Release minimap2-2.21 (r1071)

Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.

.github/workflows/ci.yaml

@@ -0,0 +1,21 @@
+name: CI
+
+on:
+  push:
+    branches:
+    - master
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout minimap2
+      uses: actions/checkout@v2
+
+    - name: Compile with ${{ matrix.compiler }}
+      run:  make CC=${{ matrix.compiler }}

MANIFEST.in

@@ -4,7 +4,6 @@ include ksw2_dispatch.c
 include main.c
 include README.md
 include sse2neon/emmintrin.h
-include python/mappy.c
 include python/cmappy.h
 include python/cmappy.pxd
 include python/mappy.pyx

Makefile

@@ -1,7 +1,9 @@
 CFLAGS=		-g -Wall -O2 -Wc++-compat #-Wextra
 CPPFLAGS=	-DHAVE_KALLOC
 INCLUDES=
-OBJS=		kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.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 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
@@ -103,26 +105,28 @@ depend:
 
 # 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
-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 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 ketopt.h
-map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h khash.h
-map.o: ksort.h
-misc.o: mmpriv.h minimap.h bseq.h ksort.h
-options.o: mmpriv.h minimap.h bseq.h
-pe.o: mmpriv.h minimap.h bseq.h kvec.h kalloc.h ksort.h
-sdust.o: kalloc.h kdq.h kvec.h ketopt.h sdust.h
-sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h
-splitidx.o: mmpriv.h minimap.h bseq.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
+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

NEWS.md

@@ -1,3 +1,65 @@
+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)
+
+
+
+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)
 ---------------------------------
 

README.md

@@ -1,7 +1,7 @@
 [![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
 ```sh
 git clone https://github.com/lh3/minimap2
@@ -12,9 +12,10 @@ cd minimap2 && make
 ./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 asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio CCS genomic reads
+./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or later)
+./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18 or earlier)
 ./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 (strand unknown)
 ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore Direct RNA-seq
@@ -26,9 +27,6 @@ cd minimap2 && make
 # man page for detailed command line options
 man ./minimap2.1
 ```
-[Unimap][unimap] is recommended 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.
 
 ## Table of Contents
 
@@ -76,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 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/v2.18/minimap2-2.18_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.18_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.21_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
@@ -98,7 +96,7 @@ with the ARM related command lines given above.
 
 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
 ```
@@ -139,13 +137,13 @@ 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
 ```
 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
+performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning
 Nanopore reads.
 
 #### <a name="map-long-splice"></a>Map long mRNA/cDNA reads
@@ -206,7 +204,7 @@ strand field. In this case, each line indicates an oriented junction.
 #### <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
@@ -253,7 +251,7 @@ 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`.
 
 **TL;DR**: if you work with ultra-long reads and use tools that only process
@@ -274,7 +272,7 @@ 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.
 

