same group
+		h = {};
+		h[max_name] = 1;
+		for (let i = 0; i < a.length; ++i) {
+			if (a[i].name1 != max_name && a[i].name2 != max_name)
+				continue;
+			const diff1 = a[i].len1 * (1.0 - a[i].cov1);
+			const diff2 = a[i].len2 * (1.0 - a[i].cov2);
+			if (a[i].min_cov >= opt.min_cov && a[i].dv <= opt.max_dv && diff1 <= opt.max_diff && diff2 <= opt.max_diff)
+				h[a[i].name1] = h[a[i].name2] = 1;
+		}
+		let n = 0;
+		for (const key in h) {
+			++n;
+			delete name2len[key];
+		}
+		print(`SD\t${max_name}\t${n}`);
+		for (const key in h) print(`CL\t${key}\t${len[key]}`);
+		print("//");
+		// filter out redundant hits
+		let b = [];
+		for (let i = 0; i < a.length; ++i)
+			if (h[a[i].name1] == null && h[a[i].name2] == null)
+				b.push(a[i]);
+		warn(`Reduced the number of hits from ${a.length} to ${b.length}`);
+		a = b;
+	}
+
+	// output remaining singletons
+	for (const key in name2len) {
+		print(`SD\t${key}\t1`);
+		print(`CL\t${key}\t${name2len[key]}`);
+		print(`//`);
+	}
+}
+
+main(arguments);

misc/sam2paf.js

@@ -1,114 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, pri_only = false;
-while ((c = getopt(arguments, "p")) != null)
-	if (c == 'p') pri_only = true;
-
-var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
-var buf = new Bytes();
-var re = /(\d+)([MIDSHNX=])/g;
-
-var len = {}, lineno = 0;
-while (file.readline(buf) >= 0) {
-	var m, n_cigar = 0, line = buf.toString();
-	++lineno;
-	if (line.charAt(0) == '@') {
-		if (/^@SQ/.test(line)) {
-			var name = (m = /\tSN:(\S+)/.exec(line)) != null? m[1] : null;
-			var l = (m = /\tLN:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
-			if (name != null && l != null) len[name] = l;
-		}
-		continue;
-	}
-	var t = line.split("\t");
-	var flag = parseInt(t[1]);
-	if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length) throw Error("ERROR at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
-	if (t[2] == '*' || (flag&4)) continue;
-	if (pri_only && (flag&0x100)) continue;
-	var tlen = len[t[2]];
-	if (tlen == null) throw Error("ERROR at line " + lineno + ": can't find the length of contig " + t[2]);
-	var nn = (m = /\tnn:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : 0;
-	var NM = (m = /\tNM:i:(\d+)/.exec(line)) != null? parseInt(m[1]) : null;
-	var have_NM = NM == null? false : true;
-	NM += nn;
-	var clip = [0, 0], I = [0, 0], D = [0, 0], M = 0, N = 0, ql = 0, tl = 0, mm = 0, ext_cigar = false;
-	while ((m = re.exec(t[5])) != null) {
-		var l = parseInt(m[1]);
-		if (m[2] == 'M') M += l, ql += l, tl += l, ext_cigar = false;
-		else if (m[2] == 'I') ++I[0], I[1] += l, ql += l;
-		else if (m[2] == 'D') ++D[0], D[1] += l, tl += l;
-		else if (m[2] == 'N') N += l, tl += l;
-		else if (m[2] == 'S') clip[M == 0? 0 : 1] = l, ql += l;
-		else if (m[2] == 'H') clip[M == 0? 0 : 1] = l;
-		else if (m[2] == '=') M += l, ql += l, tl += l, ext_cigar = true;
-		else if (m[2] == 'X') M += l, ql += l, tl += l, mm += l, ext_cigar = true;
-		++n_cigar;
-	}
-	if (n_cigar > 65535)
-		warn("WARNING at line " + lineno + ": " + n_cigar + " CIGAR operations");
-	if (tl + parseInt(t[3]) - 1 > tlen) {
-		warn("WARNING at line " + lineno + ": alignment end position larger than ref length; skipped");
-		continue;
-	}
-	if (t[9] != '*' && t[9].length != ql) {
-		warn("WARNING at line " + lineno + ": SEQ length inconsistent with CIGAR (" + t[9].length + " != " + ql + "); skipped");
-		continue;
-	}
-	if (!have_NM || ext_cigar) NM = I[1] + D[1] + mm;
-	if (NM < I[1] + D[1] + mm) {
-		warn("WARNING at line " + lineno + ": NM is less than the total number of gaps (" + NM + " < " + (I[1]+D[1]+mm) + ")");
-		NM = I[1] + D[1] + mm;
-	}
-	var extra = ["mm:i:"+(NM-I[1]-D[1]), "io:i:"+I[0], "in:i:"+I[1], "do:i:"+D[0], "dn:i:"+D[1]];
-	var match = M - (NM - I[1] - D[1]);
-	var blen = M + I[1] + D[1];
-	var qlen = M + I[1] + clip[0] + clip[1];
-	var qs, qe;
-	if (flag&16) qs = clip[1], qe = qlen - clip[0];
-	else qs = clip[0], qe = qlen - clip[1];
-	var ts = parseInt(t[3]) - 1, te = ts + M + D[1] + N;
-	var qname = t[0];
-	if ((flag&1) && (flag&0x40)) qname += '/1';
-	if ((flag&1) && (flag&0x80)) qname += '/2';
-	var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
-	print(a.join("\t"), extra.join("\t"));
-}
-
-buf.destroy();
-file.close();

misc/sim-eval.js

@@ -1,193 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.1, cap_short_mapq = false;
-while ((c = getopt(arguments, "Q:r:m:c")) != null) {
-	if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
-	else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
-	else if (c == 'm') mode = parseInt(getopt.arg);
-	else if (c == 'c') cap_short_mapq = true;
-}
-
-var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
-var buf = new Bytes();
-
-var tot = [], err = [];
-for (var q = 0; q <= max_mapq; ++q)
-	tot[q] = err[q] = 0;
-
-function is_correct(s, b)
-{
-	if (s[0] != b[0] || s[3] != b[3]) return false;
-	var o, l;
-	if (s[1] < b[1]) {
-		if (s[2] <= b[1]) return false;
-		o = (s[2] < b[2]? s[2] : b[2]) - b[1];
-		l = (s[2] > b[2]? s[2] : b[2]) - s[1];
-	} else {
-		if (b[2] <= s[1]) return false;
-		o = (s[2] < b[2]? s[2] : b[2]) - s[1];
-		l = (s[2] > b[2]? s[2] : b[2]) - b[1];
-	}
-	return o/l > ovlp_ratio? true : false;
-}
-
-function count_err(qname, a, tot, err, mode)
-{
-	if (a.length == 0) return;
-
-	var m, s;
-	if ((m = /^(\S+)!(\S+)!(\d+)!(\d+)!([\+\-])$/.exec(qname)) != null) { // pbsim single-end reads
-		s = [m[1], m[2], parseInt(m[3]), parseInt(m[4]), m[5]];
-	} else if ((m = /^(\S+)!(\S+)!(\d+)_(\d+)!(\d+)_(\d+)!([\+\-])([\+\-])\/([12])$/.exec(qname)) != null) { // mason2 paired-end reads
-		if (m[9] == '1') {
-			s = [m[1], m[2], parseInt(m[3]), parseInt(m[5]), m[7]];
-		} else {
-			s = [m[1], m[2], parseInt(m[4]), parseInt(m[6]), m[8]];
-		}
-	} else throw Error("Failed to parse simulated read names '" + qname + "'");
-	s.shift(); // skip the orginal read name
-
-	if (mode == 0 || mode == 1) { // longest only or first only
-		var max_i = 0;
-		if (mode == 0) { // longest only
-			var max = 0;
-			for (var i = 0; i < a.length; ++i)
-				if (a[i][5] > max)
-					max = a[i][5], max_i = i;
-		}
-		var mapq = a[max_i][4];
-		++tot[mapq];
-		if (!is_correct(s, a[max_i])) {
-			if (mapq >= err_out_q)
-				print('E', qname, a[max_i].join("\t"));
-			++err[mapq];
-		}
-	} else if (mode == 2) { // all primary mode
-		var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
-		if (cap_short_mapq) {
-			var max = 0, max_q = 0;
-			for (var i = 0; i < a.length; ++i)
-				if (a[i][5] > max)
-					max = a[i][5], max_q = a[i][4];
-			for (var i = 0; i < a.length; ++i)
-				a[i][4] = max_q < a[i][4]? max_q : a[i][4];
-		}
-		for (var i = 0; i < a.length; ++i) {
-			max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
-			if (!is_correct(s, a[i]))
-				if (a[i][4] > max_err_mapq)
-					max_err_mapq = a[i][4], max_err_i = i;
-		}
-		if (max_err_mapq >= 0) {
-			++tot[max_err_mapq], ++err[max_err_mapq];
-			if (max_err_mapq >= err_out_q)
-				print('E', qname, a[max_err_i].join("\t"));
-		} else ++tot[max_mapq];
-	}
-}
-
-var lineno = 0, last = null, a = [], n_unmapped = null;
-var re_cigar = /(\d+)([MIDSHN])/g;
-while (file.readline(buf) >= 0) {
-	var m, line = buf.toString();
-	++lineno;
-	if (line[0] != '@') {
-		var t = line.split("\t");
-		if (t[4] == '+' || t[4] == '-') { // PAF
-			if (last != t[0]) {
-				if (last != null) count_err(last, a, tot, err, mode);
-				a = [], last = t[0];
-			}
-			if (/\ts1:i:\d+/.test(line) && !/\ts2:i:\d+/.test(line)) // secondary alignment in minimap2 PAF
-				continue;
-			var mapq = parseInt(t[11]);
-			if (mapq > max_mapq) mapq = max_mapq;
-			a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
-		} else { // SAM
-			var flag = parseInt(t[1]);
-			var read_no = flag>>6&0x3;
-			var qname = t[0];
-			if (!/\/[12]$/.test(qname))
-				qname = read_no == 1 || read_no == 2? t[0] + '/' + read_no : t[0];
-			if (last != qname) {
-				if (last != null) count_err(last, a, tot, err, mode);
-				a = [], last = qname;
-			}
-			if (flag&0x100) continue; // secondary alignment
-			if ((flag&0x4) || t[2] == '*') { // unmapped
-				if (n_unmapped == null) n_unmapped = 0;
-				++n_unmapped;
-				continue;
-			}
-			var mapq = parseInt(t[4]);
-			if (mapq > max_mapq) mapq = max_mapq;
-			var pos = parseInt(t[3]) - 1, pos_end = pos;
-			var n_gap = 0, mlen = 0;
-			while ((m = re_cigar.exec(t[5])) != null) {
-				var len = parseInt(m[1]);
-				if (m[2] == 'M') pos_end += len, mlen += len;
-				else if (m[2] == 'I') n_gap += len;
-				else if (m[2] == 'D') n_gap += len, pos_end += len;
-			}
-			var score = pos_end - pos;
-			if ((m = /\tNM:i:(\d+)/.exec(line)) != null) {
-				var NM = parseInt(m[1]);
-				if (NM >= n_gap) score = mlen - (NM - n_gap);
-			}
-			a.push([t[2], pos, pos_end, (flag&16)? '-' : '+', mapq, score]);
-		}
-	}
-}
-if (last != null) count_err(last, a, tot, err, mode);
-
-buf.destroy();
-file.close();
-
-var sum_tot = 0, sum_err = 0, q_out = -1, sum_tot2 = 0, sum_err2 = 0;
-for (var q = max_mapq; q >= 0; --q) {
-	if (tot[q] == 0) continue;
-	if (q_out < 0 || err[q] > 0) {
-		if (q_out >= 0) print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
-		sum_tot = sum_err = 0, q_out = q;
-	}
-	sum_tot += tot[q], sum_err += err[q];
-	sum_tot2 += tot[q], sum_err2 += err[q];
-}
-print('Q', q_out, sum_tot, sum_err, (sum_err2/sum_tot2).toFixed(9), sum_tot2);
-if (n_unmapped != null) print('U', n_unmapped);

misc/sim-mason2.js

@@ -1,105 +0,0 @@
-Bytes.prototype.reverse = function()
-{
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[i];
-		this[i] = this[this.length - i - 1];
-		this[this.length - i - 1] = tmp;
-	}
-}
-
-// reverse complement a DNA string
-Bytes.prototype.revcomp = function()
-{
-	if (Bytes.rctab == null) {
-		var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
-		var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
-		Bytes.rctab = [];
-		for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
-		for (var i = 0; i < s1.length; ++i)
-			Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
-	}
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[this.length - i - 1];
-		this[this.length - i - 1] = Bytes.rctab[this[i]];
-		this[i] = Bytes.rctab[tmp];
-	}
-	if (this.length&1)
-		this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
-}
-
-if (arguments.length == 0) {
-	print("Usage: k8 sim-mason2.js <mason.sam>");
-	exit(1);
-}
-
-function print_se(a)
-{
-	print('@' + a.slice(0, 5).join("!") + " " + a[8]);
-	print(a[5]);
-	print("+");
-	print(a[6]);
-}
-
-var buf = new Bytes(), buf2 = new Bytes();
-var file = new File(arguments[0]);
-var re = /(\d+)([MIDSHN])/g;
-var last = null;
-while (file.readline(buf) >= 0) {
-	var t = buf.toString().split("\t");
-	if (t[0].charAt(0) == '@') continue;
-	var m, l_ref = 0;
-	while ((m = re.exec(t[5])) != null)
-		if (m[2] == 'D' || m[2] == 'M' || m[2] == 'N')
-			l_ref += parseInt(m[1]);
-	var flag = parseInt(t[1]);
-	var rev = !!(flag&16);
-	var seq, qual;
-	if (rev) {
-		buf2.length = 0;
-		buf2.set(t[9], 0);
-		buf2.revcomp();
-		seq = buf2.toString();
-		buf2.set(t[10], 0);
-		buf2.reverse();
-		qual = buf2.toString();
-	} else seq = t[9], qual = t[10];
-	var qname = t[0];
-	qname = qname.replace(/^simulated./, "");
-	var chr = t[2];
-	var pos = parseInt(t[3]) - 1;
-	var strand = (flag&16)? '-' : '+';
-	var read_no = flag&0xc0;
-	if (read_no == 0x40) read_no = 1;
-	else if (read_no == 0x80) read_no = 2;
-	else read_no = 0;
-	var err = 0, snp = 0, indel = 0;
-	for (var i = 11; i < t.length; ++i) {
-		if ((m = /^XE:i:(\d+)/.exec(t[i])) != null) err = m[1];
-		else if ((m = /^XS:i:(\d+)/.exec(t[i])) != null) snp = m[1];
-		else if ((m = /^XI:i:(\d+)/.exec(t[i])) != null) indel = m[1];
-	}
-	var comment = [err, snp, indel].join(":");
-	if (last == null) {
-		last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
-	} else if (last[0] != qname) {
-		print_se(last);
-		last = [qname, chr, pos, pos + l_ref, strand, seq, qual, read_no, comment];
-	} else {
-		if (read_no == 2) { // last[] is the first read
-			if (last[7] != 1) throw Error("ERROR: can't find read1");
-			var name = [qname, chr, last[2] + "_" + pos, last[3] + "_" + (pos + l_ref), last[4] + strand].join("!");
-			print('@' + name + '/1' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
-			print('@' + name + '/2' + ' ' + comment); print(seq); print("+"); print(qual);
-		} else {
-			if (last[7] != 2) throw Error("ERROR: can't find read2");
-			var name = [qname, chr, pos + "_" + last[2], (pos + l_ref) + "_" + last[3], strand + last[4]].join("!");
-			print('@' + name + '/1' + ' ' + comment); print(seq); print("+"); print(qual);
-			print('@' + name + '/2' + ' ' + last[8]); print(last[5]); print("+"); print(last[6]);
-		}
-		last = null;
-	}
-}
-if (last != null) print_se(last);
-file.close();
-buf.destroy();
-buf2.destroy();

misc/sim-pbsim.js

@@ -1,81 +0,0 @@
-Bytes.prototype.reverse = function()
-{
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[i];
-		this[i] = this[this.length - i - 1];
-		this[this.length - i - 1] = tmp;
-	}
-}
-
-// reverse complement a DNA string
-Bytes.prototype.revcomp = function()
-{
-	if (Bytes.rctab == null) {
-		var s1 = 'WSATUGCYRKMBDHVNwsatugcyrkmbdhvn';
-		var s2 = 'WSTAACGRYMKVHDBNwstaacgrymkvhdbn';
-		Bytes.rctab = [];
-		for (var i = 0; i < 256; ++i) Bytes.rctab[i] = 0;
-		for (var i = 0; i < s1.length; ++i)
-			Bytes.rctab[s1.charCodeAt(i)] = s2.charCodeAt(i);
-	}
-	for (var i = 0; i < this.length>>1; ++i) {
-		var tmp = this[this.length - i - 1];
-		this[this.length - i - 1] = Bytes.rctab[this[i]];
-		this[i] = Bytes.rctab[tmp];
-	}
-	if (this.length&1)
-		this[this.length>>1] = Bytes.rctab[this[this.length>>1]];
-}
-
-if (arguments.length < 2) {
-	print("Usage: k8 sim-pbsim.js <ref.fa.fai> <pbsim1.maf> [[pbsim2.maf] ...]");
-	exit(1);
-}
-
-var file, buf = new Bytes(), buf2 = new Bytes();
-file = new File(arguments[0]);
-var chr_list = [];
-while (file.readline(buf) >= 0) {
-	var t = buf.toString().split(/\s+/);
-	chr_list.push(t[0]);
-}
-file.close();
-
-for (var k = 1; k < arguments.length; ++k) {
-	var fn = arguments[k];
-	file = new File(fn);
-	var state = 0, reg;
-	while (file.readline(buf) >= 0) {
-		var line = buf.toString();
-		if (state == 0 && line.charAt(0) == 'a') {
-			state = 1;
-		} else if (state == 1 && line.charAt(0) == 's') {
-			var t = line.split(/\s+/);
-			var st = parseInt(t[2]);
-			reg = [st, st + parseInt(t[3])];
-			state = 2;
-		} else if (state == 2 && line.charAt(0) == 's') {
-			var m, t = line.split(/\s+/);
-			if ((m = /S(\d+)_\d+/.exec(t[1])) == null) throw Error("Failed to parse the read name");
-			var chr_id = parseInt(m[1]) - 1;
-			if (chr_id >= chr_list.length) throw Error("Index outside the chr list");
-			var name = [t[1], chr_list[chr_id], reg[0], reg[1], t[4]].join("!");
-			var seq = t[6].replace(/\-/g, "");
-			if (seq.length != parseInt(t[5])) throw Error("Inconsistent read length");
-			if (seq.indexOf("NN") < 0) {
-				if (t[4] == '-') {
-					buf2.set(seq, 0);
-					buf2.length = seq.length;
-					buf2.revcomp();
-					seq = buf2.toString();
-				}
-				print(">" + name);
-				print(seq);
-			}
-			state = 0;
-		}
-	}
-	file.close();
-}
-buf.destroy();
-buf2.destroy();

misc/splice2bed.js

@@ -1,148 +0,0 @@
-var getopt = function(args, ostr) {
-	var oli; // option letter list index
-	if (typeof(getopt.place) == 'undefined')
-		getopt.ind = 0, getopt.arg = null, getopt.place = -1;
-	if (getopt.place == -1) { // update scanning pointer
-		if (getopt.ind >= args.length || args[getopt.ind].charAt(getopt.place = 0) != '-') {
-			getopt.place = -1;
-			return null;
-		}
-		if (getopt.place + 1 < args[getopt.ind].length && args[getopt.ind].charAt(++getopt.place) == '-') { // found "--"
-			++getopt.ind;
-			getopt.place = -1;
-			return null;
-		}
-	}
-	var optopt = args[getopt.ind].charAt(getopt.place++); // character checked for validity
-	if (optopt == ':' || (oli = ostr.indexOf(optopt)) < 0) {
-		if (optopt == '-') return null; //  if the user didn't specify '-' as an option, assume it means null.
-		if (getopt.place < 0) ++getopt.ind;
-		return '?';
-	}
-	if (oli+1 >= ostr.length || ostr.charAt(++oli) != ':') { // don't need argument
-		getopt.arg = null;
-		if (getopt.place < 0 || getopt.place >= args[getopt.ind].length) ++getopt.ind, getopt.place = -1;
-	} else { // need an argument
-		if (getopt.place >= 0 && getopt.place < args[getopt.ind].length)
-			getopt.arg = args[getopt.ind].substr(getopt.place);
-		else if (args.length <= ++getopt.ind) { // no arg
-			getopt.place = -1;
-			if (ostr.length > 0 && ostr.charAt(0) == ':') return ':';
-			return '?';
-		} else getopt.arg = args[getopt.ind]; // white space
-		getopt.place = -1;
-		++getopt.ind;
-	}
-	return optopt;
-}
-
-var colors = ["0,128,255", "255,0,0", "0,192,0"];
-
-function print_lines(a, fmt) {
-	if (a.length == 0) return;
-	if (fmt == "bed") {
-		var n_pri = 0;
-		for (var i = 0; i < a.length; ++i)
-			if (a[i][8] == 0) ++n_pri;
-		if (n_pri > 1) {
-			for (var i = 0; i < a.length; ++i)
-				if (a[i][8] == 0) a[i][8] = 1;
-		} else if (n_pri == 0) {
-			warn("Warning: " + a[0][3] + " doesn't have a primary alignment");
-		}
-		for (var i = 0; i < a.length; ++i) {
-			a[i][8] = colors[a[i][8]];
-			print(a[i].join("\t"));
-		}
-	}
-	a.length = 0;
-}
-
-function main(args) {
-	var re = /(\d+)([MIDNSH])/g;
-	var c, fmt = "bed", fn_name_conv = null;
-	while ((c = getopt(args, "f:n:")) != null) {
-		if (c == 'f') fmt = getopt.arg;
-		else if (c == 'n') fn_name_conv = getopt.arg;
-	}
-	if (getopt.ind == args.length) {
-		warn("Usage: k8 splice2bed.js <in.paf>");
-		exit(1);
-	}
-
-	var conv = null;
-	if (fn_name_conv != null) {
-		conv = new Map();
-		var file = new File(fn_name_conv);
-		var buf = new Bytes();
-		while (file.readline(buf) >= 0) {
-			var t = buf.toString().split("\t");
-			conv.put(t[0], t[1]);
-		}
-		buf.destroy();
-		file.close();
-	}
-
-	var file = new File(args[getopt.ind]);
-	var buf = new Bytes();
-	var a = [];
-	while (file.readline(buf) >= 0) {
-		var line = buf.toString();
-		if (line.charAt(0) == '@') continue; // skip SAM header lines
-		var t = line.split("\t");
-		var is_pri = false, cigar = null, a1;
-		var qname = conv != null? conv.get(t[0]) : null;
-		if (qname != null) t[0] = qname;
-		if (t.length >= 10 && t[4] != '+' && t[4] != '-' && /^\d+/.test(t[1])) { // SAM
-			var flag = parseInt(t[1]);
-			if (flag&1) t[0] += '/' + (flag>>6&3);
-		}
-		if (a.length && a[0][3] != t[0]) {
-			print_lines(a, fmt);
-			a = [];
-		}
-		if (t.length >= 12 && (t[4] == '+' || t[4] == '-')) { // PAF
-			for (var i = 12; i < t.length; ++i) {
-				if (t[i].substr(0, 5) == 'cg:Z:') {
-					cigar = t[i].substr(5);
-				} else if (t[i].substr(0, 5) == 's2:i:') {
-					is_pri = true;
-				}
-			}
-			a1 = [t[5], t[7], t[8], t[0], Math.floor(t[9]/t[10]*1000), t[4]];
-		} else if (t.length >= 10) { // SAM
-			var flag = parseInt(t[1]);
-			if ((flag&4) || a[2] == '*') continue;
-			cigar = t[5];
-			is_pri = (flag&0x100)? false : true;
-			a1 = [t[2], parseInt(t[3])-1, null, t[0], 1000, (flag&16)? '-' : '+'];
-		} else {
-			throw Error("unrecognized input format");
-		}
-		if (cigar == null) throw Error("missing CIGAR");
-		var m, x0 = 0, x = 0, bs = [], bl = [];
-		while ((m = re.exec(cigar)) != null) {
-			if (m[2] == 'M' || m[2] == 'D') {
-				x += parseInt(m[1]);
-			} else if (m[2] == 'N') {
-				bs.push(x0);
-				bl.push(x - x0);
-				x += parseInt(m[1]);
-				x0 = x;
-			}
-		}
-		bs.push(x0);
-		bl.push(x - x0);
-		// write the BED12 line
-		if (a1[2] == null) a1[2] = a1[1] + x;
-		a1.push(a1[1], a1[2]); // thick start/end is the same as start/end
-		a1.push(is_pri? 0 : 2, bs.length, bl.join(",")+",", bs.join(",")+",");
-		a.push(a1);
-	}
-	print_lines(a, fmt);
-	buf.destroy();
-	file.close();
-	if (conv != null) conv.destroy();
-}
-
-main(arguments);

mmpriv.h

@@ -4,6 +4,7 @@
 #include <assert.h>
 #include "minimap.h"
 #include "bseq.h"
+#include "kseq.h"
 
 #define MM_PARENT_UNSET   (-1)
 #define MM_PARENT_TMP_PRI (-2)
@@ -12,14 +13,20 @@
 #define MM_DBG_PRINT_QNAME   0x2
 #define MM_DBG_PRINT_SEED    0x4
 #define MM_DBG_PRINT_ALN_SEQ 0x8
+#define MM_DBG_PRINT_CHAIN   0x10
+#define MM_DBG_SEED_FREQ     0x20
 
 #define MM_SEED_LONG_JOIN  (1ULL<<40)
 #define MM_SEED_IGNORE     (1ULL<<41)
 #define MM_SEED_TANDEM     (1ULL<<42)
+#define MM_SEED_SELF       (1ULL<<43)
 
 #define MM_SEED_SEG_SHIFT  48
 #define MM_SEED_SEG_MASK   (0xffULL<<(MM_SEED_SEG_SHIFT))
 
+#define MM_JUNC_ANNO 0x1
+#define MM_JUNC_MISC 0x2
+
 #ifndef kroundup32
 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
 #endif
@@ -27,17 +34,21 @@
 #define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
 #define mm_seq4_get(s, i)    ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
 
+#define MALLOC(type, len) ((type*)malloc((len) * sizeof(type)))
+#define CALLOC(type, len) ((type*)calloc((len), sizeof(type)))
+#define REALLOC(type, ptr, cnt) ((type*)realloc((ptr), (cnt) * sizeof(type)))
+
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
-	unsigned l, m;
-	char *s;
-} kstring_t;
-#endif
+typedef struct {
+	uint32_t n;
+	uint32_t q_pos;
+	uint32_t q_span:31, flt:1;
+	uint32_t seg_id:31, is_tandem:1;
+	const uint64_t *cr;
+} mm_seed_t;
 
 typedef struct {
 	int n_u, n_a;
@@ -45,8 +56,15 @@ typedef struct {
 	mm128_t *a;
 } mm_seg_t;
 
+typedef struct {
+	int32_t off, off2, cnt;
+	int16_t strand;
+	uint16_t flag;
+} mm_idx_jjump1_t;
+
 double cputime(void);
 double realtime(void);
+long peakrss(void);
 
 void radix_sort_128x(mm128_t *beg, mm128_t *end);
 void radix_sort_64(uint64_t *beg, uint64_t *end);
@@ -54,30 +72,52 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
 void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
 
-void mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
-void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag);
-void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
-void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km, int opt_flag);
+mm_seed_t *mm_collect_matches(void *km, int *_n_m, int qlen, int max_occ, int max_max_occ, int dist, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos);
+void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac);
 
+double mm_event_identity(const mm_reg1_t *r);
+int mm_write_sam_hdr(const mm_idx_t *mi, const char *rg, const char *ver, int argc, char *argv[]);
+void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag);
+void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag, int rep_len);
+void mm_write_paf4(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int64_t opt_flag, int rep_len, int n_seg, int seg_idx);
+void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs);
+void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regs, const mm_reg1_t *const* regs, void *km, int64_t opt_flag);
+void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int seg_idx, int reg_idx, int n_seg, const int *n_regss, const mm_reg1_t *const* regss, void *km, int64_t opt_flag, int rep_len);
+void mm_write_junc(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r);
+
+// indexing related in index.c
 void mm_idxopt_init(mm_idxopt_t *opt);
 const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
-int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
 int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
-mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
-mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
+int mm_idx_getseq2(const mm_idx_t *mi, int is_rev, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
+mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a, int is_qstrand);
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
+int mm_idx_jjump_read(mm_idx_t *mi, const char *fn, int flag, int min_sc);
+const mm_idx_jjump1_t *mm_idx_jump_get(const mm_idx_t *db, int32_t cid, int32_t st, int32_t en, int32_t *n);
 
-mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a);
-void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
+// chaining in lchain.c
+mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
+					  int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
+mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
+					   int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
+
+void mm_mark_alt(const mm_idx_t *mi, int n, mm_reg1_t *r);
+void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a, int is_qstrand);
 void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
 int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a);
 int mm_set_sam_pri(int n, mm_reg1_t *r);
-void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff);
-void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
+void mm_set_parent(void *km, float mask_level, int mask_len, int n, mm_reg1_t *r, int sub_diff, int hard_mask_level, float alt_diff_frac);
+void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int check_strand, int min_strand_sc, int *n_, mm_reg1_t *r);
 void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
-void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
-void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
-void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);
-void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);
+int mm_filter_strand_retained(int n_regs, mm_reg1_t *r);
+void mm_filter_regs(const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);
+void mm_hit_sort(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac);
+void mm_set_mapq2(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr, int is_splice);
+void mm_update_dp_max(int qlen, int n_regs, mm_reg1_t *regs, float frac, int a, int b);
+void mm_jump_split(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq, mm_reg1_t *r, int32_t ts_strand);
+
+mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
+void mm_enlarge_cigar(mm_reg1_t *r, uint32_t n_cigar);
 
 void mm_est_err(const mm_idx_t *mi, int qlen, int n_regs, mm_reg1_t *regs, const mm128_t *a, int32_t n, const uint64_t *mini_pos);
 
@@ -85,6 +125,27 @@ mm_seg_t *mm_seg_gen(void *km, uint32_t hash, int n_segs, const int *qlens, int
 void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
 void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
 
+void mm_jump_split(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq, mm_reg1_t *r, int32_t ts_strand);
+
+FILE *mm_split_init(const char *prefix, const mm_idx_t *mi);
+mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part);
+int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx);
+void mm_split_rm_tmp(const char *prefix, int n_splits);
+
+void mm_err_puts(const char *str);
+void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp);
+void mm_err_fread(void *p, size_t size, size_t nitems, FILE *fp);
+
+static inline float mg_log2(float x) // NB: this doesn't work when x<2
+{
+	union { float f; uint32_t i; } z = { x };
+	float log_2 = ((z.i >> 23) & 255) - 128;
+	z.i &= ~(255 << 23);
+	z.i += 127 << 23;
+	log_2 += (-0.34484843f * z.f + 2.02466578f) * z.f - 0.67487759f;
+	return log_2;
+}
+
 #ifdef __cplusplus
 }
 #endif

options.c

@@ -0,0 +1,277 @@
+#include <stdio.h>
+#include <limits.h>
+#include "mmpriv.h"
+
+void mm_idxopt_init(mm_idxopt_t *opt)
+{
+	memset(opt, 0, sizeof(mm_idxopt_t));
+	opt->k = 15, opt->w = 10, opt->flag = 0;
+	opt->bucket_bits = 14;
+	opt->mini_batch_size = 50000000;
+	opt->batch_size = 8000000000ULL;
+}
+
+void mm_mapopt_init(mm_mapopt_t *opt)
+{
+	memset(opt, 0, sizeof(mm_mapopt_t));
+	opt->seed = 11;
+	opt->mid_occ_frac = 2e-4f;
+	opt->min_mid_occ = 10;
+	opt->max_mid_occ = 1000000;
+	opt->sdust_thres = 0; // no SDUST masking
+	opt->q_occ_frac = 0.01f;
+
+	opt->min_cnt = 3;
+	opt->min_chain_score = 40;
+	opt->bw = 500, opt->bw_long = 20000;
+	opt->max_gap = 5000;
+	opt->max_gap_ref = -1;
+	opt->max_chain_skip = 25;
+	opt->max_chain_iter = 5000;
+	opt->rmq_inner_dist = 1000;
+	opt->rmq_size_cap = 100000;
+	opt->rmq_rescue_size = 1000;
+	opt->rmq_rescue_ratio = 0.1f;
+	opt->chain_gap_scale = 0.8f;
+	opt->chain_skip_scale = 0.0f;
+	opt->max_max_occ = 4095;
+	opt->occ_dist = 500;
+
+	opt->mask_level = 0.5f;
+	opt->mask_len = INT_MAX;
+	opt->pri_ratio = 0.8f;
+	opt->best_n = 5;
+
+	opt->alt_drop = 0.15f;
+
+	opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
+	opt->transition = 0;
+	opt->sc_ambi = 1;
+	opt->zdrop = 400, opt->zdrop_inv = 200;
+	opt->end_bonus = -1;
+	opt->min_dp_max = opt->min_chain_score * opt->a;
+	opt->min_ksw_len = 200;
+	opt->anchor_ext_len = 20, opt->anchor_ext_shift = 6;
+	opt->max_clip_ratio = 1.0f;
+	opt->mini_batch_size = 500000000;
+	opt->max_sw_mat = 100000000;
+	opt->cap_kalloc = 500000000;
+
+	opt->rank_min_len = 500;
+	opt->rank_frac = 0.9f;
+
+	opt->pe_ori = 0; // FF
+	opt->pe_bonus = 33;
+
+	opt->jump_min_match = 3;
+}
+
+void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
+{
+	if ((opt->flag & MM_F_SPLICE_FOR) || (opt->flag & MM_F_SPLICE_REV))
+		opt->flag |= MM_F_SPLICE;
+	if (opt->mid_occ <= 0) {
+		opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
+		if (opt->mid_occ < opt->min_mid_occ)
+			opt->mid_occ = opt->min_mid_occ;
+		if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
+			opt->mid_occ = opt->max_mid_occ;
+	}
+	if (opt->bw_long < opt->bw) opt->bw_long = opt->bw;
+	if (mm_verbose >= 3)
+		fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
+}
+
+void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len)
+{
+	if ((opt->flag & MM_F_SPLICE) && max_intron_len > 0)
+		opt->max_gap_ref = opt->bw = opt->bw_long = max_intron_len;
+}
+
+int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
+{
+	if (preset == 0) {
+		mm_idxopt_init(io);
+		mm_mapopt_init(mo);
+	} else if (strcmp(preset, "lr") == 0 || strcmp(preset, "map-ont") == 0) { // this is the same as the default
+	} else if (strcmp(preset, "ava-ont") == 0) {
+		io->flag = 0, io->k = 15, io->w = 5;
+		mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
+		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_chain_skip = 25;
+		mo->bw = mo->bw_long = 2000;
+		mo->occ_dist = 0;
+	} else if (strcmp(preset, "map10k") == 0 || strcmp(preset, "map-pb") == 0) {
+		io->flag |= MM_I_HPC, io->k = 19;
+	} else if (strcmp(preset, "ava-pb") == 0) {
+		io->flag |= MM_I_HPC, io->k = 19, io->w = 5;
+		mo->flag |= MM_F_ALL_CHAINS | MM_F_NO_DIAG | MM_F_NO_DUAL | MM_F_NO_LJOIN;
+		mo->min_chain_score = 100, mo->pri_ratio = 0.0f, mo->max_chain_skip = 25;
+		mo->bw_long = mo->bw;
+		mo->occ_dist = 0;
+	} else if (strcmp(preset, "lr:hq") == 0 || strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
+		io->flag = 0, io->k = 19, io->w = 19;
+		mo->max_gap = 10000;
+		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
+		if (strcmp(preset, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 0) {
+			mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
+			mo->min_dp_max = 200;
+		}
+	} else if (strcmp(preset, "lr:hqae") == 0) { // high-quality assembly evaluation
+		io->flag = 0, io->k = 25, io->w = 51;
+		mo->flag |= MM_F_RMQ;
+		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
+		mo->rmq_inner_dist = 5000;
+		mo->occ_dist = 200;
+		mo->best_n = 100;
+		mo->chain_gap_scale = 5.0f;
+	} else if (strcmp(preset, "map-iclr-prerender") == 0) {
+		io->flag = 0, io->k = 15;
+		mo->b = 6, mo->transition = 1;
+		mo->q = 10, mo->q2 = 50;
+	} else if (strcmp(preset, "map-iclr") == 0) {
+		io->flag = 0, io->k = 19;
+		mo->b = 6, mo->transition = 4;
+		mo->q = 10, mo->q2 = 50;
+	} else if (strncmp(preset, "asm", 3) == 0) {
+		io->flag = 0, io->k = 19, io->w = 19;
+		mo->bw = 1000, mo->bw_long = 100000;
+		mo->max_gap = 10000;
+		mo->flag |= MM_F_RMQ;
+		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
+		mo->min_dp_max = 200;
+		mo->best_n = 50;
+		if (strcmp(preset, "asm5") == 0) {
+			mo->a = 1, mo->b = 19, mo->q = 39, mo->q2 = 81, mo->e = 3, mo->e2 = 1, mo->zdrop = mo->zdrop_inv = 200;
+		} else if (strcmp(preset, "asm10") == 0) {
+			mo->a = 1, mo->b = 9, mo->q = 16, mo->q2 = 41, mo->e = 2, mo->e2 = 1, mo->zdrop = mo->zdrop_inv = 200;
+		} else if (strcmp(preset, "asm20") == 0) {
+			mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1, mo->zdrop = mo->zdrop_inv = 200;
+			io->w = 10;
+		} else return -1;
+	} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
+		io->flag = 0, io->k = 21, io->w = 11;
+		mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT;
+		mo->pe_ori = 0<<1|1; // FR
+		mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 24, mo->e2 = 1;
+		mo->zdrop = mo->zdrop_inv = 100;
+		mo->end_bonus = 10;
+		mo->max_frag_len = 800;
+		mo->max_gap = 100;
+		mo->bw = mo->bw_long = 100;
+		mo->pri_ratio = 0.5f;
+		mo->min_cnt = 2;
+		mo->min_chain_score = 25;
+		mo->min_dp_max = 40;
+		mo->best_n = 20;
+		mo->mid_occ = 1000;
+		mo->max_occ = 5000;
+		mo->mini_batch_size = 50000000;
+	} else if (strcmp(preset, "splice") == 0 || strcmp(preset, "splice:hq") == 0 || strcmp(preset, "splice:sr") == 0 || strcmp(preset, "cdna") == 0) {
+		io->flag = 0, io->k = 15, io->w = 5;
+		mo->flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV | MM_F_SPLICE_FLANK;
+		mo->max_sw_mat = 0;
+		mo->max_gap = 2000, mo->max_gap_ref = mo->bw = mo->bw_long = 200000;
+		mo->a = 1, mo->b = 2, mo->q = 2, mo->e = 1, mo->q2 = 32, mo->e2 = 0;
+		mo->noncan = 9;
+		mo->junc_bonus = 9;
+		mo->junc_pen = 5;
+		mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved
+		if (strcmp(preset, "splice:hq") == 0) {
+			mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
+		} else if (strcmp(preset, "splice:sr") == 0) {
+			mo->flag |= MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT | MM_F_FRAG_MODE | MM_F_WEAK_PAIRING | MM_F_SR_RNA;
+			mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
+			mo->min_chain_score = 25;
+			mo->min_dp_max = 40;
+			mo->min_ksw_len = 20;
+			mo->pe_ori = 0<<1|1; // FR
+			mo->best_n = 10;
+			mo->mini_batch_size = 100000000;
+		}
+	} else return -1;
+	return 0;
+}
+
+int mm_max_spsc_bonus(const mm_mapopt_t *mo)
+{
+	int max_sc = (mo->q2 + 1) / 2 - 1;
+	max_sc = max_sc > mo->q2 - mo->q? max_sc : mo->q2 - mo->q;
+	return max_sc;
+}
+
+int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
+{
+	if (mo->bw > mo->bw_long) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m with '-rNUM1,NUM2', NUM1 (%d) can't be larger than NUM2 (%d)\033[0m\n", mo->bw, mo->bw_long);
+		return -8;
+	}
+	if ((mo->flag & MM_F_RMQ) && (mo->flag & (MM_F_SR|MM_F_SPLICE))) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m --rmq doesn't work with --sr or --splice\033[0m\n");
+		return -7;
+	}
+	if (mo->split_prefix && (mo->flag & (MM_F_OUT_CS|MM_F_OUT_MD))) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m --cs or --MD doesn't work with --split-prefix\033[0m\n");
+		return -6;
+	}
+	if (io->k <= 0 || io->w <= 0) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -k and -w must be positive\033[0m\n");
+		return -5;
+	}
+	if (mo->best_n < 0) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -N must be no less than 0\033[0m\n");
+		return -4;
+	}
+	if (mo->best_n == 0 && mm_verbose >= 2)
+		fprintf(stderr, "[WARNING]\033[1;31m '-N 0' reduces mapping accuracy. Please use '--secondary=no' instead.\033[0m\n");
+	if (mo->pri_ratio < 0.0f || mo->pri_ratio > 1.0f) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -p must be within 0 and 1 (including 0 and 1)\033[0m\n");
+		return -4;
+	}
+	if ((mo->flag & MM_F_FOR_ONLY) && (mo->flag & MM_F_REV_ONLY)) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m --for-only and --rev-only can't be applied at the same time\033[0m\n");
+		return -3;
+	}
+	if (mo->e <= 0 || mo->q <= 0) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -O and -E must be positive\033[0m\n");
+		return -1;
+	}
+	if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");
+		return -2;
+	}
+	if ((mo->q + mo->e) + (mo->q2 + mo->e2) > 127) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m scoring system violating ({-O}+{-E})+({-O2}+{-E2}) <= 127\033[0m\n");
+		return -1;
+	}
+	if (mo->sc_ambi < 0 || mo->sc_ambi >= mo->b) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m --score-N should be within [0,{-B})\033[0m\n");
+		return -1;
+	}
+	if (mo->zdrop < mo->zdrop_inv) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m Z-drop should not be less than inversion-Z-drop\033[0m\n");
+		return -5;
+	}
+	if ((mo->flag & MM_F_NO_PRINT_2ND) && (mo->flag & MM_F_ALL_CHAINS)) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -X/-P and --secondary=no can't be applied at the same time\033[0m\n");
+		return -5;
+	}
+	if ((mo->flag & MM_F_QSTRAND) && ((mo->flag & (MM_F_OUT_SAM|MM_F_SPLICE|MM_F_FRAG_MODE)) || (io->flag & MM_I_HPC))) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m --qstrand doesn't work with -a, -H, --frag or --splice\033[0m\n");
+		return -5;
+	}
+	return 0;
+}