align.c

@@ -53,16 +53,16 @@ static int mm_test_zdrop(void *km, const mm_mapopt_t *opt, const uint8_t *qseq,
 	// find the score and the region where score drops most along diagonal
 	for (k = 0, score = 0; k < n_cigar; ++k) {
 		uint32_t l, op = cigar[k]&0xf, len = cigar[k]>>4;
-		if (op == 0) {
+		if (op == MM_CIGAR_MATCH) {
 			for (l = 0; l < len; ++l) {
 				score += mat[tseq[i + l] * 5 + qseq[j + l]];
 				update_max_zdrop(score, i+l, j+l, &max, &max_i, &max_j, opt->e, &max_zdrop, pos);
 			}
 			i += len, j += len;
-		} else if (op == 1 || op == 2 || op == 3) {
+		} else if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL || op == MM_CIGAR_N_SKIP) {
 			score -= opt->q + opt->e * len;
-			if (op == 1) j += len; // insertion
-			else i += len;         // deletion
+			if (op == MM_CIGAR_INS) j += len;
+			else i += len;
 			update_max_zdrop(score, i, j, &max, &max_i, &max_j, opt->e, &max_zdrop, pos);
 		}
 	}
@@ -98,12 +98,12 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
 	for (k = 0; k < p->n_cigar; ++k) { // indel left alignment
 		uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
 		if (len == 0) to_shrink = 1;
-		if (op == 0) {
+		if (op == MM_CIGAR_MATCH) {
 			toff += len, qoff += len;
-		} else if (op == 1 || op == 2) { // insertion or deletion
+		} else if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL) {
 			if (k > 0 && k < p->n_cigar - 1 && (p->cigar[k-1]&0xf) == 0 && (p->cigar[k+1]&0xf) == 0) {
 				int l, prev_len = p->cigar[k-1] >> 4;
-				if (op == 1) {
+				if (op == MM_CIGAR_INS) {
 					for (l = 0; l < prev_len; ++l)
 						if (qseq[qoff - 1 - l] != qseq[qoff + len - 1 - l])
 							break;
@@ -116,9 +116,9 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
 					p->cigar[k-1] -= l<<4, p->cigar[k+1] += l<<4, qoff -= l, toff -= l;
 				if (l == prev_len) to_shrink = 1;
 			}
-			if (op == 1) qoff += len;
+			if (op == MM_CIGAR_INS) qoff += len;
 			else toff += len;
-		} else if (op == 3) {
+		} else if (op == MM_CIGAR_N_SKIP) {
 			toff += len;
 		}
 	}
@@ -128,13 +128,13 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
 			uint32_t l, s[3] = {0,0,0};
 			for (l = k; l < p->n_cigar; ++l) { // count number of adjacent I and D
 				uint32_t op = p->cigar[l]&0xf;
-				if (op == 1 || op == 2 || p->cigar[l]>>4 == 0)
+				if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL || p->cigar[l]>>4 == 0)
 					s[op] += p->cigar[l] >> 4;
 				else break;
 			}
 			if (s[1] > 0 && s[2] > 0 && l - k > 2) { // turn to a single I and a single D
-				p->cigar[k]   = s[1]<<4|1;
-				p->cigar[k+1] = s[2]<<4|2;
+				p->cigar[k]   = s[1]<<4|MM_CIGAR_INS;
+				p->cigar[k+1] = s[2]<<4|MM_CIGAR_DEL;
 				for (k += 2; k < l; ++k)
 					p->cigar[k] &= 0xf;
 				to_shrink = 1;
@@ -154,9 +154,9 @@ static void mm_fix_cigar(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *tseq,
 			else p->cigar[k+1] += p->cigar[k]>>4<<4; // add length to the next CIGAR operator
 		p->n_cigar = l;
 	}
-	if ((p->cigar[0]&0xf) == 1 || (p->cigar[0]&0xf) == 2) { // get rid of leading I or D
+	if ((p->cigar[0]&0xf) == MM_CIGAR_INS || (p->cigar[0]&0xf) == MM_CIGAR_DEL) { // get rid of leading I or D
 		int32_t l = p->cigar[0] >> 4;
-		if ((p->cigar[0]&0xf) == 1) {
+		if ((p->cigar[0]&0xf) == MM_CIGAR_INS) {
 			if (r->rev) r->qe -= l;
 			else r->qs += l;
 			*qshift = l;
@@ -174,7 +174,7 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 	if (r->p == 0) return;
 	for (k = 0; k < r->p->n_cigar; ++k) {
 		uint32_t op = r->p->cigar[k]&0xf, len = r->p->cigar[k]>>4;
-		if (op == 0) {
+		if (op == MM_CIGAR_MATCH) {
 			while (len > 0) {
 				for (l = 0; l < len && qseq[qoff + l] == tseq[toff + l]; ++l) {} // run of "="; TODO: N<=>N is converted to "="
 				if (l > 0) { ++n_EQX; len -= l; toff += l; qoff += l; }
@@ -183,11 +183,11 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 				if (l > 0) { ++n_EQX; len -= l; toff += l; qoff += l; }
 			}
 			++n_M;
-		} else if (op == 1) { // insertion
+		} else if (op == MM_CIGAR_INS) {
 			qoff += len;
-		} else if (op == 2) { // deletion
+		} else if (op == MM_CIGAR_DEL) {
 			toff += len;
-		} else if (op == 3) { // intron
+		} else if (op == MM_CIGAR_N_SKIP) {
 			toff += len;
 		}
 	}
@@ -195,7 +195,7 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 	if (n_EQX == n_M) {
 		for (k = 0; k < r->p->n_cigar; ++k) {
 			uint32_t op = r->p->cigar[k]&0xf, len = r->p->cigar[k]>>4;
-			if (op == 0) r->p->cigar[k] = len << 4 | 7;
+			if (op == MM_CIGAR_MATCH) r->p->cigar[k] = len << 4 | MM_CIGAR_EQ_MATCH;
 		}
 		return;
 	}
@@ -209,25 +209,25 @@ static void mm_update_cigar_eqx(mm_reg1_t *r, const uint8_t *qseq, const uint8_t
 	toff = qoff = m = 0;
 	for (k = 0; k < r->p->n_cigar; ++k) {
 		uint32_t op = r->p->cigar[k]&0xf, len = r->p->cigar[k]>>4;
-		if (op == 0) { // match/mismatch
+		if (op == MM_CIGAR_MATCH) {
 			while (len > 0) {
 				// match
 				for (l = 0; l < len && qseq[qoff + l] == tseq[toff + l]; ++l) {}
-				if (l > 0) p->cigar[m++] = l << 4 | 7;
+				if (l > 0) p->cigar[m++] = l << 4 | MM_CIGAR_EQ_MATCH;
 				len -= l;
 				toff += l, qoff += l;
 				// mismatch
 				for (l = 0; l < len && qseq[qoff + l] != tseq[toff + l]; ++l) {}
-				if (l > 0) p->cigar[m++] = l << 4 | 8;
+				if (l > 0) p->cigar[m++] = l << 4 | MM_CIGAR_X_MISMATCH;
 				len -= l;
 				toff += l, qoff += l;
 			}
 			continue;
-		} else if (op == 1) { // insertion
+		} else if (op == MM_CIGAR_INS) {
 			qoff += len;
-		} else if (op == 2) { // deletion
+		} else if (op == MM_CIGAR_DEL) {
 			toff += len;
-		} else if (op == 3) { // intron
+		} else if (op == MM_CIGAR_N_SKIP) {
 			toff += len;
 		}
 		p->cigar[m++] = r->p->cigar[k];
@@ -248,7 +248,7 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
 	r->blen = r->mlen = 0;
 	for (k = 0; k < p->n_cigar; ++k) {
 		uint32_t op = p->cigar[k]&0xf, len = p->cigar[k]>>4;
-		if (op == 0) { // match/mismatch
+		if (op == MM_CIGAR_MATCH) {
 			int n_ambi = 0, n_diff = 0;
 			for (l = 0; l < len; ++l) {
 				int cq = qseq[qoff + l], ct = tseq[toff + l];
@@ -260,7 +260,7 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
 			}
 			r->blen += len - n_ambi, r->mlen += len - (n_ambi + n_diff), p->n_ambi += n_ambi;
 			toff += len, qoff += len;
-		} else if (op == 1) { // insertion
+		} else if (op == MM_CIGAR_INS) {
 			int n_ambi = 0;
 			for (l = 0; l < len; ++l)
 				if (qseq[qoff + l] > 3) ++n_ambi;
@@ -268,7 +268,7 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
 			s -= q + e * len;
 			if (s < 0) s = 0;
 			qoff += len;
-		} else if (op == 2) { // deletion
+		} else if (op == MM_CIGAR_DEL) {
 			int n_ambi = 0;
 			for (l = 0; l < len; ++l)
 				if (tseq[toff + l] > 3) ++n_ambi;
@@ -276,7 +276,7 @@ static void mm_update_extra(mm_reg1_t *r, const uint8_t *qseq, const uint8_t *ts
 			s -= q + e * len;
 			if (s < 0) s = 0;
 			toff += len;
-		} else if (op == 3) { // intron
+		} else if (op == MM_CIGAR_N_SKIP) {
 			toff += len;
 		}
 	}
@@ -333,7 +333,7 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 		int i;
 		fprintf(stderr, "score=%d, cigar=", ez->score);
 		for (i = 0; i < ez->n_cigar; ++i)
-			fprintf(stderr, "%d%c", ez->cigar[i]>>4, "MIDN"[ez->cigar[i]&0xf]);
+			fprintf(stderr, "%d%c", ez->cigar[i]>>4, MM_CIGAR_STR[ez->cigar[i]&0xf]);
 		fprintf(stderr, "\n");
 	}
 }
@@ -567,7 +567,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	int is_sr = !!(opt->flag & MM_F_SR), is_splice = !!(opt->flag & MM_F_SPLICE);
 	int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63, as1, cnt1;
 	uint8_t *tseq, *qseq, *junc;
-	int32_t i, l, bw, dropped = 0, extra_flag = 0, rs0, re0, qs0, qe0;
+	int32_t i, l, bw, bw_long, dropped = 0, extra_flag = 0, rs0, re0, qs0, qe0;
 	int32_t rs, re, qs, qe;
 	int32_t rs1, qs1, re1, qe1;
 	int8_t mat[25];
@@ -578,6 +578,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	if (r->cnt == 0) return;
 	ksw_gen_simple_mat(5, mat, opt->a, opt->b, opt->sc_ambi);
 	bw = (int)(opt->bw * 1.5 + 1.);
+	bw_long = (int)(opt->bw_long * 1.5 + 1.);
+	if (bw_long < bw) bw_long = bw;
 