pe.c

@@ -8,7 +8,8 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
 	if (pri_ratio > 0.0f && *n_ > 0) {
 		int i, k, n = *n_, n_2nd = 0;
 		int max_dist = n_segs == 2? qlens[0] + qlens[1] + max_gap_ref : 0;
-		for (i = k = 0; i < n; ++i) {
+		uint8_t *keep = (uint8_t*)kmalloc(km, n);
+		for (i = 0; i < n; ++i) {
 			int to_keep = 0;
 			if (r[i].parent == i) { // primary
 				to_keep = 1;
@@ -34,9 +35,13 @@ void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int
 			if (to_keep && r[i].parent != i) {
 				if (n_2nd++ >= best_n) to_keep = 0; // don't keep if there are too many secondary hits
 			}
-			if (to_keep) r[k++] = r[i];
+			keep[i] = to_keep;
+		}
+		for (i = k = 0; i < n; ++i) {
+			if (keep[i]) r[k++] = r[i];
 			else if (r[i].p) free(r[i].p);
 		}
+		kfree(km, keep);
 		if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
 		*n_ = k;
 	}
@@ -54,7 +59,7 @@ void mm_set_pe_thru(const int *qlens, int *n_regs, mm_reg1_t **regs)
 	if (n_pri[0] == 1 && n_pri[1] == 1) {
 		mm_reg1_t *p = &regs[0][pri[0]];
 		mm_reg1_t *q = &regs[1][pri[1]];
-		if (p->rid == q->rid && p->rev == q->rev && abs(p->rs - q->rs) < 3 && abs(p->re - p->re) < 3
+		if (p->rid == q->rid && p->rev == q->rev && abs(p->rs - q->rs) < 3 && abs(p->re - q->re) < 3
 			&& ((p->qs == 0 && qlens[1] - q->qe == 0) || (q->qs == 0 && qlens[0] - p->qe == 0)))
 		{
 			p->pe_thru = q->pe_thru = 1;
@@ -105,7 +110,7 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 	max = -1;
 	max_idx[0] = max_idx[1] = -1;
 	last[0] = last[1] = -1;
-	kv_resize(uint64_t, km, sc, n);
+	kv_resize(uint64_t, km, sc, (size_t)n);
 	for (i = 0; i < n; ++i) {
 		if (a[i].key & 1) { // reverse first read or forward second read
 			mm_reg1_t *q, *r;
@@ -151,8 +156,8 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 			}
 		}
 		mapq_pe = r[0]->mapq > r[1]->mapq? r[0]->mapq : r[1]->mapq;
-		for (i = 0; i < sc.n; ++i)
-			if ((sc.a[i]>>32) + sub_diff >= max>>32)
+		for (i = 0; i < (int)sc.n; ++i)
+			if ((sc.a[i]>>32) + sub_diff >= (uint64_t)max>>32)
 				++n_sub;
 		if (sc.n > 1) {
 			int mapq_pe_alt;
@@ -164,7 +169,7 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
 		if (sc.n == 1) {
 			if (r[0]->mapq < 2) r[0]->mapq = 2;
 			if (r[1]->mapq < 2) r[1]->mapq = 2;
-		} else if (max>>32 > sc.a[sc.n - 2]>>32) {
+		} else if ((uint64_t)max>>32 > sc.a[sc.n - 2]>>32) {
 			if (r[0]->mapq < 1) r[0]->mapq = 1;
 			if (r[1]->mapq < 1) r[1]->mapq = 1;
 		}

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython"]

python/README.rst

@@ -34,6 +34,8 @@ The following Python script demonstrates the key functionality of mappy:
 	import mappy as mp
 	a = mp.Aligner("test/MT-human.fa")  # load or build index
 	if not a: raise Exception("ERROR: failed to load/build index")
+	s = a.seq("MT_human", 100, 200)     # retrieve a subsequence from the index
+	print(mp.revcomp(s))                # reverse complement
 	for name, seq, qual in mp.fastx_read("test/MT-orang.fa"): # read a fasta/q sequence
 		for hit in a.map(seq): # traverse alignments
 			print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
@@ -41,20 +43,24 @@ The following Python script demonstrates the key functionality of mappy:
 APIs
 ----
 
-Mappy implements two classes and one global function.
+Mappy implements two classes and two global function.
 
 Class mappy.Aligner
 ~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
-	mappy.Aligner(fn_idx_in, preset=None, ...)
+	mappy.Aligner(fn_idx_in=None, preset=None, ...)
 
 This constructor accepts the following arguments:
 
 * **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the
   file type. If a sequence file is provided, minimap2 builds an index. The
-  sequence file can be optionally gzip'd.
+  sequence file can be optionally gzip'd. This option has no effect if **seq**
+  is set.
+
+* **seq**: a single sequence to index. The sequence name will be set to
+  :code:`N/A`.
 
 * **preset**: minimap2 preset. Currently, minimap2 supports the following
   presets: **sr** for single-end short reads; **map-pb** for PacBio
@@ -71,20 +77,50 @@ This constructor accepts the following arguments:
 
 * **min_chain_score**: minimum chaing score
 
-* **bw**: chaining and alignment band width
+* **bw**: chaining and alignment band width (initial chaining and extension)
+
+* **bw_long**: chaining and alignment band width (RMQ-based rechaining and closing gaps)
 
 * **best_n**: max number of alignments to return
 
 * **n_threads**: number of indexing threads; 3 by default
 
-* **fn_idx_out**: name of file to which the index is written
+* **extra_flags**: additional flags defined in minimap.h
+
+* **fn_idx_out**: name of file to which the index is written. This parameter
+  has no effect if **seq** is set.
+
+* **scoring**: scoring system. It is a tuple/list consisting of 4, 6 or 7
+  positive integers. The first 4 elements specify match scoring, mismatch
+  penalty, gap open and gap extension penalty. The 5th and 6th elements, if
+  present, set long-gap open and long-gap extension penalty. The 7th sets a
+  mismatch penalty involving ambiguous bases.
 
 .. code:: python
 
-	mappy.Aligner.map(seq)
+	mappy.Aligner.map(seq, seq2=None, cs=False, MD=False)
 
 This method aligns :code:`seq` against the index. It is a generator, *yielding*
-a series of :code:`mappy.Alignment` objects.
+a series of :code:`mappy.Alignment` objects. If :code:`seq2` is present, mappy
+performs paired-end alignment, assuming the two ends are in the FR orientation.
+Alignments of the two ends can be distinguished by the :code:`read_num` field
+(see Class mappy.Alignment below). Argument :code:`cs` asks mappy to generate
+the :code:`cs` tag; :code:`MD` is similar. These two arguments might slightly
+degrade performance and are not enabled by default.
+
+.. code:: python
+
+	mappy.Aligner.seq(name, start=0, end=0x7fffffff)
+
+This method retrieves a (sub)sequence from the index and returns it as a Python
+string. :code:`None` is returned if :code:`name` is not present in the index or
+the start/end coordinates are invalid.
+
+.. code:: python
+
+	mappy.Aligner.seq_names
+
+This property gives the array of sequence names in the index.
 
 Class mappy.Alignment
 ~~~~~~~~~~~~~~~~~~~~~
@@ -110,7 +146,7 @@ properties:
 * **mlen**: length of the matching bases in the alignment, excluding ambiguous
   base matches.
 
-* **NM**: number of mismatches, gaps and ambiguous poistions in the alignment
+* **NM**: number of mismatches, gaps and ambiguous positions in the alignment
 
 * **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
   reverse strand; 0 if unknown
@@ -118,11 +154,19 @@ properties:
 * **is_primary**: if the alignment is primary (typically the best and the first
   to generate)
 
+* **read_num**: read number that the alignment corresponds to; 1 for the first
+  read and 2 for the second read
+
 * **cigar_str**: CIGAR string
 
 * **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
   numbers give the length and the operator of each CIGAR operation.
 
+* **MD**: the :code:`MD` tag as in the SAM format. It is an empty string unless
+  the :code:`MD` argument is applied when calling :code:`mappy.Aligner.map()`.
+
+* **cs**: the :code:`cs` tag.
+
 An :code:`Alignment` object can be converted to a string with :code:`str()` in
 the following format:
 
@@ -133,13 +177,22 @@ the following format:
 It is effectively the PAF format without the QueryName and QueryLength columns
 (the first two columns in PAF).
 
-Function mappy.fastx_read
-~~~~~~~~~~~~~~~~~~~~~~~~~
+Miscellaneous Functions
+~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code:: python
 
-	mappy.fastx_read(fn)
+	mappy.fastx_read(fn, read_comment=False)
 
 This generator function opens a FASTA/FASTQ file and *yields* a
 :code:`(name,seq,qual)` tuple for each sequence entry. The input file may be
-optionally gzip'd.
+optionally gzip'd. If :code:`read_comment` is True, this generator yields
+a :code:`(name,seq,qual,comment)` tuple instead.
+
+.. code:: python
+
+	mappy.revcomp(seq)
+
+Return the reverse complement of DNA string :code:`seq`. This function
+recognizes IUB code and preserves the letter cases. Uracil :code:`U` is
+complemented to :code:`A`.

python/cmappy.h

@@ -15,6 +15,7 @@ typedef struct {
 	int32_t blen, mlen, NM, ctg_len;
 	uint8_t mapq, is_primary;
 	int8_t strand, trans_strand;
+	int32_t seg_id;
 	int32_t n_cigar32;
 	uint32_t *cigar32;
 } mm_hitpy_t;
@@ -32,6 +33,7 @@ static inline void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
 	h->NM = r->blen - r->mlen + r->p->n_ambi;
 	h->trans_strand = r->p->trans_strand == 1? 1 : r->p->trans_strand == 2? -1 : 0;
 	h->is_primary = (r->id == r->parent);
+	h->seg_id = r->seg_id;
 	h->n_cigar32 = r->p->n_cigar;
 	h->cigar32 = r->p->cigar;
 }
@@ -68,4 +70,83 @@ static inline void mm_reset_timer(void)
 	mm_realtime0 = realtime();
 }
 
+extern unsigned char seq_comp_table[256];
+static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char* seqname, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
+{
+	mm_reg1_t *r;
+
+	Py_BEGIN_ALLOW_THREADS
+	if (seq2 == 0) {
+		r = mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, seqname);
+	} else {
+		int _n_regs[2];
+		mm_reg1_t *regs[2];
+		char *seq[2];
+		int i, len[2];
+
+		len[0] = strlen(seq1);
+		len[1] = strlen(seq2);
+		seq[0] = (char*)seq1;
+		seq[1] = strdup(seq2);
+		for (i = 0; i < len[1]>>1; ++i) {
+			int t = seq[1][len[1] - i - 1];
+			seq[1][len[1] - i - 1] = seq_comp_table[(uint8_t)seq[1][i]];
+			seq[1][i] = seq_comp_table[t];
+		}
+		if (len[1]&1) seq[1][len[1]>>1] = seq_comp_table[(uint8_t)seq[1][len[1]>>1]];
+		mm_map_frag(mi, 2, len, (const char**)seq, _n_regs, regs, b, opt, seqname);
+		for (i = 0; i < _n_regs[1]; ++i)
+			regs[1][i].rev = !regs[1][i].rev;
+		*n_regs = _n_regs[0] + _n_regs[1];
+		regs[0] = (mm_reg1_t*)realloc(regs[0], sizeof(mm_reg1_t) * (*n_regs));
+		memcpy(&regs[0][_n_regs[0]], regs[1], _n_regs[1] * sizeof(mm_reg1_t));
+		free(regs[1]);
+		r = regs[0];
+	}
+	Py_END_ALLOW_THREADS
+
+	return r;
+}
+
+static inline char *mappy_revcomp(int len, const uint8_t *seq)
+{
+	int i;
+	char *rev;
+	rev = (char*)malloc(len + 1);
+	for (i = 0; i < len; ++i)
+		rev[len - i - 1] = seq_comp_table[seq[i]];
+	rev[len] = 0;
+	return rev;
+}
+
+static char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int en, int *len)
+{
+	int i, rid;
+	char *s;
+	*len = 0;
+	rid = mm_idx_name2id(mi, name);
+	if (rid < 0) return 0;
+	if ((uint32_t)st >= mi->seq[rid].len || st >= en) return 0;
+	if (en < 0 || (uint32_t)en > mi->seq[rid].len)
+		en = mi->seq[rid].len;
+	s = (char*)malloc(en - st + 1);
+	*len = mm_idx_getseq(mi, rid, st, en, (uint8_t*)s);
+	for (i = 0; i < *len; ++i)
+		s[i] = "ACGTN"[(uint8_t)s[i]];
+	s[*len] = 0;
+	return s;
+}
+
+static mm_idx_t *mappy_idx_seq(int w, int k, int is_hpc, int bucket_bits, const char *seq, int len)
+{
+	const char *fake_name = "N/A";
+	char *s;
+	mm_idx_t *mi;
+	s = (char*)calloc(len + 1, 1);
+	memcpy(s, seq, len);
+	mi = mm_idx_str(w, k, is_hpc, bucket_bits, 1, (const char**)&s, (const char**)&fake_name);
+	free(s);
+	return mi;
+}
+
 #endif

python/cmappy.pxd

@@ -6,36 +6,64 @@ cdef extern from "minimap.h":
 	#
 	ctypedef struct mm_idxopt_t:
 		short k, w, flag, bucket_bits
-		int mini_batch_size
+		int64_t mini_batch_size
 		uint64_t batch_size
 
 	ctypedef struct mm_mapopt_t:
+		int64_t flag
 		int seed
 		int sdust_thres
-		int flag
-		int bw
+
+		int max_qlen
+
+		int bw, bw_long
 		int max_gap, max_gap_ref
 		int max_frag_len
-		int max_chain_skip
+		int max_chain_skip, max_chain_iter
 		int min_cnt
 		int min_chain_score
+		float chain_gap_scale
+		float chain_skip_scale
+		int rmq_size_cap, rmq_inner_dist
+		int rmq_rescue_size
+		float rmq_rescue_ratio
+
 		float mask_level
+		int mask_len
 		float pri_ratio
 		int best_n
-		int max_join_long, max_join_short
-		int min_join_flank_sc
+
+		float alt_drop
+
 		int a, b, q, e, q2, e2
+		int transition
+		int sc_ambi
 		int noncan
-		int zdrop
+		int junc_bonus, junc_pen
+		int zdrop, zdrop_inv
 		int end_bonus
 		int min_dp_max
 		int min_ksw_len
 		int anchor_ext_len, anchor_ext_shift
+		float max_clip_ratio
+
+		int rank_min_len
+		float rank_frac
+
 		int pe_ori, pe_bonus
+
+		int jump_min_match;
+
 		float mid_occ_frac
+		float q_occ_frac
+		int32_t min_mid_occ
 		int32_t mid_occ
 		int32_t max_occ
-		int mini_batch_size
+		int64_t mini_batch_size
+		int64_t max_sw_mat
+		int64_t cap_kalloc
+
+		const char *split_prefix
 
 	int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 	int mm_verbose
@@ -58,6 +86,7 @@ cdef extern from "minimap.h":
 		uint32_t *S
 		mm_idx_bucket_t *B
 		void *km
+		void *h
 
 	ctypedef struct mm_idx_reader_t:
 		pass
@@ -68,6 +97,8 @@ cdef extern from "minimap.h":
 	void mm_idx_destroy(mm_idx_t *mi)
 	void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 
+	int mm_idx_index_name(mm_idx_t *mi)
+
 	#
 	# Mapping (key struct defined in cmappy.h below)
 	#
@@ -79,7 +110,10 @@ cdef extern from "minimap.h":
 
 	mm_tbuf_t *mm_tbuf_init()
 	void mm_tbuf_destroy(mm_tbuf_t *b)
-	mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name)
+	void *mm_tbuf_get_km(mm_tbuf_t *b)
+	int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden)
+	int mm_gen_ds(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden)
+	int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq)
 
 #
 # Helper header (because it is hard to expose mm_reg1_t with Cython)
@@ -92,11 +126,15 @@ cdef extern from "cmappy.h":
 		int32_t blen, mlen, NM, ctg_len
 		uint8_t mapq, is_primary
 		int8_t strand, trans_strand
+		int32_t seg_id
 		int32_t n_cigar32
 		uint32_t *cigar32
 
 	void mm_reg2hitpy(const mm_idx_t *mi, mm_reg1_t *r, mm_hitpy_t *h)
 	void mm_free_reg1(mm_reg1_t *r)
+	mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char* seqname, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
+	char *mappy_fetch_seq(const mm_idx_t *mi, const char *name, int st, int en, int *l)
+	mm_idx_t *mappy_idx_seq(int w, int k, int is_hpc, int bucket_bits, const char *seq, int l)
 
 	ctypedef struct kstring_t:
 		unsigned l, m
@@ -114,5 +152,6 @@ cdef extern from "cmappy.h":
 	void mm_fastx_close(kseq_t *ks)
 	int kseq_read(kseq_t *seq)
 
+	char *mappy_revcomp(int l, const uint8_t *seq)
 	int mm_verbose_level(int v)
 	void mm_reset_timer()

python/mappy.pyx

@@ -1,6 +1,9 @@
 from libc.stdint cimport uint8_t, int8_t
 from libc.stdlib cimport free
 cimport cmappy
+import sys
+
+__version__ = '2.31'
 
 cmappy.mm_reset_timer()
 
@@ -10,9 +13,10 @@ cdef class Alignment:
 	cdef int _NM, _mlen, _blen
 	cdef int8_t _strand, _trans_strand
 	cdef uint8_t _mapq, _is_primary
-	cdef _ctg, _cigar # these are python objects
+	cdef int _seg_id
+	cdef _ctg, _cigar, _cs, _ds, _MD # these are python objects
 
-	def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand):
+	def __cinit__(self, ctg, cl, cs, ce, strand, qs, qe, mapq, cigar, is_primary, mlen, blen, NM, trans_strand, seg_id, cs_str, ds_str, MD_str):
 		self._ctg = ctg if isinstance(ctg, str) else ctg.decode()
 		self._ctg_len, self._r_st, self._r_en = cl, cs, ce
 		self._strand, self._q_st, self._q_en = strand, qs, qe
@@ -21,6 +25,10 @@ cdef class Alignment:
 		self._cigar = cigar
 		self._is_primary = is_primary
 		self._trans_strand = trans_strand
+		self._seg_id = seg_id
+		self._cs = cs_str
+		self._ds = ds_str
+		self._MD = MD_str
 
 	@property
 	def ctg(self): return self._ctg
@@ -64,9 +72,21 @@ cdef class Alignment:
 	@property
 	def cigar(self): return self._cigar
 
+	@property
+	def read_num(self): return self._seg_id + 1
+
+	@property
+	def cs(self): return self._cs
+
+	@property
+	def ds(self): return self._ds
+
+	@property
+	def MD(self): return self._MD
+
 	@property
 	def cigar_str(self):
-		return "".join(map(lambda x: str(x[0]) + 'MIDNSH'[x[1]], self._cigar))
+		return "".join(map(lambda x: str(x[0]) + 'MIDNSHP=XB'[x[1]], self._cigar))
 
 	def __str__(self):
 		if self._strand > 0: strand = '+'
@@ -77,8 +97,12 @@ cdef class Alignment:
 		if self._trans_strand > 0: ts = 'ts:A:+'
 		elif self._trans_strand < 0: ts = 'ts:A:-'
 		else: ts = 'ts:A:.'
-		return "\t".join([str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
-				str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str])
+		a = [str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
+			str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str]
+		if self._cs != "": a.append("cs:Z:" + self._cs)
+		if self._ds != "": a.append("ds:Z:" + self._ds)
+		if self._MD != "": a.append("MD:Z:" + self._MD)
+		return "\t".join(a)
 
 cdef class ThreadBuffer:
 	cdef cmappy.mm_tbuf_t *_b
@@ -94,7 +118,8 @@ cdef class Aligner:
 	cdef cmappy.mm_idxopt_t idx_opt
 	cdef cmappy.mm_mapopt_t map_opt
 
-	def __cinit__(self, fn_idx_in, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, best_n=None, n_threads=3, fn_idx_out=None):
+	def __cinit__(self, fn_idx_in=None, preset=None, k=None, w=None, min_cnt=None, min_chain_score=None, min_dp_score=None, bw=None, bw_long=None, best_n=None, n_threads=3, fn_idx_out=None, max_frag_len=None, extra_flags=None, seq=None, scoring=None, sc_ambi=None, max_chain_skip=None):
+		self._idx = NULL
 		cmappy.mm_set_opt(NULL, &self.idx_opt, &self.map_opt) # set the default options
 		if preset is not None:
 			cmappy.mm_set_opt(str.encode(preset), &self.idx_opt, &self.map_opt) # apply preset
@@ -106,17 +131,37 @@ cdef class Aligner:
 		if min_chain_score is not None: self.map_opt.min_chain_score = min_chain_score
 		if min_dp_score is not None: self.map_opt.min_dp_max = min_dp_score
 		if bw is not None: self.map_opt.bw = bw
-		if best_n is not None: self.best_n = best_n
+		if bw_long is not None: self.map_opt.bw_long = bw_long
+		if best_n is not None: self.map_opt.best_n = best_n
+		if max_frag_len is not None: self.map_opt.max_frag_len = max_frag_len
+		if extra_flags is not None: self.map_opt.flag |= extra_flags
+		if scoring is not None and len(scoring) >= 4:
+			self.map_opt.a, self.map_opt.b = scoring[0], scoring[1]
+			self.map_opt.q, self.map_opt.e = scoring[2], scoring[3]
+			self.map_opt.q2, self.map_opt.e2 = self.map_opt.q, self.map_opt.e
+			if len(scoring) >= 6:
+				self.map_opt.q2, self.map_opt.e2 = scoring[4], scoring[5]
+				if len(scoring) >= 7:
+					self.map_opt.sc_ambi = scoring[6]
+		if sc_ambi is not None: self.map_opt.sc_ambi = sc_ambi
+		if max_chain_skip is not None: self.map_opt.max_chain_skip = max_chain_skip
 
 		cdef cmappy.mm_idx_reader_t *r;
-		if fn_idx_out is None:
-			r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, NULL)
+
+		if seq is None:
+			if fn_idx_out is None:
+				r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, NULL)
+			else:
+				r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, str.encode(fn_idx_out))
+			if r is not NULL:
+				self._idx = cmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
+				cmappy.mm_idx_reader_close(r)
+				cmappy.mm_mapopt_update(&self.map_opt, self._idx)
+				cmappy.mm_idx_index_name(self._idx)
 		else:
-			r = cmappy.mm_idx_reader_open(str.encode(fn_idx_in), &self.idx_opt, fn_idx_out)
-		if r is not NULL:
-			self._idx = cmappy.mm_idx_reader_read(r, n_threads) # NB: ONLY read the first part
-			cmappy.mm_idx_reader_close(r)
+			self._idx = cmappy.mappy_idx_seq(self.idx_opt.w, self.idx_opt.k, self.idx_opt.flag&1, self.idx_opt.bucket_bits, str.encode(seq), len(seq))
 			cmappy.mm_mapopt_update(&self.map_opt, self._idx)
+			self.map_opt.mid_occ = 1000 # don't filter high-occ seeds
 
 	def __dealloc__(self):
 		if self._idx is not NULL:
@@ -125,28 +170,104 @@ cdef class Aligner:
 	def __bool__(self):
 		return (self._idx != NULL)
 
-	def map(self, seq, buf=None):
+	def map(self, seq, seq2=None, name=None, buf=None, cs=False, ds=False, MD=False, max_frag_len=None, extra_flags=None):
 		cdef cmappy.mm_reg1_t *regs
 		cdef cmappy.mm_hitpy_t h
 		cdef ThreadBuffer b
 		cdef int n_regs
+		cdef char *cs_str = NULL
+		cdef int l_cs_str, m_cs_str = 0
+		cdef void *km
+		cdef cmappy.mm_mapopt_t map_opt
+
+		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
+		map_opt = self.map_opt
+		if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
+		if extra_flags is not None: map_opt.flag |= extra_flags
 
 		if self._idx is NULL: return None
 		if buf is None: b = ThreadBuffer()
 		else: b = buf
-		regs = cmappy.mm_map(self._idx, len(seq), str.encode(seq), &n_regs, b._b, &self.map_opt, NULL)
 
-		for i in range(n_regs):
-			cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)
-			cigar = []
-			for k in range(h.n_cigar32):
-				c = h.cigar32[k]
-				cigar.append([c>>4, c&0xf])
-			yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand)
-			cmappy.mm_free_reg1(&regs[i])
-		free(regs)
+		_seq = seq if isinstance(seq, bytes) else seq.encode()
+		if name is not None:
+			_name = name if isinstance(name, bytes) else name.encode()
 
-def fastx_read(fn):
+		if seq2 is None:
+			if name is None:
+				regs = cmappy.mm_map_aux(self._idx, NULL, _seq, NULL,  &n_regs, b._b, &map_opt)
+			else:
+				regs = cmappy.mm_map_aux(self._idx, _name, _seq, NULL,  &n_regs, b._b, &map_opt)
+		else:
+			_seq2 = seq2 if isinstance(seq2, bytes) else seq2.encode()
+			if name is None:
+				regs = cmappy.mm_map_aux(self._idx, NULL, _seq, _seq2, &n_regs, b._b, &map_opt)
+			else:
+				regs = cmappy.mm_map_aux(self._idx, _name, _seq, _seq2, &n_regs, b._b, &map_opt)
+
+		try:
+			i = 0
+			while i < n_regs:
+				cmappy.mm_reg2hitpy(self._idx, &regs[i], &h)
+				cigar, _cs, _ds, _MD = [], '', '', ''
+				for k in range(h.n_cigar32): # convert the 32-bit CIGAR encoding to Python array
+					c = h.cigar32[k]
+					cigar.append([c>>4, c&0xf])
+				if cs or ds or MD: # generate the cs/ds and/or the MD tag, if requested
+					km = cmappy.mm_tbuf_get_km(b._b)
+					_cur_seq = _seq2 if h.seg_id > 0 and seq2 is not None else _seq
+					if cs:
+						l_cs_str = cmappy.mm_gen_cs(km, &cs_str, &m_cs_str, self._idx, &regs[i], _cur_seq, 1)
+						_cs = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
+					if ds:
+						l_cs_str = cmappy.mm_gen_ds(km, &cs_str, &m_cs_str, self._idx, &regs[i], _cur_seq, 1)
+						_ds = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
+					if MD:
+						l_cs_str = cmappy.mm_gen_MD(km, &cs_str, &m_cs_str, self._idx, &regs[i], _cur_seq)
+						_MD = cs_str[:l_cs_str] if isinstance(cs_str, str) else cs_str[:l_cs_str].decode()
+				yield Alignment(h.ctg, h.ctg_len, h.ctg_start, h.ctg_end, h.strand, h.qry_start, h.qry_end, h.mapq, cigar, h.is_primary, h.mlen, h.blen, h.NM, h.trans_strand, h.seg_id, _cs, _ds, _MD)
+				cmappy.mm_free_reg1(&regs[i])
+				i += 1
+		finally:
+			while i < n_regs:
+				cmappy.mm_free_reg1(&regs[i])
+				i += 1
+			free(regs)
+			free(cs_str)
+
+	def seq(self, str name, int start=0, int end=0x7fffffff):
+		cdef int l
+		cdef char *s
+		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
+		s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