 	if (is_sr && !(mi->flag & MM_I_HPC)) {
 		mm_max_stretch(r, a, &as1, &cnt1);
@@ -714,7 +716,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		} else mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
 		re1 = re, qe1 = qe;
 		if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || (qe - qs >= opt->min_ksw_len && re - rs >= opt->min_ksw_len)) {
-			int j, bw1 = bw, zdrop_code;
+			int j, bw1 = bw_long, zdrop_code;
 			if (a[as1+i].y & MM_SEED_LONG_JOIN)
 				bw1 = qe - qs > re - rs? qe - qs : re - rs;
 			// perform alignment
@@ -728,7 +730,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 					if (qseq[j] >= 4 || tseq[j] >= 4) ez->score += opt->e2;
 					else ez->score += qseq[j] == tseq[j]? opt->a : -opt->b;
 				}
-				ez->cigar = ksw_push_cigar(km, &ez->n_cigar, &ez->m_cigar, ez->cigar, 0, qe - qs);
+				ez->cigar = ksw_push_cigar(km, &ez->n_cigar, &ez->m_cigar, ez->cigar, MM_CIGAR_MATCH, qe - qs);
 			} else { // perform normal gapped alignment
 				mm_align_pair(km, opt, qe - qs, qseq, re - rs, tseq, junc, mat, bw1, -1, opt->zdrop, extra_flag|KSW_EZ_APPROX_MAX, ez); // first pass: with approximate Z-drop
 			}