+		if l == 0: return None
+		r = s[:l] if isinstance(s, str) else s[:l].decode()
+		free(s)
+		return r
+
+	@property
+	def k(self): return self._idx.k
+
+	@property
+	def w(self): return self._idx.w
+
+	@property
+	def n_seq(self): return self._idx.n_seq
+
+	@property
+	def seq_names(self):
+		cdef char *p
+		if self._idx == NULL: return
+		sn = []
+		for i in range(self._idx.n_seq):
+			p = self._idx.seq[i].name
+			s = p if isinstance(p, str) else p.decode()
+			sn.append(s)
+		return sn
+
+def fastx_read(fn, read_comment=False):
 	cdef cmappy.kseq_t *ks
 	ks = cmappy.mm_fastx_open(str.encode(fn))
 	if ks is NULL: return None
@@ -155,9 +276,22 @@ def fastx_read(fn):
 		else: qual = None
 		name = ks.name.s if isinstance(ks.name.s, str) else ks.name.s.decode()
 		seq = ks.seq.s if isinstance(ks.seq.s, str) else ks.seq.s.decode()
-		yield name, seq, qual
+		if read_comment:
+			if ks.comment.l > 0: comment = ks.comment.s if isinstance(ks.comment.s, str) else ks.comment.s.decode()
+			else: comment = None
+			yield name, seq, qual, comment
+		else:
+			yield name, seq, qual
 	cmappy.mm_fastx_close(ks)
 
+def revcomp(seq):
+	l = len(seq)
+	bseq = seq if isinstance(seq, bytes) else seq.encode()
+	cdef char *s = cmappy.mappy_revcomp(l, bseq)
+	r = s[:l] if isinstance(s, str) else s[:l].decode()
+	free(s)
+	return r
+
 def verbose(v=None):
 	if v is None: v = -1
 	return cmappy.mm_verbose_level(v)

python/minimap2.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
-import sys, getopt
+import sys
+import getopt
 import mappy as mp
 
 def main(argv):
-	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:")
+	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cdM")
 	if len(args) < 2:
 		print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
 		print("Options:")
@@ -14,9 +15,13 @@ def main(argv):
 		print("  -k INT      k-mer length")
 		print("  -w INT      minimizer window length")
 		print("  -r INT      band width")
+		print("  -c          output the cs tag")
+		print("  -d          output the ds tag")
+		print("  -M          output the MD tag")
 		sys.exit(1)
 
-	preset, min_cnt, min_sc, k, w, bw = None, None, None, None, None, None
+	preset = min_cnt = min_sc = k = w = bw = None
+	out_cs = out_ds = out_MD = False
 	for opt, arg in opts:
 		if opt == '-x': preset = arg
 		elif opt == '-n': min_cnt = int(arg)
@@ -24,11 +29,14 @@ def main(argv):
 		elif opt == '-r': bw = int(arg)
 		elif opt == '-k': k = int(arg)
 		elif opt == '-w': w = int(arg)
+		elif opt == '-c': out_cs = True
+		elif opt == '-d': out_ds = True
+		elif opt == '-M': out_MD = True
 
 	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
 	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
 	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
-		for h in a.map(seq): # traverse hits
+		for h in a.map(seq, cs=out_cs, ds=out_ds, MD=out_MD): # traverse hits
 			print('{}\t{}\t{}'.format(name, len(seq), h))
 
 if __name__ == "__main__":

sdust.c

@@ -70,10 +70,10 @@ void sdust_buf_destroy(sdust_buf_t *buf)
 static inline void shift_window(int t, kdq_t(int) *w, int T, int W, int *L, int *rw, int *rv, int *cw, int *cv)
 {
 	int s;
-	if (kdq_size(w) >= W - SD_WLEN + 1) { // TODO: is this right for SD_WLEN!=3?
+	if ((int)kdq_size(w) >= W - SD_WLEN + 1) { // TODO: is this right for SD_WLEN!=3?
 		s = *kdq_shift(int, w);
 		*rw -= --cw[s];
-		if (*L > kdq_size(w))
+		if (*L > (int)kdq_size(w))
 			--*L, *rv -= --cv[s];
 	}
 	kdq_push(int, w, t);
@@ -114,7 +114,7 @@ static void find_perfect(void *km, perf_intv_v *P, const kdq_t(int) *w, int T, i
 		r += c[t]++;
 		new_r = r, new_l = kdq_size(w) - i - 1;
 		if (new_r * 10 > T * new_l) {
-			for (j = 0; j < P->n && P->a[j].start >= i + start; ++j) { // find insertion position
+			for (j = 0; j < (int)P->n && P->a[j].start >= i + start; ++j) { // find insertion position
 				perf_intv_t *p = &P->a[j];
 				if (max_r == 0 || p->r * max_l > max_r * p->l)
 					max_r = p->r, max_l = p->l;
@@ -177,7 +177,7 @@ uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n)
 #ifdef _SDUST_MAIN
 #include <zlib.h>
 #include <stdio.h>
-#include "getopt.h"
+#include "ketopt.h"
 #include "kseq.h"
 KSEQ_INIT(gzFile, gzread)
 
@@ -186,16 +186,17 @@ int main(int argc, char *argv[])
 	gzFile fp;
 	kseq_t *ks;
 	int W = 64, T = 20, c;
+	ketopt_t o = KETOPT_INIT;
 
-	while ((c = getopt(argc, argv, "w:t:")) >= 0) {
-		if (c == 'w') W = atoi(optarg);
-		else if (c == 't') T = atoi(optarg);
+	while ((c = ketopt(&o, argc, argv, 1, "w:t:", 0)) >= 0) {
+		if (c == 'w') W = atoi(o.arg);
+		else if (c == 't') T = atoi(o.arg);
 	}
-	if (optind == argc) {
+	if (o.ind == argc) {
 		fprintf(stderr, "Usage: sdust [-w %d] [-t %d] <in.fa>\n", W, T);
 		return 1;
 	}
-	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+	fp = strcmp(argv[o.ind], "-")? gzopen(argv[o.ind], "r") : gzdopen(fileno(stdin), "r");
 	ks = kseq_init(fp);
 	while (kseq_read(ks) >= 0) {
 		uint64_t *r;

seed.c

@@ -0,0 +1,132 @@
+#include "mmpriv.h"
+#include "kalloc.h"
+#include "ksort.h"
+
+void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac)
+{
+	mm128_t *a;
+	size_t i, j, st;
+	if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
+	a = Kmalloc(km, mm128_t, mv->n);
+	for (i = 0; i < mv->n; ++i)
+		a[i].x = mv->a[i].x, a[i].y = i;
+	radix_sort_128x(a, a + mv->n);
+	for (st = 0, i = 1; i <= mv->n; ++i) {
+		if (i == mv->n || a[i].x != a[st].x) {
+			int32_t cnt = i - st;
+			if (cnt > q_occ_max && cnt > mv->n * q_occ_frac)
+				for (j = st; j < i; ++j)
+					mv->a[a[j].y].x = 0;
+			st = i;
+		}
+	}
+	kfree(km, a);
+	for (i = j = 0; i < mv->n; ++i)
+		if (mv->a[i].x != 0)
+			mv->a[j++] = mv->a[i];
+	mv->n = j;
+}
+
+mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv, int32_t *n_m_)
+{
+	mm_seed_t *m;
+	size_t i;
+	int32_t k;
+	m = (mm_seed_t*)kmalloc(km, mv->n * sizeof(mm_seed_t));
+	for (i = k = 0; i < mv->n; ++i) {
+		const uint64_t *cr;
+		mm_seed_t *q;
+		mm128_t *p = &mv->a[i];
+		uint32_t q_pos = (uint32_t)p->y, q_span = p->x & 0xff;
+		int t;
+		cr = mm_idx_get(mi, p->x>>8, &t);
+		if (t == 0) continue;
+		q = &m[k++];
+		q->q_pos = q_pos, q->q_span = q_span, q->cr = cr, q->n = t, q->seg_id = p->y >> 32;
+		q->is_tandem = q->flt = 0;
+		if (i > 0 && p->x>>8 == mv->a[i - 1].x>>8) q->is_tandem = 1;
+		if (i < mv->n - 1 && p->x>>8 == mv->a[i + 1].x>>8) q->is_tandem = 1;
+	}
+	*n_m_ = k;
+	return m;
+}
+
+#define MAX_MAX_HIGH_OCC 128
+
+void mm_seed_select(int32_t n, mm_seed_t *a, int len, int max_occ, int max_max_occ, int dist)
+{ // for high-occ minimizers, choose up to max_high_occ in each high-occ streak
+	extern void ks_heapdown_uint64_t(size_t i, size_t n, uint64_t*);
+	extern void ks_heapmake_uint64_t(size_t n, uint64_t*);
+	int32_t i, last0, m;
+	uint64_t b[MAX_MAX_HIGH_OCC]; // this is to avoid a heap allocation
+
+	if (n == 0 || n == 1) return;
+	for (i = m = 0; i < n; ++i)
+		if (a[i].n > max_occ) ++m;
+	if (m == 0) return; // no high-frequency k-mers; do nothing
+	for (i = 0, last0 = -1; i <= n; ++i) {
+		if (i == n || a[i].n <= max_occ) {
+			if (i - last0 > 1) {
+				int32_t ps = last0 < 0? 0 : (uint32_t)a[last0].q_pos>>1;
+				int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1;
+				int32_t j, k, st = last0 + 1, en = i;
+				int32_t max_high_occ = (int32_t)((double)(pe - ps) / dist + .499);
+				if (max_high_occ > 0) {
+					if (max_high_occ > MAX_MAX_HIGH_OCC)
+						max_high_occ = MAX_MAX_HIGH_OCC;
+					for (j = st, k = 0; j < en && k < max_high_occ; ++j, ++k)
+						b[k] = (uint64_t)a[j].n<<32 | j;
+					ks_heapmake_uint64_t(k, b); // initialize the binomial heap
+					for (; j < en; ++j) { // if there are more, choose top max_high_occ
+						if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap
+							b[0] = (uint64_t)a[j].n<<32 | j;
+							ks_heapdown_uint64_t(0, k, b);
+						}
+					}
+					for (j = 0; j < k; ++j) a[(uint32_t)b[j]].flt = 1;
+				}
+				for (j = st; j < en; ++j) a[j].flt ^= 1;
+				for (j = st; j < en; ++j)
+					if (a[j].n > max_max_occ)
+						a[j].flt = 1;
+			}
+			last0 = i;
+		}
+	}
+}
+
+mm_seed_t *mm_collect_matches(void *km, int *_n_m, int qlen, int max_occ, int max_max_occ, int dist, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos)
+{
+	int rep_st = 0, rep_en = 0, n_m, n_m0;
+	size_t i;
+	mm_seed_t *m;
+	*n_mini_pos = 0;
+	*mini_pos = (uint64_t*)kmalloc(km, mv->n * sizeof(uint64_t));
+	m = mm_seed_collect_all(km, mi, mv, &n_m0);
+	if (dist > 0 && max_max_occ > max_occ) {
+		mm_seed_select(n_m0, m, qlen, max_occ, max_max_occ, dist);
+	} else {
+		for (i = 0; i < n_m0; ++i)
+			if (m[i].n > max_occ)
+				m[i].flt = 1;
+	}
+	for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) {
+		mm_seed_t *q = &m[i];
+		if (mm_dbg_flag & MM_DBG_SEED_FREQ)
+			fprintf(stderr, "SF\t%d\t%d\t%d\n", q->q_pos>>1, q->n, q->flt);
+		if (q->flt) {
+			int en = (q->q_pos >> 1) + 1, st = en - q->q_span;
+			if (st > rep_en) {
+				*rep_len += rep_en - rep_st;
+				rep_st = st, rep_en = en;
+			} else rep_en = en;
+		} else {
+			*n_a += q->n;
+			(*mini_pos)[(*n_mini_pos)++] = (uint64_t)q->q_span<<32 | q->q_pos>>1;
+			m[n_m++] = *q;
+		}
+	}
+	*rep_len += rep_en - rep_st;
+	*_n_m = n_m;
+	return m;
+}

setup.py

@@ -4,26 +4,26 @@ except ImportError:
 	from distutils.core import setup
 	from distutils.extension import Extension
 
-cmdclass = {}
+import sys, platform
 
-try:
-	from Cython.Build import build_ext
-except ImportError: # without Cython
-	module_src = 'python/mappy.c'
-else: # with Cython
-	module_src = 'python/mappy.pyx'
-	cmdclass['build_ext'] = build_ext
-
-import sys
 sys.path.append('python')
 
+extra_compile_args = ['-DHAVE_KALLOC']
+include_dirs = ["."]
+
+if platform.machine() in ["aarch64", "arm64"]:
+	include_dirs.append("sse2neon/")
+	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
+else:
+	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
+
 def readme():
-    with open('python/README.rst') as f:
-        return f.read()
+	with open('python/README.rst') as f:
+		return f.read()
 
 setup(
 	name = 'mappy',
-	version = '2.7',
+	version = '2.31',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -32,18 +32,18 @@ setup(
 	license = 'MIT',
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
-    ext_modules = [Extension('mappy',
-		sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'pe.c',
+	ext_modules = [Extension('mappy',
+		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'jump.c', 'options.c',
 				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
-				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c'],
+				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
 		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
 				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
 				   'python/cmappy.h', 'python/cmappy.pxd'],
-		extra_compile_args = ['-msse4'], # WARNING: ancient x86_64 CPUs don't have SSE4
-		include_dirs = ['.'],
+		extra_compile_args = extra_compile_args,
+		include_dirs = include_dirs,
 		libraries = ['z', 'm', 'pthread'])],
 	classifiers = [
-		'Development Status :: 4 - Beta',
+		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',
 		'Operating System :: POSIX',
 		'Programming Language :: C',
@@ -52,4 +52,4 @@ setup(
 		'Programming Language :: Python :: 3',
 		'Intended Audience :: Science/Research',
 		'Topic :: Scientific/Engineering :: Bio-Informatics'],
-	cmdclass = cmdclass)
+	setup_requires=["cython"])

sketch.c

@@ -2,8 +2,9 @@
 #include <stdlib.h>
 #include <assert.h>
 #include <string.h>
+#define __STDC_LIMIT_MACROS
 #include "kvec.h"
-#include "minimap.h"
+#include "mmpriv.h"
 
 unsigned char seq_nt4_table[256] = {
 	0, 1, 2, 3,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,

splitidx.c

@@ -0,0 +1,84 @@
+#include <string.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <errno.h>
+#include "mmpriv.h"
+
+FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
+{
+	char *fn;
+	FILE *fp;
+	uint32_t i, k = mi->k;
+	fn = (char*)calloc(strlen(prefix) + 10, 1);
+	sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
+	if ((fp = fopen(fn, "wb")) == NULL) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m failed to write to temporary file '%s'\033[0m: %s\n", fn, strerror(errno));
+		exit(1);
+	}
+	mm_err_fwrite(&k, 4, 1, fp);
+	mm_err_fwrite(&mi->n_seq, 4, 1, fp);
+	for (i = 0; i < mi->n_seq; ++i) {
+		uint32_t l;
+		l = strlen(mi->seq[i].name);
+		mm_err_fwrite(&l, 1, 4, fp);
+		mm_err_fwrite(mi->seq[i].name, 1, l, fp);
+		mm_err_fwrite(&mi->seq[i].len, 4, 1, fp);
+	}
+	free(fn);
+	return fp;
+}
+
+mm_idx_t *mm_split_merge_prep(const char *prefix, int n_splits, FILE **fp, uint32_t *n_seq_part)
+{
+	mm_idx_t *mi = 0;
+	char *fn;
+	int i, j;
+
+	if (n_splits < 1) return 0;
+	fn = CALLOC(char, strlen(prefix) + 10);
+	for (i = 0; i < n_splits; ++i) {
+		sprintf(fn, "%s.%.4d.tmp", prefix, i);
+		if ((fp[i] = fopen(fn, "rb")) == 0) {
+			if (mm_verbose >= 1)
+				fprintf(stderr, "ERROR: failed to open temporary file '%s': %s\n", fn, strerror(errno));
+			for (j = 0; j < i; ++j)
+				fclose(fp[j]);
+			free(fn);
+			return 0;
+		}
+	}
+	free(fn);
+
+	mi = CALLOC(mm_idx_t, 1);
+	for (i = 0; i < n_splits; ++i) {
+		mm_err_fread(&mi->k, 4, 1, fp[i]); // TODO: check if k is all the same
+		mm_err_fread(&n_seq_part[i], 4, 1, fp[i]);
+		mi->n_seq += n_seq_part[i];
+	}
+	mi->seq = CALLOC(mm_idx_seq_t, mi->n_seq);
+	for (i = j = 0; i < n_splits; ++i) {
+		uint32_t k;
+		for (k = 0; k < n_seq_part[i]; ++k, ++j) {
+			uint32_t l;
+			mm_err_fread(&l, 1, 4, fp[i]);
+			mi->seq[j].name = (char*)calloc(l + 1, 1);
+			mm_err_fread(mi->seq[j].name, 1, l, fp[i]);
+			mm_err_fread(&mi->seq[j].len, 4, 1, fp[i]);
+		}
+	}
+	return mi;
+}
+
+void mm_split_rm_tmp(const char *prefix, int n_splits)
+{
+	int i;
+	char *fn;
+	fn = CALLOC(char, strlen(prefix) + 10);
+	for (i = 0; i < n_splits; ++i) {
+		sprintf(fn, "%s.%.4d.tmp", prefix, i);
+		remove(fn);
+	}
+	free(fn);
+}

test/MT-orang.fa

@@ -1,4 +1,4 @@
->MT_orang
+>MT_orang co:Z:comment
 GTTTATGTAGCTTATTCTATCCAAAGCAATGCACTGAAAATGTCTCGACGGGCCCACACG
 CCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTGAGGTTACACAT
 GCAAGCATCCCCGCCCCAGTGAGTCGCCCTCCAAGTCACTCTGACTAAGAGGAGCAAGCA

test/t-inv.fa

@@ -0,0 +1,127 @@
+>ref
+TGCGGAGGCTGAAGCAACTCCATCTTGGAAGCTAATCTACCATGTTGGCTTCTGATTAAC
+ATCAGTTCTGGGAAGGCTTGTAAGATTTCCTGTTTGTCTATTATTTCCTAGGTAAGAGCA
+GATACTTACTGTAAATCCTGCCCCTAGATTAAACAACCTTGGTGTTATCGTACTTCCATT
+GTCCTATACATCCCTTCGGAATCCCCCTTTCCCTATGGTCCTCAAGCCCTTGGTCTGGGG
+AGTAACAGCATAGGGATCAACCATCTCGTCTTGCCACTGCCCGAAATACAGACATGGCTT
+CTGTTCCTAAGTCCCTATTCAACTTTTCTTTCTAAGAAACTGGATTTGTCAGCCTCTTTC
+TTCACCTCTCAGCTTCCTTGGACTTTGGGGGTAGGTTTGCGTAGACATGCTCACCACAGA
+CACAATATCAGCTTCATTCTACAGATGAGGAAGGCAAGCCTTGGGGAGCTTAACCAACTT
+GTCGAGACTCATGTATATACCAACACTGAAAAGCAGATATTCCAGACTCCCAGTCATGCC
+ACAGGCACACCCCTCAGTGAGAGGTGGGGTTTGTAGTTGAGGCTATTTCCTGCCCAGGGA
+GCAGGGAGGCACTCTAGCTTCCCTGAGCTAACGTGGTTCTGCTTGTGTCTGACTTCCAGG
+TCTCTGCCCTTTCCAAGCTCACTAGGATGGGCTTCGGGTGTGTCAAATGCCTCAGACAGT
+ACAGATCCACACAGAATGGGCATATGCAACCAATCAGTGTCATAAAAAAGAAGGAAATGA
+CTCGGGCCCCCTGTGTGTTCAACATGTCGAAGGTATCTGTGCAGCAGAAGAAAGAGGGGC
+AAAAGCCCCCAGTGCCACAGGCCAGAGGCAGCAGCTTGGGCCCATGTGGGAGGGTTTGCT
+TTCCCCTGCCAAAGTGATGGGCTGCTGCAGCCTGGGGCTTGTGGGAATCCTTCCTGGGCC
+TGTGTGGGAAGTGTAGGCAGGGAGAGTGCTGCTTTCCCAAGCTCATCCCAGCTACAGCTA
+CCTTTGTGCTCTGGGATTCAGGACCCCCGAGGGGGCTGGCAGGAGAGTCTCTGTTCTCGG
+ATGGGTTGTCACCAGGGCATACATGGGAAGTGGGCTCTCTGGAGTCACCCTCCAGGGGAC
+AATGCCAATTCCAGACACATTTACTGGAACCCCTACACTGATGACCTTTTGTTGAGGGTT
+GAATTATGTCCCCAAAAAAGATACATTGAAGTCCAAACCTCTGGTGTCTATAAATGTGAT
+TTTATTTGAAAATGAGGTTTCTATGGACTAAATTGTGTCCCTCCCAAATTCATATTTTGA
+AGCCCTAGCCCCCAGTGTGACTATACCTAGAGACAGAGATCTTTAGGAGGTAATTAAGGT
+TCAATGAGGTCAGGTGGGTGGGGCCCTAAACCAACAGGAAGGACTGTGGCCTTACTAGAA
+AAGGAAGAAAAAGCATTTCCTCTCTTCTAGTATAAAAGGACACAGAAAGAAGGCAGATAT
+CTACAAGCCACGAAGAGAGACGTCACTGAGAACTGAATTTGTGTACATTGATCTGGAACT
+TCCAGCCTCCAGAACTTGAGAAATACATTTCTGTTGTTTATTTTTTTTTCATGTAATCAA
+TTCATTTATCATATATTTATTGAGTGCCTACTATGTGCCAGAGGATACAGCAGTAACAAA
+ACTAGGCAAAAATTGTGCCTAAAAGAGGGAAGATGACTTTTCTTAAAGTGTGGAATAAAG
+AAAAGTAAGATAGCGGATAGAAGCTTGAAGTGAAAGCAGGTTCACAGGAAGTTTCTTTGG
+TCATTTGTTTTGTTTTTAAATAGTGGAAAGATGTATATGTTTATGGAGAAAGATTGCCTT
+GAAGATGCAAGAGGAAGAGATGATCAAAATTCAAGAAGAAGCAGAAAGTGATAGAATAAA
+GAGCACAAGTGGAGAATTAGTGTTAATGAAAAGAAGGATGCTTCCTTTGATATGAAGTGA
+AGGAAGAGAGAATGAGTAAAGACCAAGACTTGAAGTCCCTAGTTTAATAGAGGGAGATTT
+CTTCTTTTGATAGCAACAATGGTATTCTGAATTATTTGAAGACATGTCATATTTCTCTTG
+TGCCATTTTCCTCCCAGTTTAAACATTCTCATAACCTCTATTCCTCACATGATGTTTTTC
+CAGGTCCTTTATTCTTTGGCACTCTCTTCTCTGGACACATTGTATTCTGTCATTGGTCCT
+AAAATTTAGATACCCACAATTGAACATACTCCTCTAGATATGGTCTAGCTAATGCAAAAG
+AACTGCTGCCTTCCAACTTGTTCAGACATCATATGTTTGTTGTCAAACGCTAAGTTGAGT
+TGTTATCTTTTAAGTTTTGTTTTTGTTTTTTTTTTTTTTTTTTAATTCCAAGAGGTGCCC
+ACGTTGGCTAAGTACCAAACAGGGTACTAGGGAATTTTACTTCTGAGTTAAATGCCATTC