chain.c

@@ -1,164 +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)
-{
-	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 max_iter, int min_cnt, int min_sc, float gap_scale, 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;
-	if (n == 0 || a == 0) {
-		kfree(km, a);
-		return 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;
-		if (i - st > max_iter) st = i - max_iter;
-		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, gap_cost;
-			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;
-			gap_cost = 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) gap_cost = c_lin < c_log? c_lin : c_log;
-				else gap_cost = c_lin + (c_log>>1);
-			} else gap_cost = (int)(dd * .01 * avg_qspan) + (log_dd>>1);
-			sc -= (int)((double)gap_cost * gap_scale + .499);
-			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;
-	}
-	if (n_u) memcpy(u, u2, n_u * 8);
-	if (k) 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

@@ -31,8 +31,8 @@ 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/v2.18/minimap2-2.18_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.18_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.21_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 -

example.c

@@ -47,7 +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, "MIDNSH"[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

@@ -144,8 +144,8 @@ static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 	if (write_tag) mm_sprintf_lite(s, "\tcs: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 >= 0 && op <= 3) || op == 7 || op == 8);
-		if (op == 0 || op == 7 || op == 8) { // match
+		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]) {
@@ -166,12 +166,12 @@ static void write_cs_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 				} else mm_sprintf_lite(s, ":%d", l_tmp);
 			}
 			q_off += len, t_off += len;
-		} else if (op == 1) { // insertion to ref
+		} else if (op == MM_CIGAR_INS) {
 			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) { // deletion from ref
+		} 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, "-%s", tmp);
@@ -192,8 +192,8 @@ static void write_MD_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 	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 >= 0 && op <= 3) || op == 7 || op == 8);
-		if (op == 0 || op == 7 || op == 8) { // match
+		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]]);
@@ -201,15 +201,15 @@ static void write_MD_core(kstring_t *s, const uint8_t *tseq, const uint8_t *qseq
 				} else ++l_MD;
 			}
 			q_off += len, t_off += len;
-		} else if (op == 1) { // insertion to ref
+		} else if (op == MM_CIGAR_INS) {
 			q_off += len;
-		} else if (op == 2) { // deletion from ref
+		} 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 == 3) { // reference skip
+		} else if (op == MM_CIGAR_N_SKIP) {
 			t_off += len;
 		}
 	}
@@ -271,7 +271,7 @@ double mm_event_identity(const mm_reg1_t *r)
 	if (r->p == 0) return -1.0f;
 	for (i = 0; i < r->p->n_cigar; ++i) {
 		int32_t op = r->p->cigar[i] & 0xf, len = r->p->cigar[i] >> 4;
-		if (op == 1 || op == 2)
+		if (op == MM_CIGAR_INS || op == MM_CIGAR_DEL)
 			++n_gapo, n_gap += len;
 	}
 	return (double)r->mlen / (r->blen + r->p->n_ambi - n_gap + n_gapo);
@@ -325,7 +325,7 @@ void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const
 		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, "MIDNSHP=XB"[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|MM_F_OUT_MD)))
 		write_cs_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD, 1);
@@ -382,7 +382,7 @@ static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, co
 			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, "MIDNSHP=XB"[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);
 		}
 	}

hit.c

@@ -312,64 +312,6 @@ 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, min_flank_len;
-
-		// 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 = a0e->x + max_gap > a1s->x? max_gap : a1s->x - a0e->x;
-		min_gap = a0e->x + min_gap < a1s->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
-		min_flank_len = (int)(max_gap * opt->min_join_flank_ratio);
-		if (r0->re - r0->rs < min_flank_len || r0->qe - r0->qs < min_flank_len) continue; // require enough flanking length
-		if (r1->re - r1->rs < min_flank_len || r1->qe - r1->qs < min_flank_len) 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(opt, qlen, 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;

kalloc.h

@@ -34,4 +34,43 @@ void km_stat(const void *_km, km_stat_t *s);
 		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; \
+		KCALLOC(km, mp, 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, 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

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

ksw2.h

@@ -16,6 +16,13 @@
 #define KSW_EZ_SPLICE_REV  0x200
 #define KSW_EZ_SPLICE_FLANK 0x400
 
+// 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
+
 #ifdef __cplusplus
 extern "C" {
 #endif
@@ -137,13 +144,13 @@ static inline void ksw_backtrack(void *km, int is_rot, int is_rev, int min_intro
 		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;

lchain.c

@@ -0,0 +1,354 @@
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <assert.h>
+#include "mmpriv.h"
+#include "kalloc.h"
+#include "krmq.h"
+
+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;
+}
+
+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 *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;
+	KMALLOC(km, z, 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
+		int64_t n_v0 = n_v;
+		int32_t sc;
+		for (i = z[k].y; i >= 0 && t[i] == 0; 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;
+	}
+	KMALLOC(km, u, n_u);
+	memset(t, 0, n * 4);
+	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
+		int64_t n_v0 = n_v;
+		int32_t sc;
+		for (i = z[k].y; i >= 0 && t[i] == 0; 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[]
+	KMALLOC(km, b, 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
+	KMALLOC(km, w, 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);
+	KMALLOC(km, u2, 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: tid<<33 | rev<<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;
+	int64_t *p, i, j, max_ii, st = 0, n_iter = 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;
+	KMALLOC(km, p, n);
+	KMALLOC(km, f, n);
+	KMALLOC(km, v, n);
+	KCALLOC(km, 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);
+			++n_iter;
+			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;
+	}
+
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &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;
+	int64_t *p, i, i0, st = 0, st_inner = 0, n_iter = 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 >= max_dist) max_dist_inner = 0;
+	KMALLOC(km, p, n);
+	KMALLOC(km, f, n);
+	KCALLOC(km, t, n);
+	KMALLOC(km, v, 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, n_rmq_iter = 0;
+					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;
+						++n_rmq_iter;
+						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;
+					}
+					n_iter += n_rmq_iter;
+				}
+			}
+		}
+		// 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, &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

@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.18-r1015"
+#define MM_VERSION "2.21-r1071"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -71,6 +71,7 @@ static ko_longopt_t long_options[] = {
 	{ "alt",            ko_required_argument, 344 },
 	{ "alt-drop",       ko_required_argument, 345 },
 	{ "mask-len",       ko_required_argument, 346 },
+	{ "rmq",            ko_optional_argument, 347 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -82,17 +83,23 @@ static ko_longopt_t long_options[] = {
 	{ 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(str, &p);
-	if (*p == 'G' || *p == 'g') x *= 1e9;
-	else if (*p == 'M' || *p == 'm') x *= 1e6;
-	else if (*p == 'K' || *p == 'k') x *= 1e3;
+	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, int flag, int long_idx, const char *arg, int yes_to_set)
 {
 	if (yes_to_set) {
@@ -108,7 +115,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
 