+TAGTTGTTTTTTCTTCATCTCCAGTAAGGTTATCTTTATTCACCAGTTGTTACAATAGCT
+GTGGGTCTTGCTTCTCACAGTTTTATGCTGTCTGTGCTATTTTCTCTACTGATCATCACC
+ACAATCATTATTGCTTATCATAATTGTTATCTTTATTTTCTCCTTTAATCAAGAATCAGT
+CTTCCTTTATCTCATTATTCTCTTTTGCAGGCTTCAGGATAATTATGGTTGGAGTGCACT
+GGGGGAACCAGTGCAGCTAAGCTCTGACATCTTTGCATCCCTTTTCCATCTGCTGTTTTG
+GCACTCTGGTAGAATAGATAACCTAAAAACGACTTTAAAACATCTAGAAATTTTGGATAA
+AATATAACAAACATCCCTTTAAATGCACAACTGATCTTCCATGGAAGTCACAGAAATATA
+TAACGCCAAAAAGAAGGGAAGCTGAAACCCAGGGCTGTAAACATGAACATCATCTTCTCT
+CCCTTTTTCTTGTGACTTATCTTGTTTTTCTCAGCTTTGGTGCTACCAAGGCTTGACTTT
+AATAGGCATTTCCAATCAATGAGAGAATTTCTTTTGCTTTCATCAACAATTCAGTTATTG
+ATGTTAACATATATATCATTTGAGTACTTTTCTTTTTTTTATTATTATTATACTTTAAGT
+TTTAGGGTCCATGTGCACAATGTGCAGGTTAGTTACGTATGTATACATGTGCCATGCTGG
+TGTGCTGCACCCATTAACTCATCATTTAGCATTAGGTATATCTCCTAATGCTATCCCTTC
+CCCCTCTCCCCACCCCACAACAGTCCCCAGAGTGTTCCCCTTCCTGTGTCCATGTGTTCT
+CATTGTTCAATCCCCATCTATGAGTGAGAACATGCGGTGTTTGGTTTTTTGTCCTTGCAA
+TAGTTTACTGAGAATGATGATTTCTAATTTCATCCATGTCCCTAAAGAGCTTCTGCACAG
+CAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTCACAA
+CCTGCTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACA
+AGAAAAAAACAAACAACCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA
+AAGAAGACATTTATGCAGCCAAAAGACACATGAAAAAATGCTCATCATCACTGGCCATCA
+GAGAAATGCAAACCAAAACCACAATGAGATACCATCTCACACCAGTTAAAATGGCAATCA
+TTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAACAGGAACACTTTTAC
+ACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGCTGATTCCTCA
+GGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAA
+AGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTAT
+TCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGA
+AAATGTGGCACATATACACCACGGAATACTGTGCAGCCATAAAAAATGATGAGTTCATGT
+CCTTTGTAGGGACACGGATGAAATTGGAAATCATTTCTGTTGTTTAAACCACGAAGTCTA
+TGGTATCTGGTTATGACAACCTGAGAATACTAACTCAAGGGTCTTTCGCAGATGTCATTA
+AGTTGTTAAAGTGAGGTCATTATGGTGGGTCCTAATCCAAGAGAAGAGATGCATGGACAG
+ACGTGCACAACGGGAGGACCAAGCCAAGACACACAGGGAGAATGGCCATGGGAAGATGGA
+GGCAGAGATCAAAGTGAGGCACCCACAAGCCAAGAAATGGCAGGAGCTACCAGCAGCTGG
+AAGATGCAGAGAAGCATTCCTTCTTAGAGGTTTCAGAGAGAGTATGGTGCTACTGACACC
+TTGATTTTGAACTTCTAGTCTCCAGAACTATGAGAGAATAAATTTCTGTTGGTTAAGCCA
+TCGAGTTTGTGTAAGTTTGTTATAAGAGCCCTAGGAAATAAACATATCCATTTATTCAGG
+AAAGCCTGCTAGAGTGCAAATATTTGGAAAAGATACTACTATGCAAATGTTTGAAAAAGA
+TATTGCTCTTGATTCTGCCTTATGGGTTTTTCATTTCTGTAAGCTATTCTCAAAGTTTTG
+TTCTTGGACTACTATTGGTAATTAAGACTGCAACATGTTTGGCAACATCAGTTGAGAACT
+GTTGCTCTGGGAACGTTTTCGGCAAGCCTCAGCCCTTCTTTTCCCTTGGCTTGCATTGAG
+GAGTTAGGTGATACTCTGCTGCTCAGGCCCAGCACCTTTATGGACCGTATTCCCCTGGTG
+GAATGACCATCTCTGCTTGCTCTGATTGGCTGTTGGGGTTTTCTAGCATGCCCTATTTAA
+TATGTATGATTTATCTCTTACTTCAGTTGGAAGGTACAGTTGCTCTGTAGTTGGCATGCA
+GTCATGGTGACTATGAAAATATAAAATAATGTTTTGGTTTACAGACACTTAGAAATAAGT
+TGTGTCTCAAAATTGGGTGACTATTCTAGTTATCTGCTACTCAATATCCTTGTGCGAGCC
+CTCTTTACCCAGAATCAAACTAAACCATGAGGGGCACTATAGAATGTCACCCCTGGGTCC
+AGGATACTATGGGGACTCAGAAGCCAAGCTCCCACTGGGGGATCTAGGGCATGCCCCCAA
+GGTAAGATTCCCACCTCTTTGTTCAGCAGGAAGCACCCATCACACAAGGAGGTAGGAATA
+AACAAGCATTCGTCAAGAACAAAAGATACAGATGTTCTGCTGGAGCTTGGATACATAGCA
+TAAGAGGGAACAGTTCTCACAGGTAAGAGTAAGTTTTCCTCTGGTGGTGACAGTGGGACC
+TGTGGGGGAGAGAATTGGGAGTACTGACAGGAAGGCAGAGTGGCTGTCCAAATGAACGGA
+TTGTTTGCACATGGCCTTTAGGGCACGTTGTGTTAGCCTTCCATTGCTGCTTATATTAGT
+CTGTTTTCACACTGCCCATAAATGCATACCTGAGACTGGATAATTTATAAAGAAAAAGAG
+CCTTAATGTACTCATAGTTGCATGTGGCTGGGGAGGCCTCACAATCATGGCAGAAGGTGA
+AAGGCACATCTTACATGGAAGCAGACAAGAGAGAATTGAGGACCAAGTGAAAGGGGTTTC
+CCCTTATAAAACCATCAGATCACATGAGACTTTTTCACCACCATGAGAACAGTAAGGGGA
+AAACTATGCTCATGATTCAATTGTCTCCCACTGGATTCCTCCCACAACACATAGGAATTA
+TGGGAGCTAAAATTCAAGATGAGATTTGGGTGAGGACACAGCCAAACCCTATCACTGCTG
+TAATCAATTCCCACCAACTTAGTGGCTCGAAACATCACAGATTTATGATCTTATGACGGT
+GGAGGTCCCCAAATGGATCTTCTAGGTCTAGAATCAAGGTATCAGCAGACCACTTCTTTT
+GGAGGCTCTGGTGGAGAAACCATTTCCTCGCCTTTTCCAGCTTCTAGAGGCTGCCCTTCT
+CATTCCTTGGTTCACGGCCACACTCATTTCCATCTCTGCTTCCACTGTGACAACTTCTCT
+GCCTCAGACCCTCCTGCTTTGCCTTTGTAAGGACCCTTGTGATGAGATCAGGCCCATCCA
+GGATTATCCCTCATCTCAAGACCTTTACCTTAATCACATTTGCAAGGTCTCTTCCACTGT
+GTCAGGTAACATTTTCACAGGTTCCAGGGATTAGGGTGTGGACATCTTGGGGAGCTGGAG
+GATATTATTTCATCTACCACACACATCTCTACCTTGTACAGGCAAGCACTTGCAAAGTGC
+AATGTGATCCTCTGGAGCCACTGTCCTCCCAGAGCTTATATATACTCTGAAAGTCAACTC
+TCAGACCACAGCCTCCTGTCCATGCACCACTCTCATCAACACCCCCACCCGAAACACTTT
+CACTCCACCCTCTTTGTCCCCTAACTCATGGAGAAGAAAATCTAATTAGTAGGAGTGGAA
+TTTGGCTTTCATCTTTACCAGTACTAGAAATATGGTGTGTGTCTTTTTGTAAAAATTCTC
+TCAACTAAATTGTTTTTATTAATTTCTGCAAAATGTGAACATCAACTCCCTTCATGTGAA
+TGTCAATAAGATTAAATGAGCTGTCTCAGCTCCTAGCCTGTGCAAGCTAACAGCTCAGGA
+GATGTTTATTTCTTTCCCTCTTCTTTCCTTAATGAAGCCCTCTCCTTTGACATCTTCAAT
+TCTGGAGCGCTTCTTTTCTGAGGCCTTGGCTCCCCCACATTGCCCACCCTTTTCCTGCTC
+GTCCACATTTCTGGCTTCTATTCTCTTGTCTTTACCATCTCCCTGAACAATGTTATCCGT
+TCCAATGACTTCAACAGTCTCTCCGCTTACATATGATGCCTCTCAAACTCTGATCTCCAA
+CTCTTCCAAAGAGCTCTGGACCTTTGTTCCAATTACCTGAAAAACATCTTCTTGGATGTC
+CCATTAGCACTGTTAAATCAAACAAGAATTTCCCTCCCTCCTGCCTTGCTGTAGTTCCCC
+TAGGGATTCGGTTGTGTGGGAAGATGTGTGGAGAGCTCTTAGTTGACTCCCTTCTCTGCA
+GTTCTACCTCTCTAGAGACTTGGAGGACCCACTGTTTCCGCCTCGCTTTTTCAGGCCTAG
+AGATTGCTCGCTCCTGGGCTGGCTGCTTCATAATTCCTTATTAGTAGTTTCCCAAGCTTA
+CATATCTGTAAATATTTACTTTAGTTAAATTCTCCCCAATTTCCACAATATGTTGGCTGC
+ACATGCTTTCTACTAGGAGTCACACAACTATGATAAGAACCAAGAAATATTAGTAAACGT
+TTTTTACCATTATTGGCCTATACCCTGGAATAGCCAACAATAACCTAGAACCTATGCAAC
+AAGAATATCCAACAAGAACCTAGAGACCTGTCAGTCTATAGGTGGGAACTACAGGATGAG
+A

test/x3s-aln.txt

@@ -0,0 +1,5 @@
+mm2: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCAC......................................................................................................................................CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
+     |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                                                                                                      |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+ref: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCACTCACctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCCGAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGTTAGGCTAACCTCacCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT
+     ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||                                                                                                                                      ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+sta: TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAGTGCA......................................................................................................................................CTCACCACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCACGGTT

test/x3s-qry.fa

@@ -0,0 +1,5 @@
+>query
+AACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCC
+AAGTG
+GTGAGTGCA
+CTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA

test/x3s-ref.fa

@@ -0,0 +1,10 @@
+>ref
+TGATCCAACATCGAGGTCGTAAACCCTATTGTTGATATGGACTCTAGAATAGGATTGCGC
+TGTTATCCCTAGGGTAACTTGTTCCGTTGGTCAAGTTATTGGATCAATTGAGTATAGTAG
+TGCACTCAC
+ctGCTTCGCTTTGACTGGTGAAGTCTTAGCATGTACTGCTCGGAGGTTGGGTTCTGCTCC
+GAGGTCGCCCCAACCGAAATTTTTAATGCAGGTTTGGTAGTTTAGGACCTGTGGGTTTGT
+TAGGCTAACCTCac
+CACTTGGAGCCATTCATACAGGTCCCTATTTAAGGAACAAGTGATTATGCTACCTTTGCA
+CGGTTAGGGTACCGCGGCCGTTAAACATGTGTCACTGGGCAGGCGGTGCCTCTAATACTG
+GTGAT

tex/minimap2.bib

@@ -61,13 +61,6 @@
 	Volume = {32},
 	Year = {2016}}
 
-@misc{Suzuki:2016,
-	title = {Fast and accurate alignment tool for PacBio and Nanopore long reads},
-	author = {Hajime Suzuki},
-	journal = {Unpublished},
-	howpublished = {\href{https://github.com/ocxtal/minialign}{https://github.com/ocxtal/minialign}},
-	year = {2016}}
-
 @misc{Ruan:2016,
 	title = {Ultra-fast de novo assembler using long noisy reads},
 	author = {Jue Ruan},
@@ -172,14 +165,6 @@
 	Volume = {29},
 	Year = {2011}}
 
-@article {Suzuki130633,
-	author = {Suzuki, Hajime and Kasahara, Masahiro},
-	title = {Acceleration Of Nucleotide Semi-Global Alignment With Adaptive Banded Dynamic Programming},
-	year = {2017},
-	note = {doi:10.1101/130633},
-	publisher = {Cold Spring Harbor Labs Journals},
-	journal = {bioRxiv}}
-
 @article{Gotoh:1982aa,
 	Author = {Gotoh, O},
 	Journal = {J Mol Biol},
@@ -313,3 +298,163 @@
 	Title = {Assembling large genomes with single-molecule sequencing and locality-sensitive hashing},
 	Volume = {33},
 	Year = {2015}}
+
+@article{Gurevich:2013aa,
+	Author = {Gurevich, Alexey and others},
+	Journal = {Bioinformatics},
+	Pages = {1072-5},
+	Title = {{QUAST}: quality assessment tool for genome assemblies},
+	Volume = {29},
+	Year = {2013}}
+
+@article{Li:2010fk,
+	Author = {Li, Heng and Durbin, Richard},
+	Journal = {Bioinformatics},
+	Pages = {589-95},
+	Title = {Fast and accurate long-read alignment with {Burrows-Wheeler} transform},
+	Volume = {26},
+	Year = {2010}}
+
+@article{Marcais:2018aa,
+	Author = {Mar{\c c}ais, Guillaume and others},
+	Journal = {PLoS Comput Biol},
+	Pages = {e1005944},
+	Title = {{MUMmer4}: A fast and versatile genome alignment system},
+	Volume = {14},
+	Year = {2018}}
+
+@article{Li:2009ys,
+	Author = {Li, Heng and others},
+	Journal = {Bioinformatics},
+	Pages = {2078-9},
+	Title = {The {Sequence Alignment/Map format and SAMtools}},
+	Volume = {25},
+	Year = {2009}}
+
+@article{Suzuki:2018aa,
+	Author = {Suzuki, Hajime and Kasahara, Masahiro},
+	Journal = {BMC Bioinformatics},
+	Pages = {45},
+	Title = {Introducing difference recurrence relations for faster semi-global alignment of long sequences},
+	Volume = {19},
+	Year = {2018}}
+
+@article{Li:2018ab,
+	Author = {Li, Heng},
+	Journal = {Bioinformatics},
+	Pages = {3094-3100},
+	Title = {Minimap2: pairwise alignment for nucleotide sequences},
+	Volume = {34},
+	Year = {2018}}
+
+@article{Jain:2020aa,
+	Author = {Jain, Chirag and others},
+	Journal = {Bioinformatics},
+	Pages = {i111-i118},
+	Title = {Weighted minimizer sampling improves long read mapping},
+	Volume = {36},
+	Year = {2020}}
+
+@article{Miga:2020aa,
+	Author = {Miga, Karen H and others},
+	Journal = {Nature},
+	Pages = {79-84},
+	Title = {Telomere-to-telomere assembly of a complete human {X} chromosome},
+	Volume = {585},
+	Year = {2020}}
+
+@article {Jain2020.11.01.363887,
+	author = {Jain, Chirag and others},
+	title = {A long read mapping method for highly repetitive reference sequences},
+	elocation-id = {2020.11.01.363887},
+	year = {2020},
+	doi = {10.1101/2020.11.01.363887},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2020/11/02/2020.11.01.363887},
+	eprint = {https://www.biorxiv.org/content/early/2020/11/02/2020.11.01.363887.full.pdf},
+	journal = {bioRxiv}
+}
+
+@article{Li:2020aa,
+	Author = {Li, Heng and others},
+	Journal = {Genome Biol},
+	Pages = {265},
+	Title = {The design and construction of reference pangenome graphs with minigraph},
+	Volume = {21},
+	Year = {2020}}
+
+@article{Ren:2021aa,
+	Author = {Ren, Jingwen and Chaisson, Mark J P},
+	Journal = {PLoS Comput Biol},
+	Pages = {e1009078},
+	Title = {lra: A long read aligner for sequences and contigs},
+	Volume = {17},
+	Year = {2021}}
+
+@inproceedings{DBLP:conf/wabi/AbouelhodaO03,
+	Author = {Mohamed Ibrahim Abouelhoda and Enno Ohlebusch},
+	Booktitle = {Algorithms in Bioinformatics, Third International Workshop, {WABI} 2003, Budapest, Hungary, September 15-20, 2003, Proceedings},
+	Crossref = {DBLP:conf/wabi/2003},
+	Pages = {1--16},
+	Title = {A Local Chaining Algorithm and Its Applications in Comparative Genomics},
+	Year = {2003}}
+
+@article{Ono:2021aa,
+	Author = {Ono, Yukiteru and others},
+	Journal = {Bioinformatics},
+	Pages = {589-595},
+	Title = {{PBSIM2}: a simulator for long-read sequencers with a novel generative model of quality scores},
+	Volume = {37},
+	Year = {2021}}
+
+@article{Sedlazeck:2018ab,
+	Author = {Sedlazeck, Fritz J and others},
+	Journal = {Nat Methods},
+	Pages = {461-468},
+	Title = {Accurate detection of complex structural variations using single-molecule sequencing},
+	Volume = {15},
+	Year = {2018}}
+
+@article{Jeffares:2017aa,
+	Author = {Jeffares, Daniel C and others},
+	Journal = {Nat Commun},
+	Pages = {14061},
+	Title = {Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast},
+	Volume = {8},
+	Year = {2017}}
+
+@article{Zook:2020aa,
+	Author = {Zook, Justin M and others},
+	Journal = {Nat Biotechnol},
+	Pages = {1347-1355},
+	Title = {A robust benchmark for detection of germline large deletions and insertions},
+	Volume = {38},
+	Year = {2020}}
+
+@article{Harpak:2017aa,
+	Author = {Harpak, Arbel and others},
+	Journal = {Proc Natl Acad Sci U S A},
+	Pages = {12779-12784},
+	Title = {Frequent nonallelic gene conversion on the human lineage and its effect on the divergence of gene duplicates},
+	Volume = {114},
+	Year = {2017}}
+
+@article{Li:2018aa,
+	Author = {Li, Heng and others},
+	Journal = {Nat Methods},
+	Month = {Aug},
+	Number = {8},
+	Pages = {595-597},
+	Title = {A synthetic-diploid benchmark for accurate variant-calling evaluation},
+	Volume = {15},
+	Year = {2018}}
+
+@article{Gu:1995wt,
+	author = {Gu, X and Li, W H},
+	journal = {J Mol Evol},
+	month = {Apr},
+	number = {4},
+	pages = {464-73},
+	title = {The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment},
+	volume = {40},
+	year = {1995}}

tex/minimap2.tex

@@ -1,6 +1,6 @@
 \documentclass{bioinfo}
-\copyrightyear{2017}
-\pubyear{2017}
+\copyrightyear{2018}
+\pubyear{2018}
 
 \usepackage{graphicx}
 \usepackage{hyperref}
@@ -19,7 +19,7 @@
 \begin{document}
 \firstpage{1}
 
-\title[Aligning nucleotide sequences with minimap2]{Minimap2: versatile pairwise alignment for nucleotide sequences}
+\title[Aligning nucleotide sequences with minimap2]{Minimap2: pairwise alignment for nucleotide sequences}
 \author[Li]{Heng Li}
 \address{Broad Institute, 415 Main Street, Cambridge, MA 02142, USA}
 
@@ -40,9 +40,10 @@ full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely
 related full chromosomes of hundreds of megabases in length. Minimap2 does
 split-read alignment, employs concave gap cost for long insertions and
 deletions (INDELs) and introduces new heuristics to reduce spurious alignments.
-It is 3--4 times faster than mainstream short-read mappers at comparable
-accuracy and $\ge$30 times faster at higher accuracy for both genomic and mRNA
-reads, surpassing most aligners specialized in one type of alignment.
+It is 3--4 times as fast as mainstream short-read mappers at comparable
+accuracy, and is $\ge$30 times faster than long-read genomic or cDNA
+mappers at higher accuracy, surpassing most aligners specialized in one type of
+alignment.
 
 \section{Availability and implementation:}
 \href{https://github.com/lh3/minimap2}{https://github.com/lh3/minimap2}
@@ -63,7 +64,7 @@ the thought that 10kb long sequences should be easier to map than 100bp reads
 because we can more effectively skip repetitive regions, which are often the
 bottleneck of short-read alignment. We confirmed our speculation by achieving
 approximate mapping 50 times faster than BWA-MEM~\citep{Li:2016aa}.
-\citet{Suzuki130633} extended our work with a fast and novel algorithm on
+\citet{Suzuki:2018aa} extended our work with a fast and novel algorithm on
 generating base-level alignment, which in turn inspired us to develop minimap2
 with added functionality.
 
@@ -87,12 +88,14 @@ the versatility of minimap2.
 
 Minimap2 follows a typical seed-chain-align procedure as is used by most
 full-genome aligners. It collects minimizers~\citep{Roberts:2004fv} of the
-reference sequences and indexes them in a hash table. Then for each query
-sequence, minimap2 takes query minimizers as \emph{seeds}, finds matches to the
-reference, and identifies sets of colinear seeds, which are called
+reference sequences and indexes them in a hash table, with the key being the
+hash of a minimizer and the value being a list of locations of the minimizer
+copies. Then for each query
+sequence, minimap2 takes query minimizers as \emph{seeds}, finds exact matches
+(i.e. \emph{anchors}) to the reference, and identifies sets of colinear anchors as
 \emph{chains}. If base-level alignment is requested, minimap2 applies dynamic
-programming (DP) to extend from the ends of chains and to close unseeded
-regions between adjacent seeds in chains.
+programming (DP) to extend from the ends of chains and to close
+regions between adjacent anchors in chains.
 
 Minimap2 uses indexing and seeding algorithms similar to
 minimap~\citep{Li:2016aa}, and furthers the predecessor with more accurate
@@ -119,10 +122,13 @@ distance between two anchors is too large); otherwise
 \end{equation}
 In implementation, a gap of length $l$ costs
 \[
-\gamma_c(l)=0.01\cdot \bar{w}\cdot|l|+0.5\log_2|l|
+\gamma_c(l)=\left\{\begin{array}{ll}
+0.01\cdot \bar{w}\cdot|l|+0.5\log_2|l| & (l\not=0) \\
+0 & (l=0)
+\end{array}\right.
 \]
-where $\bar{w}$ is the average seed length. For $m$ anchors, directly computing all $f(\cdot)$ with
-Eq.~(\ref{eq:chain}) takes $O(m^2)$ time. Although theoretically faster