 int main(int argc, char *argv[])
 {
-	const char *opt_str = "2aSDw: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:yYPo:";
+	const char *opt_str = "2aSDw: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:yYPo:e:U:";
 	ketopt_t o = KETOPT_INIT;
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
@@ -144,7 +151,6 @@ int main(int argc, char *argv[])
 		else if (c == 'k') ipt.k = atoi(o.arg);
 		else if (c == 'H') ipt.flag |= MM_I_HPC;
 		else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
-		else if (c == 'r') opt.bw = (int)mm_parse_num(o.arg);
 		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);
@@ -171,6 +177,7 @@ int main(int argc, char *argv[])
 		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;
@@ -203,7 +210,6 @@ int main(int argc, char *argv[])
 		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 == 330) opt.min_join_flank_ratio = atof(o.arg); // --lj-min-ratio
 		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
@@ -219,7 +225,9 @@ int main(int argc, char *argv[])
 		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 == 314) { // --frag
+		else if (c == 330) {
+			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\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);
@@ -240,6 +248,8 @@ int main(int argc, char *argv[])
 			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
+			yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
 		} else if (c == 'S') {
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
 			if (mm_verbose >= 2)
@@ -247,6 +257,12 @@ 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;
@@ -301,7 +317,7 @@ int main(int argc, char *argv[])
 		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
@@ -332,7 +348,8 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    --version    show version number\n");
 		fprintf(fp_help, "  Preset:\n");
 		fprintf(fp_help, "    -x STR       preset (always applied before other options; see minimap2.1 for details) []\n");
-		fprintf(fp_help, "                 - map-pb/map-ont - PacBio/Nanopore vs reference mapping\n");
+		fprintf(fp_help, "                 - map-pb/map-ont - PacBio CLR/Nanopore vs reference mapping\n");
+		fprintf(fp_help, "                 - map-hifi - PacBio HiFi reads vs reference mapping\n");
 		fprintf(fp_help, "                 - ava-pb/ava-ont - PacBio/Nanopore read overlap\n");
 		fprintf(fp_help, "                 - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
 		fprintf(fp_help, "                 - splice/splice:hq - long-read/Pacbio-CCS spliced alignment\n");
@@ -389,6 +406,7 @@ int main(int argc, char *argv[])
 		if (mm_verbose >= 3) mm_idx_stat(mi);
 		if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
 		if (alt_list) mm_idx_alt_read(mi, alt_list);
+		if (argc - (o.ind + 1) == 0) continue; // no query files
 		ret = 0;
 		if (!(opt.flag & MM_F_FRAG_MODE)) {
 			for (i = o.ind + 1; i < argc; ++i) {

map.c

@@ -80,49 +80,7 @@ static void collect_minimizers(void *km, const mm_mapopt_t *opt, const mm_idx_t
 #define heap_lt(a, b) ((a).x > (b).x)
 KSORT_INIT(heap, mm128_t, heap_lt)
 
-typedef struct {
-	uint32_t n;
-	uint32_t q_pos, q_span;
-	uint32_t seg_id:31, is_tandem:1;
-	const uint64_t *cr;
-} mm_match_t;
-
-static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, 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;
-	size_t i;
-	mm_match_t *m;
-	*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, n_m = 0, *rep_len = 0, *n_a = 0; i < mv->n; ++i) {
-		const uint64_t *cr;
-		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 >= max_occ) {
-			int en = (q_pos >> 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;
-		} else {
-			mm_match_t *q = &m[n_m++];
-			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 = 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_a += q->n;
-			(*mini_pos)[(*n_mini_pos)++] = (uint64_t)q_span<<32 | q_pos>>1;
-		}
-	}
-	*rep_len += rep_en - rep_st;
-	*_n_m = n_m;
-	return m;
-}
-
-static inline int skip_seed(int flag, uint64_t r, const mm_match_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
+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))) {
@@ -151,10 +109,10 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
 {
 	int i, n_m, heap_size = 0;
 	int64_t j, n_for = 0, n_rev = 0;
-	mm_match_t *m;
+	mm_seed_t *m;
 	mm128_t *a, *heap;
 
-	m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
+	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));
@@ -168,7 +126,7 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
 	}
 	ks_heapmake_heap(heap_size, heap);
 	while (heap_size > 0) {
-		mm_match_t *q = &m[heap->y>>32];
+		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;
@@ -216,12 +174,12 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
 								  int *n_mini_pos, uint64_t **mini_pos)
 {
 	int i, n_m;
-	mm_match_t *m;
+	mm_seed_t *m;
 	mm128_t *a;
-	m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
+	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 = 0, *n_a = 0; i < n_m; ++i) {
-		mm_match_t *q = &m[i];
+		mm_seed_t *q = &m[i];
 		const uint64_t *r = q->cr;
 		uint32_t k;
 		for (k = 0; k < q->n; ++k) {
@@ -252,8 +210,6 @@ static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_i
 		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, 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|MM_F_SR|MM_F_NO_LJOIN))) // long join not working well without primary chains
-			mm_join_long(km, opt, qlen, n_regs, regs, a);
 	}
 }
 
@@ -313,9 +269,25 @@ 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->max_chain_iter, opt->min_cnt, opt->min_chain_score, opt->chain_gap_scale, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
+	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,
+						  opt->chain_gap_scale * 0.01 * mi->k, 0.0f, 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,
+						 opt->chain_gap_scale * 0.01 * mi->k, 0.0f, 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,
+							  opt->chain_gap_scale * 0.01 * mi->k, 0.0f, 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;
@@ -335,7 +307,8 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 			kfree(b->km, mini_pos);
 			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 = mm_chain_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, opt->chain_gap_scale, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
+			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,
+							 opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
 		}
 	}
 	b->frag_gap = max_chain_gap_ref;

minimap.h

@@ -36,6 +36,7 @@
 #define MM_F_NO_END_FLT    0x10000000
 #define MM_F_HARD_MLEVEL   0x20000000
 #define MM_F_SAM_HIT_ONLY  0x40000000
+#define MM_F_RMQ           0x80000000LL
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
@@ -45,6 +46,18 @@
 
 #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
@@ -113,23 +126,22 @@ typedef struct {
 
 	int max_qlen;    // max query length
 
-	int bw;          // bandwidth
+	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, max_chain_iter;
 	int min_cnt;         // min number of minimizers on each chain
 	int min_chain_score; // min chaining score
 	float chain_gap_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 min_join_flank_ratio;
-
 	float alt_drop;
 
 	int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
@@ -146,9 +158,9 @@ typedef struct {
 	int pe_ori, pe_bonus;
 
 	float mid_occ_frac;  // only used by mm_mapopt_update(); see below
-	int32_t min_mid_occ;
+	int32_t min_mid_occ, max_mid_occ;
 	int32_t mid_occ;     // ignore seeds with occurrences above this threshold
-	int32_t max_occ;
+	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;
 

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "9 April 2021" "minimap2-2.18 (r1015)" "Bioinformatics tools"
+.TH minimap2 1 "6 July 2021" "minimap2-2.21 (r1071)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -145,22 +145,32 @@ or
 .B -xsr
 mode, which sets the threshold for a second round of seeding.
 .TP
-.BI --min-occ-floor \ INT
-Force minimap2 to always use k-mers occurring
+.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. It deprecates
+.B --min-occ-floor
+in earlier versions of minimap2.
+.TP
+.BI -e \ INT
+Sample a high-frequency minimizer every
 .I INT
-times or less [0]. In effect, the max occurrence threshold is set to
-the
-.RI max{ INT ,
-.BR -f }.
+basepairs [500].
 .TP
-.BI -g \ INT
+.BI -g \ NUM
 Stop chain enlongation if there are no minimizers within
-.IR INT -bp
-[10000].
+.IR NUM -bp
+[10k].
 .TP
-.BI -r \ INT
-Bandwidth used in chaining and DP-based alignment [500]. This option
-approximately controls the maximum gap size.
+.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
@@ -234,6 +244,10 @@ 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
 .B --hard-mask-level
 Honor option
 .B -M
@@ -268,10 +282,6 @@ Disable the long gap patching heuristic. When this option is applied, the
 maximum alignment gap is mostly controlled by
 .BR -r .
 .TP
-.BI --lj-min-ratio \ FLOAT
-Fraction of query sequence length required to bridge a long gap [0.5]. A
-smaller value helps to recover longer gaps, at the cost of more false gaps.
-.TP
 .B --splice
 Enable the splice alignment mode.
 .TP
@@ -412,7 +422,7 @@ alignment.
 .BI --cap-sw-mem \ NUM
 Skip alignment if the DP matrix size is above
 .IR NUM .
-Set 0 to disable [0].
+Set 0 to disable [100m].
 .SS Input/output options
 .TP 10
 .B -a
@@ -523,60 +533,47 @@ 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 map-hifi
+Align PacBio high-fidelity (HiFi) reads to a reference genome
+.RB ( -k19
+.B -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1
+.BR -s200 ).
+.TP
+.B map-pb
+Align older PacBio continuous long (CLR) reads to a reference genome
+.RB ( -Hk19 ).
 .TP
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 -N50
-.BR --min-occ-floor=100 ).
+.B -w19 -U50,500 --rmq -r100k -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%.
 .TP
 .B asm10
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 -N50
-.BR --min-occ-floor=100 ).
+.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
+.BR -N50 ).
 Up to 10% sequence divergence.
 .TP
 .B asm20
 Long assembly to reference mapping
 .RB ( -k19
-.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200 -N50
-.BR --min-occ-floor=100 ).
+.B -w10 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
+.BR -N50 ).
 Up to 20% sequence divergence.
 .TP
-.B ava-pb
-PacBio all-vs-all overlap mapping
-.RB ( -Hk19
-.B -Xw5 -m100 -g10000 --max-chain-skip
-.BR 25 ).
-.TP
-.B ava-ont
-Oxford Nanopore all-vs-all overlap mapping
-.RB ( -k15
-.B -Xw5 -m100 -g10000 -r2000 --max-chain-skip
-.BR 25 ).
-Similarly, the major difference from
-.B ava-pb
-is that this preset is not using HPC minimizers.
-.TP
 .B splice
 Long-read spliced alignment
 .RB ( -k15
-.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9
+.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
@@ -595,9 +592,21 @@ Long-read splice alignment for PacBio CCS reads
 .B sr
 Short single-end reads without splicing
 .RB ( -k21
-.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
-.B -s40 -g200 -2K50m --heap-sort=yes
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
+.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

misc.c

@@ -159,3 +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/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.18-r1015';
+var paftools_version = '2.21-r1071';
 