+where $\bar{w}$ is the average seed length. For $N$ anchors, directly computing all $f(\cdot)$ with
+Eq.~(\ref{eq:chain}) takes $O(N^2)$ time. Although theoretically faster
 chaining algorithms exist~\citep{Abouelhoda:2005aa}, they
 are inapplicable to generic gap cost, complex to implement and usually
 associated with a large constant. We introduced a simple heuristic to
@@ -132,7 +138,7 @@ We note that if anchor $i$ is chained to $j$, chaining $i$ to a predecessor
 of $j$ is likely to yield a lower score. When evaluating Eq.~(\ref{eq:chain}),
 we start from anchor $i-1$ and stop the process if we cannot find a better
 score after up to $h$ iterations. This approach reduces the average time to
-$O(h\cdot m)$. In practice, we can almost always find the optimal chain with
+$O(hN)$. In practice, we can almost always find the optimal chain with
 $h=50$; even if the heuristic fails, the optimal chain is often close.
 
 \subsubsection{Backtracking}
@@ -146,9 +152,11 @@ in more than one chains.
 \subsubsection{Identifying primary chains}\label{sec:primary}
 In the absence of copy number changes, each query segment should not be mapped
 to two places in the reference. However, chains found at the previous step may
-have significant or complete overlaps due to repeats in the reference.
+have significant or complete overlaps due to repeats in the reference~\citep{Li:2010fk}.
 Minimap2 used the following procedure to identify \emph{primary chains} that do
-not greatly overlap on the query. Let $Q$ be an empty set initially. For each
+not greatly overlap on the query.
+
+Let $Q$ be an empty set initially. For each
 chain from the best to the worst according to their chaining scores: if on the
 query, the chain overlaps with a chain in $Q$ by 50\% or higher percentage of
 the shorter chain, mark the chain as secondary to the chain in $Q$; otherwise,
@@ -156,6 +164,16 @@ add the chain to $Q$. In the end, $Q$ contains all the primary chains. We did
 not choose a more sophisticated data structure (e.g. range tree or k-d tree)
 because this step is not the performance bottleneck.
 
+For each primary chain, minimap2 estimates its mapping quality with an
+empirical formula:
+\[
+{\rm mapQ}=40\cdot (1-f_2/f_1)\cdot\min\{1,m/10\}\cdot\log f_1
+\]
+where $\log$ denotes natural logarithm, $m$ is the number of anchors on the primary chain, $f_1$ is the chaining
+score, and $f_2\le f_1$ is the score of the best chain that is secondary to the
+primary chain. Intuitively, a chain is assigned to a higher mapping quality if
+it is long and its best secondary chain is weak.
+
 \subsubsection{Estimating per-base sequence divergence}
 Suppose a query sequence harbors $n$ seeds of length $k$, $m$ of which are
 present in a chain. We want to estimate the sequence divergence $\epsilon$
@@ -186,7 +204,7 @@ $0.9$.
 \subsubsection{Indexing with homopolymer compressed $k$-mers}
 SmartDenovo
 (\href{https://github.com/ruanjue/smartdenovo}{https://github.com/ruanjue/smartdenovo};
-J Ruan, personal communication) indexes reads with homopolymer-compressed (HPC)
+J. Ruan, personal communication) indexes reads with homopolymer-compressed (HPC)
 $k$-mers and finds the strategy improves overlap sensitivity for SMRT reads.
 Minimap2 adopts the same heuristic.
 
@@ -199,9 +217,9 @@ To demonstrate the effectiveness of HPC $k$-mers, we performed read overlapping
 for the example {\it E. coli} SMRT reads from PBcR~\citep{Berlin:2015xy}, using
 different types of $k$-mers. With normal 15bp minimizers per 5bp window,
 minimap2 finds 90.9\% of $\ge$2kb overlaps inferred from the read-to-reference
-alignment. With HPC 19-mers, minimap2 finds 97.4\% of overlaps. It achieves this
+alignment. With HPC 19-mers per 5bp window, minimap2 finds 97.4\% of overlaps. It achieves this
 higher sensitivity by indexing 1/3 fewer minimizers, which further helps
-performance. HPC-based indexing reduces the sensitivity for ONT reads, though.
+performance. HPC-based indexing reduces the sensitivity for current ONT reads, though.
 
 \subsection{Aligning genomic DNA}\label{sec:genomic}
 
@@ -240,14 +258,14 @@ performance of minimap2. Traditional SSE implementations~\citep{Farrar:2007hs}
 based on Eq.~(\ref{eq:ae86}) can achieve 16-way parallelization for short
 sequences, but only 4-way parallelization when the peak alignment score reaches
 32767. Long sequence alignment may exceed this threshold. Inspired by
-\citet{Wu:1996aa} and the following work, \citet{Suzuki130633} proposed a
+\citet{Wu:1996aa} and the following work, \citet{Suzuki:2018aa} proposed a
 difference-based formulation that lifted this limitation.
 In case of 2-piece gap cost, define
 \[
 \left\{\begin{array}{ll}
 u_{ij}\triangleq H_{ij}-H_{i-1,j} & v_{ij}\triangleq H_{ij}-H_{i,j-1} \\
-x_{ij}\triangleq E_{i+1,j}-H_{ij} & \tilde{x}_{ij}\triangleq \tilde{E}_{i+1,j}-\tilde{H}_{ij} \\
-y_{ij}\triangleq F_{i,j+1}-H_{ij} & \tilde{y}_{ij}\triangleq \tilde{F}_{i,j+1}-\tilde{H}_{ij}
+x_{ij}\triangleq E_{i+1,j}-H_{ij} & \tilde{x}_{ij}\triangleq \tilde{E}_{i+1,j}-H_{ij} \\
+y_{ij}\triangleq F_{i,j+1}-H_{ij} & \tilde{y}_{ij}\triangleq \tilde{F}_{i,j+1}-H_{ij}
 \end{array}\right.
 \]
 We can transform Eq.~(\ref{eq:ae86}) to
@@ -307,11 +325,11 @@ y_{rt}&=&\max\{0,y_{r-1,t}+u_{r-1,t}-z_{rt}+q\}-q-e\\
 \end{equation*}
 In this formulation, cells with the same diagonal index $r$ are independent of
 each other. This allows us to fully vectorize the computation of all cells on
-the same anti-diagonal in one inner loop. It also simplifies banded alignment,
+the same anti-diagonal in one inner loop. It also simplifies banded alignment (500bp band width by default),
 which would be difficult with striped vectorization~\citep{Farrar:2007hs}.
 
 On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, the initial
-values in the diagonal-antidiagonal formuation is
+values in the diagonal-antidiagonal formuation are
 \[
 \left\{\begin{array}{l}
 x_{r-1,-1}=y_{r-1,r}=-q-e\\
@@ -330,12 +348,19 @@ r\cdot(e-\tilde{e})-(\tilde{q}-q)-\tilde{e} & (r=\lceil\frac{\tilde{q}-q}{e-\til
 \]
 These can be derived from the initial values for Eq.~(\ref{eq:ae86}).
 
+When performing global alignment, we do not need to compute $H_{rt}$ in each cell.
+We use 16-way vectorization throughout the alignment process. When extending
+alignments from ends of chains, we need to find the cell $(r,t)$ where $H_{rt}$
+reaches the maximum. We resort to 4-way vectorization to compute
+$H_{rt}=H_{r-1,t}+u_{rt}$. Because this computation is simple,
+Eq.~(\ref{eq:suzuki}) is still the dominant performance bottleneck.
+
 In practice, our 16-way vectorized implementation of global alignment is three
 times as fast as Parasail's 4-way vectorization~\citep{Daily:2016aa}.  Without
 banding, our implementation is slower than Edlib~\citep{Sosic:2017aa}, but with
 a 1000bp band, it is considerably faster. When performing global alignment
 between anchors, we expect the alignment to stay close to the diagonal of the
-DP matrix. Banding is applicable most of time.
+DP matrix. Banding is applicable most of the time.
 
 \subsubsection{The Z-drop heuristic}
 
@@ -359,6 +384,16 @@ alignment between the two subsequences involved in the global alignment, but
 this time with the one subsequence reverse complemented. This additional
 alignment step may identify short inversions that are missed during chaining.
 
+\subsubsection{Filtering out misplaced anchors}
+Due to sequencing errors and local homology, some anchors in a chain may be
+wrong. If we blindly align regions between two misplaced anchors, we will
+produce a suboptimal alignment. To reduce this artifact, we filter out
+anchors that lead to a $>$10bp insertion and a $>$10bp deletion at the same
+time, and filter out terminal anchors that lead to a long gap towards the ends
+of a chain. These heuristics greatly alleviate the issues with misplaced
+anchors, but they are unable to fix all such errors. Local misalignment is a
+limitation of minimap2 which we hope to address in future.
+
 \subsection{Aligning spliced sequences}
 
 The algorithm described above can be adapted to spliced alignment. In this
@@ -397,7 +432,7 @@ p/2 & \mbox{if $T[i+1,i+3]$ is ${\tt GTC}$ or ${\tt GTT}$} \\
 p & \mbox{otherwise}
 \end{array}\right.\]
 where $T[i,j]$ extracts a substring of $T$ between $i$ and $j$ inclusively.
-$d(i)$ penalizes non-canonical donor sites with $p$ and less frequent Eukayotic
+$d(i)$ penalizes non-canonical donor sites with $p$ and less frequent Eukaryotic
 splicing signal ${\tt GT[C/T]}$ with $p/2$~\citep{Irimia:2008aa}. Similarly,
 \[a(i)=\left\{\begin{array}{ll}
 0 & \mbox{if $T[i-2,i]$ is ${\tt CAG}$ or ${\tt TAG}$} \\
@@ -424,13 +459,13 @@ alignment.
 
 \subsection{Aligning short paired-end reads}
 
-During chainging, minimap2 takes a pair of reads as one fragment with a gap of
+During chaining, minimap2 takes a pair of reads as one fragment with a gap of
 unknown length in the middle. It applies a normal gap cost between seeds on the
 same read but is a more permissive gap cost between seeds on different reads.
-More precisely, the gap cost during chaining is:
+More precisely, the gap cost during chaining is ($l\not=0$):
 \[
 \gamma_c(l)=\left\{\begin{array}{ll}
-0.01\cdot\bar{w}\cdot l+0.5\log_2 l & \mbox{if two seeds on the same read} \\
+0.01\cdot\bar{w}\cdot |l|+0.5\log_2 |l| & \mbox{if two seeds on the same read} \\
 \min\{0.01\cdot\bar{w}\cdot|l|,\log_2|l|\} & \mbox{otherwise}
 \end{array}\right.
 \]
@@ -443,6 +478,17 @@ consistent paired-end alignments.
 
 \section{Results}
 
+Minimap2 is implemented in the C programming language and comes with APIs in
+both C and Python. It is distributed under the MIT license, free to both
+commercial and academic uses. Minimap2 uses the same base algorithm for all
+applications, but it has to apply different sets of parameters depending on
+input data types. Similar to BWA-MEM, minimap2 introduces `presets' that
+modify multiple parameters with a simple invocation. Detailed settings
+and command-line options can be found in the minimap2 manpage. In addition to
+the applications evaluated in the following sections, minimap2 also retains
+minimap's functionality to find overlaps between long reads and to search
+against large multi-species databases such as \emph{nt} from NCBI.
+
 \subsection{Aligning long genomic reads}\label{sec:long-genomic}
 
 \begin{figure}[!tb]
@@ -450,19 +496,22 @@ consistent paired-end alignments.
 \includegraphics[width=.5\textwidth]{roc-color.pdf}
 \caption{Evaluation on aligning simulated reads. Simulated reads were mapped 
 to the primary assembly of human genome GRCh38. A read is considered correctly
-mapped if the true position overlaps with the best mapping position by 10\% of
-the read length. Read alignments are sorted by mapping quality in the
-descending order. For each mapping quality threshold, the fraction of
-alignments with mapping quality above the threshold and their error rate are
+mapped if its longest alignment overlaps with the true interval, and the
+overlap length is $\ge$10\% of the true interval length.  Read alignments are
+sorted by mapping quality in the descending order. For each mapping quality
+threshold, the fraction of alignments (out of the number of input reads) with
+mapping quality above the threshold and their error rate are
 plotted along the curve. (a) long-read alignment evaluation. 33,088 $\ge$1000bp
 reads were simulated using pbsim~\citep{Ono:2013aa} with error profile sampled
 from file `m131017\_060208\_42213\_*.1.*' downloaded at
 \href{http://bit.ly/chm1p5c3}{http://bit.ly/chm1p5c3}. The N50 read length is
 11,628. Aligners were run under the default setting for SMRT reads.
-(b) short-read alignment evaluation. 10 million pairs of 150bp reads were
-simulated using mason2~\citep{Holtgrewe:2010aa} with option
-`\mbox{--illumina-prob-mismatch-scale 2.5}'. Short-read aligners were run under the
-default setting except for changing the maximum fragment length to
+Kart outputted all alignments at mapping quality 60, so is not shown in the
+figure. It mapped nearly all reads with 4.1\% of alignments being wrong, less
+accurate than others.  (b) short-read alignment evaluation. 10 million pairs of
+150bp reads were simulated using mason2~\citep{Holtgrewe:2010aa} with option
+`\mbox{--illumina-prob-mismatch-scale 2.5}'. Short-read aligners were run under
+the default setting except for changing the maximum fragment length to
 800bp.}\label{fig:eval}
 \end{figure}
 
@@ -471,7 +520,7 @@ BLASR~(v1.MC.rc64; \citealp{Chaisson:2012aa}),
 BWA-MEM~(v0.7.15; \citealp{Li:2013aa}),
 GraphMap~(v0.5.2; \citealp{Sovic:2016aa}),
 Kart~(v2.2.5; \citealp{Lin:2017aa}),
-minialign~(v0.5.3; \citealp{Suzuki:2016}) and
+minialign~(v0.5.3; \href{https://github.com/ocxtal/minialign}{https://github.com/ocxtal/minialign}) and
 NGMLR~(v0.2.5; \citealp{Sedlazeck169557}). We excluded rHAT~\citep{Liu:2016ab}
 and LAMSA~\citep{Liu:2017aa} because they either
 crashed or produced malformatted output. In this evaluation, minimap2 has
@@ -480,11 +529,11 @@ higher mapping accuracy (Fig.~\ref{fig:eval}a). Minimap2 and
 NGMLR provide better mapping quality estimate: they rarely give repetitive hits
 high mapping quality.  Apparently, other aligners may
 occasionally miss close suboptimal hits and be overconfident in wrong mappings.
-On run time, minialign is slightly faster than minimap2 and Kart. They are over
-30 times faster than the rest.  Minimap2 consumed 6.1GB memory at the peak,
-more than BWA-MEM but less than others.
+On run time, minimap2 took 200 CPU seconds, comparable to minialign and Kart, and is over
+30 times faster than the rest.  Minimap2 consumed 6.8GB memory at the peak,
+more than BWA-MEM (5.4GB), similar to NGMLR and less than others.
 
-On real human SMRT reads, the relative performance and sensitivity of
+On real human SMRT reads, the relative performance and fraction of mapped reads reported by
 these aligners are broadly similar to the metrics on simulated data. We are
 unable to provide a good estimate of mapping error rate due to the lack of the
 truth.  On ONT $\sim$100kb human reads~\citep{Jain128835}, BWA-MEM failed.
@@ -526,7 +575,7 @@ Peak RAM (GByte)          & 8.9      & 14.5     & 3.2      & 29.2\vspace{1em}\\
 \% approx. introns        & 91.8\%   & 96.9\%   & 92.5\%   & 82.4\% \\
 \botrule
 \end{tabular}
-}{Mouse reads (AC:SRR5286960) were mapped to the primary assembly of mouse
+}{Mouse cDNA reads (AC:SRR5286960; R9.4 chemistry) were mapped to the primary assembly of mouse
 genome GRCm38 with the following tools and command options: minimap2 (`-ax
 splice'); GMAP (`-n 0 --min-intronlength 30 --cross-species'); SpAln (`-Q7 -LS
 -S3'); STARlong (according to
@@ -535,7 +584,7 @@ compared to the EnsEMBL gene annotation, release 89. A predicted intron
 is \emph{novel} if it has no overlaps with any annotated introns. An intron
 is \emph{exact} if it is identical to an annotated intron. An intron is
 \emph{approximate} if both its 5'- and 3'-end are within 10bp around the ends
-of an annotated intron.}
+of an annotated intron. Chimeric alignments are defined in the SAM spec~\citep{Li:2009ys}.}
 \end{table}
 
 We next aligned real mouse reads~\citep{Byrne:2017aa} with GMAP~(v2017-06-20;
@@ -592,7 +641,7 @@ simulated data set than Bowtie2 and SNAP but less accurate than BWA-MEM
 (Fig.~\ref{fig:eval}b). Closer investigation reveals that BWA-MEM achieves
 a higher accuracy partly because it tries to locally align a read in a small
 region close to its mate. If we disable this feature, BWA-MEM becomes slightly
-less accurate than minimap2. We might consider to implement a similar heuristic
+less accurate than minimap2. We might implement a similar heuristic
 in minimap2 in future.
 
 To evaluate the accuracy of minimap2 on real data, we aligned human reads
@@ -603,19 +652,29 @@ across the whole genome and have been \emph{de novo} assembled with SMRT reads
 to high quality. This allowed us to construct an independent truth variant
 dataset~\citep{Li223297} for
 ERR1341796. In this evaluation, minimap2 has higher SNP false negative rate
-(FNR; 2.5\% of minimap2 vs 2.2\% of BWA-MEM), but fewer false positive SNPs per
-million bases (FPPM; 3.0 vs 3.9), lower 2--50bp INDEL FNR (7.3\% vs 7.5\%) and
-similar INDEL FPPM (both 1.0). Minimap2 is broadly similar to BWA-MEM in the
+(FNR; 2.6\% of minimap2 vs 2.3\% of BWA-MEM), but fewer false positive SNPs per
+million bases (FPPM; 7.0 vs 8.8), similar INDEL FNR (11.2\% vs 11.3\%) and
+similar INDEL FPPM (6.4 vs 6.5). Minimap2 is broadly comparable to BWA-MEM in the
 context of small variant calling.
 
-\subsection{Other applications}
+\subsection{Aligning long-read assemblies}
 
-Minimap2 retains minimap's functionality to find overlaps between long reads
-and to search against large multi-species databases such as \emph{nt} from
-NCBI. Minimap2 can also align similar genomes or different assemblies of the
-same species. It took 7 wall-clock minutes over 8 CPU cores to align a human
-SMRT assembly (AC:GCA\_001297185.1) to GRCh38, over 20 times faster
-MUMmer4~\citep{Kurtz:2004zr}.
+Minimap2 can align a SMRT assembly (AC:GCA\_001297185.1) against GRCh38 in 7
+minutes using 8 CPU cores, over 20 times faster than nucmer from
+MUMmer4~\citep{Marcais:2018aa}. With the paftools.js script from the minimap2
+package, we called 2.67 million single-base substitutions out of 2.78Gbp
+genomic regions. The transition-to-transversion ratio (ts/tv) is 2.01. In
+comparison, using MUMmer4's dnadiff pipeline, we called 2.86 million
+substitutions in 2.83Gbp at ts/tv=1.87. Given that ts/tv averaged across the
+human genome is about 2 but ts/tv averaged over random errors is 0.5, the
+minimap2 callset arguably has higher precision at lower sensitivity.
+
+The sample being assembled is a female. Minimap2 still called 201 substitutions
+on the Y chromosome. These substitutions all come from one contig aligned at
+96.8\% sequence identity. The contig could be a segmental duplication
+absent from GRCh38. In constrast, dnadiff called 9070 substitutions on the Y
+chromosome across 73 SMRT contigs. This again implies our minimap2-based
+pipeline has higher precision.
 
 \section{Discussions}
 
@@ -633,9 +692,9 @@ involving $>$100kb introns, which was impractically slow ten years ago.  The
 minimap2 chaining algorithm is fast and highly accurate by itself.  In fact,
 chaining alone is more accurate than all the other long-read mappers in
 Fig.~\ref{fig:eval}a (data not shown). This accuracy helps to reduce downstream
-base-level alignment of candidate chains, which is still times slower than
+base-level alignment of candidate chains, which is still several times slower than
 chaining even with the Suzuki-Kasahara improvement. In addition, taking a
-general form, minimap2 chaining can be adapted to non-typical data types such
+general form, minimap2 chaining can be adapted to non-typical data types such as
 spliced reads and multiple reads per fragment. This gives us the opportunity to
 extend the same base algorithm to a variety of use cases.
 
@@ -647,8 +706,9 @@ k-mers with a hash table instead. Such fixed-length seeds are inferior to
 variable-length seeds in theory, but can be computed much more efficiently in
 practice. When a query sequence has multiple seed hits, we can afford to skip
 highly repetitive seeds without affecting the final accuracy. This further
-alleviates the concern with the uniqueness of seeds. Hash table is the ideal
-data structure for mapping long query sequences.
+alleviates the concern with the seeding uniqueness. At the same time, at low
+sequence identity, it is rare to see long seeds anyway. Hash table is the ideal
+data structure for mapping long noisy sequences.
 
 \section*{Acknowledgements}
 We owe a debt of gratitude to H. Suzuki and M. Kasahara for releasing their
@@ -657,6 +717,8 @@ Schatz, P. Rescheneder and F. Sedlazeck for pointing out the limitation of
 BWA-MEM. We are also grateful to minimap2 users who have greatly helped to
 suggest features and to fix various issues.
 
+\paragraph{Funding\textcolon} NHGRI 1R01HG010040-01
+
 \bibliography{minimap2}
 
 \end{document}

tex/mm2-update.tex

@@ -0,0 +1,240 @@
+\documentclass{bioinfo}
+\copyrightyear{2021}
+\pubyear{2021}
+
+\usepackage{graphicx}
+\usepackage{hyperref}
+\usepackage{url}
+\usepackage{amsmath}
+\usepackage[ruled,vlined]{algorithm2e}
+\newcommand\mycommfont[1]{\footnotesize\rmfamily{\it #1}}
+\SetCommentSty{mycommfont}
+\SetKwComment{Comment}{$\triangleright$\ }{}
+
+\usepackage{natbib}
+\bibliographystyle{apalike}
+
+\DeclareMathOperator*{\argmax}{argmax}
+
+\begin{document}
+\firstpage{1}
+
+\title[Improvements to minimap2]{New strategies to improve minimap2 alignment accuracy}
+\author[Li]{Heng Li$^{1,2}$}
+\address{$^1$Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA,
+$^2$Harvard Medical School, 10 Shattuck St, Boston, MA 02215, USA}
+
+\maketitle
+
+\begin{abstract}
+
+\section{Summary:} We present several recent improvements to minimap2, a
+versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can
+more accurately map long reads to highly repetitive regions and align through
+insertions or deletions up to 100kb by default, addressing major weakness in
+minimap2 v2.18 or earlier.
+
+\section{Availability and implementation:}
+\href{https://github.com/lh3/minimap2}{https://github.com/lh3/minimap2}
+
+\section{Contact:} hli@ds.dfci.harvard.edu
+\end{abstract}
+
+\section{Introduction}
+Minimap2~\citep{Li:2018ab} is widely used for maping long sequence
+reads and assembly contigs. \citet{Jain:2020aa} found minimap2 v2.18 or earlier occasionally
+misaligned reads from highly repetitive regions as minimap2 ignored seeds of
+high occurrence. They also noticed minimap2 may misplace reads with structural
+variations (SVs) in such regions~\citep{Jain2020.11.01.363887}. These
+misalignments have become a pressing issue in the advent of
+temolere-to-telomore human assembly~\citep{Miga:2020aa}. Meanwhile, old minimap2
+was unable to efficiently align long insertions/deletions (INDELs) and often
+breaks an alignment around variable-number tandem repeats (VNTRs). This has
+inspired new chaining algorithms~\citep{Li:2020aa,Ren:2021aa} which are not
+integrated into minimap2. Here we will describe recent efforts implemented
+in v2.19 through v2.22 to improve mapping results.
+
+\begin{methods}
+\section{Methods}
+
+\subsection{Rescuing high-occurrence $k$-mers}\label{sec:high-occ}
+Minimap2 keeps all $k$-mer minimizers~\citep{Roberts:2004fv} during indexing. Its original
+implementation only selected low-occurrence minimizers during mapping. The
+cutoff is a few hundred for mapping long reads against a human genome. If a
+read habors only a few or even no low-occurrence minimizers, it will fail
+chaining due to insufficient anchors.
+
+To resolve this issue, we implemented a new heuristic to add additional
+minimizers. Suppose we are looking at two adjacent low-occurence $k$-mers
+located at position $x_1$ and $x_2$, respectively. If $|x_1-x_2|\ge L$,
+minimap2 v2.22 additionally selects $\lfloor|x_1-x_2|/L\rfloor$ minimizers
+of the lowest occurrence among minimizers between $x_1$ and $x_2$. Here
+parameter $L$ controls the frequency of sampling. It defaults to 500.
+This strategy adds necessary anchors at the cost of increasing total alignment
+time by a few percent on real data.
+
+\subsection{Aligning through longer INDELs}
+The original minimap2 may fail to align long INDELs due to its chaining
+heuristics. Briefly, minimap2 applies dynamic programming (DP) to chain
+minimizer anchors. This is a quadratic algorithm, slow for chaining
+contigs. For acceptable performance, the original minimap2 uses a 500bp band by
+default, which means a gap longer than 500bp will stop chaining.
+To align through longer gaps, older minimap2 implemented a long-join heurstic as follows.
+If there is an INDEL longer than 500bp and the two chains around the INDEL
+have no overlaps on either the query or the reference sequence, minimap2 may
+join the two short chains later.
+This heuristic may fail around VNTRs because short chains
+often have overlaps in VNTRs. More subtly, minimap2 may escape the inner DP
+loop early, again for performance, if the chaining result is not improved for
+50 iterations. When there is a copy number change in a long segmental
+duplication, the early escape may break around the event even if users
+specify a large band.
+
+In minigraph~\citep{Li:2020aa}, we developed a new chaining algorithm that
+finds up to 1kb INDELs with DP-based chaining and goes through longer INDELs with a
+subquadratic algorithm~\citep{DBLP:conf/wabi/AbouelhodaO03}. We ported the same
+algorithm to minimap2 for contig mapping. For long-read mapping, the minigraph
+algorithm is slower. Minimap2 v2.22 still uses the DP-based algorithm to
+find short chains and then invokes the minigraph algorithm to rechain anchors in
+these short chains. The rechaining step achieves the same goal as long-join
+but is more reliable because it can resolve overlaps between short chains. The old
+long-join heuristic has since been removed.
+
+\subsection{Properly mapping long reads with SVs}
+The original minimap2 ranks an alignment by its Smith-Waterman score and
+outputs the best scoring alignment. However, when there are SVs on the read,
+the best scoring alignment is sometimes not the correct alignment.
+\citet{Jain2020.11.01.363887} resolved this dilemma by altering the mapping
+algorithm.
+
+In our view, this problem is rooted in inapropriate scoring: affine-gap penalty
+over-penalizes a long INDEL that was often evolutionarily created in one event.
+We should not penalize a SV by a function linear in the SV length. Minimap2 v2.22 instead rescores
+an alignment with the following scoring function. Suppose an alignment consists
+of $M$ matching bases, $N$ substitutions and $G$ gap opens, we empirically
+score the alignment with
+$$
+S=M-\frac{N+G}{2d}-\sum_{i=1}^G\log_2(1+g_i)
+$$
+where $g_i\ge1$ is the length of the $i$-th gap and
+$$
+d=\max\left\{\frac{N+G}{M+N+G},0.02\right\}
+$$
+It approximates per-base sequence divergence except with the smallest value set
+to 2\%. As an analogy to affine-gap scoring, the matching score in our scheme
+is 1, the mismatch and gap open penalties are both $1/2d$ and the gap extension
+penalty is a logarithm function of the gap length~\citep{Gu:1995wt}. Our scoring gives a long SV
+a much milder penalty. In terms of time complexity, scoring an alignment is
+linear in the length of the alignment. The time spent on rescoring is negligible in
+practice.
+
+%If we assume sequences evolve under a duplication-mutation model, we may have a
+%better way to choose the best alignment. If a long read can be mapped to $n$
+%loci, we can take the read as the template and build a
+%pseudo-multi-sequence-alignment (pMSA) of $n+1$ sequences. In this pMSA, we say
+%a site on the read is informative if the $n$ reference subsequences differ at
+%the position.
+
+\end{methods}
+
+\section{Results}
+
+\begin{table}
+\processtable{Evaluation of minimap2 v2.22}
+{\footnotesize\label{tab:1}\begin{tabular}{p{4.2cm}rrrr}
+\toprule
+$[$Benchmark$]$ Metric & v2.22 & v2.18 & Winno & lra \\
+\midrule
+$[$sim-map$]$ \% mapped reads at Q10      & 97.9       & 97.6      & {\bf 99.0}& 97.3 \\
+$[$sim-map$]$ err. rate at Q10 (phredQ)   & {\bf 52}   & {\bf 52}  & 38        & 24 \\
+$[$winno-cmp$]$ rate of diff. (phredQ)    & {\bf 41}   & 37        & truth     & 18 \\
+$[$winno-cmp$]$ CPU time (hour)           & {\bf 5.0}  & 5.3       & 71.8      & 13.1 \\
+$[$winno-cmp$]$ peak RAM (Gb)             & 17.1       & 14.4      & {\bf 9.6} & 12.4 \\
+$[$sim-sv$]$  \% false negative rate      & {\bf 0.5}  & 2.0       & {\bf 0.5} & 1.4  \\
+$[$sim-sv$]$  \% false discovery rate     & {\bf 0.0}  & 0.1       & {\bf 0.0} & 0.1  \\
+$[$real-sv-1k$]$ \% false negative rate   & {\bf 7.3}  & 20.0      & 13.0      & N/A \\
+$[$real-sv-1k$]$ \% false discovery rate  & 2.7        & {\bf 2.4} & 2.7       & N/A \\
+\botrule
+\end{tabular}}
+{In $[$sim-map$]$, 152,713 reads were simulated from the CHM13 telomere-to-telomere assembly v1.1
+(AC: GCA\_009914755.3) with pbsim2~\citep{Ono:2021aa}: ``pbsim2 -{}-hmm\_model R94.model -{}-length-min
+5000 -{}-length-mean 20000 -{}-accuracy-mean 0.95''. Alignments of mapping quality
+10 or higher were evaluated by ``paftools.js mapeval''. The mapping error rate
+is measured in the phred scale: if the error rate is $e$, $-10\log_{10}e$ is
+reported in the table. In $[$winno-cmp$]$, 1.39 million CHM13 HiFi reads from
+SRR11292121 were mapped against the same CHM13 assembly. 99.3\% of them were mapped by Winnowmap2
+at mapping quality 10 or higher and were taken as ground truth to evaluate
+minimap2 and lra with ``paftools.js pafcmp''. $[$sim-sv$]$ simulated 1,000
+50bp to 1000bp INDELs from chr8 in CHM13 using SURVIVOR~\citep{Jeffares:2017aa} and simulated Nanopore
+reads at 30-fold coverage with the same pbsim2 command line. SVs were called with
+``sniffles -q 10''~\citep{Sedlazeck:2018ab} and compared to the simulated truth with ``SURVIVOR eval
+call.vcf truth.bed 50''. In $[$real-sv-1k$]$, small and long variants were
+called by dipcall-0.3~\citep{Li:2018aa} for HG002 assemblies (AC: GCA\_018852605.1 and
+GCA\_018852615.1) and compared to the GIAB truth~\citep{Zook:2020aa} using ``truvari -r 2000 -s
+1000 -S 400 -{}-multimatch -{}-passonly'' which sets the minimum INDEL size to 1kb in evaluation. }
+\end{table}
+
+We evaluated minimap2 v2.22 along with v2.18, Winnowmap2 v2.03 and lra v1.3.2
+(Table~\ref{tab:1}), using the default setting of each mapper according to the input data types.
+Both versions of minimap2 achieved high mapping accuracy on
+simulated Nanopore reads (sim-map). Winnowmap2 aligned more reads at mapping
+quality 10 or higher (mapQ10). However, it may occasionally assign a high mapping
+quality to a read with multiple identical best alignments. This reduced its
+mapping accuracy.
+
+In lack of groud truth for real data, we took Winnowmap2 mapping as ground
+truth to evaluate other mappers (winno-cmp in Table~\ref{tab:1}). Out of 1,378,092 reads with mapQ10
+alignments by Winnowmap2, minimap2 v2.22 could map all of them. 118 reads, less
+than 0.01\% of all reads, were mapped differently by v2.22. 51 of them have
+multiple identical best alignments. We believe these are more likely to be
+Winnowmap2 errors. Most of the remaining 67 (=118-51) reads have multiple
+highly similar but not identical alignments.
+Minimap2 v2.18 is less consistent with 275 differences including 30 unmapped
+reads mappable by both Winnowmap2 and v2.22.
+
+For the minimizer rescuing parameter $L$ in Section~\ref{sec:high-occ},
+we set its default to 500 such that v2.22 has comparable performance to v2.18 given simulated PacBio and Nanopore human reads.
+To see the effect of this parameter on real data, we tried several different $L$ values.
+v2.22 gave 99 mapping differences at $L=200$,
+118 at $L=500$ (default), 167 at $L=750$ and 224 differences at $L=1000$ in comparison to Winnowmap2.
+$L=200$ is 28\% slower than the default while $L=1000$ is 9\% faster.
+Changing the default minimizer window size (option ``-w'')
+and the initial minimizer occurrence cutoff (option ``-f'')
+also affects performance and accuracy to a similar magnitude.
+
+The two benchmarks above only evaluate read mappings when there are no variations between the reads and the reference.
+To measure the mapping accuracy in the presence of SVs (sim-sv), we reproduced
+the results by~\citep{Jain2020.11.01.363887}. Minimap2 v2.22 is as good as
+Winnowmap2 now. Note that we were setting the Sniffles mapping quality
+threshold to 10 in consistent with the benchmarks above. If we used the
+default threshold 20, v2.22 would miss additional five SVs (accounting for
+0.5\% of simulated SVs). For four out of these five missing SVs, minimap2 v2.22
+mapped more variant reads than Winnowmap2. Sniffles did not call these SVs
+because minimap2 tended to give them conservative mapping quality. It is worth
+noting that the simulation here only considers a simple scenario in evolution.
+Non-allelic gene conversions, which happen often in segmental
+duplications~\citep{Harpak:2017aa}, would obscure the optimal mapping
+strategies. How much such simple SV simulation informs real-world SV calling
+remains a question.
+
+To see if minimap2 v2.22 could improve long INDEL alignment, we ran dipcall on
+contig-to-reference alignments and focused on INDELs longer than 1kb
+(real-sv-1k). v2.22 is more sensitive at comparable specificity, confirming its
+advantage in more contiguous alignment. We could not get dipcall to work well with lra,
+so did not report the numbers.
+
+Minimap2 spends most computing time on base alignment. As recent improvements
+in v2.22 incur little additional computing and do not change the base alignment
+algorithm, the new version has similar performance to older versions. It is
+consistently faster than Winnowmap2 by several times. Sometimes simple
+heuristics can be as effective as more sophisticated yet slower solutions.
+
+\section*{Acknowledgements}
+We thank Arang Rhie and Chirag Jain for providing motivating examples for which
+older minimap2 underperforms.
+
+\paragraph{Funding\textcolon} This work is funded by NHGRI grant R01HG010040.
+
+\bibliography{minimap2}
+
+\end{document}