 /*****************************
  ***** Library functions *****
@@ -1419,7 +1419,7 @@ function paf_view(args)
 
 	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 re_cg = /(\d+)([MIDNSHP=X])/g;
 
 	var buf = new Bytes();
 	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
@@ -1899,7 +1899,7 @@ function paf_splice2bed(args)
 		a.length = 0;
 	}
 
-	var re = /(\d+)([MIDNSH])/g;
+	var re = /(\d+)([MIDNSHP=X])/g;
 	var c, fmt = "bed", fn_name_conv = null, keep_multi = false;
 	while ((c = getopt(args, "f:n:m")) != null) {
 		if (c == 'f') fmt = getopt.arg;
@@ -2369,28 +2369,43 @@ function paf_junceval(args)
 
 	file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]);
 	var last_qname = null;
-	var re_cigar = /(\d+)([MIDNSHX=])/g;
+	var re_cigar = /(\d+)([MIDNSHP=X])/g;
 	while (file.readline(buf) >= 0) {
 		var m, t = buf.toString().split("\t");
+		var ctg_name = null, cigar = null, pos = null, qname = t[0];
 
 		if (t[0].charAt(0) == '@') continue;
-		if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(t[2])) continue;
-		var flag = parseInt(t[1]);
-		if (flag&0x100) continue;
-		if (first_only && last_qname == t[0]) continue;
-		if (t[2] == '*') {
+		if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
+			ctg_name = t[5], pos = parseInt(t[7]);
+			var type = 'P';
+			for (i = 12; i < t.length; ++i) {
+				if ((m = /^(tp:A|cg:Z):(\S+)/.exec(t[i])) != null) {
+					if (m[1] == 'tp:A') type = m[2];
+					else cigar = m[2];
+				}
+			}
+			if (type == 'S') continue; // secondary
+		} else { // SAM
+			ctg_name = t[2], pos = parseInt(t[3]) - 1, cigar = t[5];
+			var flag = parseInt(t[1]);
+			if (flag&0x100) continue; // secondary
+		}
+
+		if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(ctg_name)) continue;
+		if (first_only && last_qname == qname) continue;
+		if (ctg_name == '*') { // unmapped
 			++n_unmapped;
 			continue;
 		} else {
 			++n_pri;
-			if (last_qname != t[0]) {
+			if (last_qname != qname) {
 				++n_mapped;
-				last_qname = t[0];
+				last_qname = qname;
 			}
 		}
 
-		var pos = parseInt(t[3]) - 1, intron = [];
-		while ((m = re_cigar.exec(t[5])) != null) {
+		var intron = [];
+		while ((m = re_cigar.exec(cigar)) != null) {
 			var len = parseInt(m[1]), op = m[2];
 			if (op == 'N') {
 				intron.push([pos, pos + len]);
@@ -2403,7 +2418,7 @@ function paf_junceval(args)
 		}
 		n_splice += intron.length;
 
-		var chr = anno[t[2]];
+		var chr = anno[ctg_name];
 		if (chr != null) {
 			for (var i = 0; i < intron.length; ++i) {
 				var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
@@ -2427,12 +2442,12 @@ function paf_junceval(args)
 							x += '(' + o[j][0] + "," + o[j][1] + ')';
 						}
 						x += ']';
-						print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x);
+						print(type, qname, i+1, ctg_name, 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]);
+						print('N',  qname, i+1, ctg_name, intron[i][0], intron[i][1]);
 				}
 			}
 		} else {
@@ -2718,16 +2733,40 @@ function paf_misjoin(args)
 	print("# candidate inversions at contig ends: " + n_inv_end.join(","));
 }
 
+function _paf_get_alen(t)
+{
+	var svlen = null, alen = null;
+	if ((m = /(^|;)SVLEN=(-?\d+)/.exec(t[7])) != null)
+		svlen = parseInt(m[2]);
+	var s = t[4].split(",");
+	var min_abs_diff = 1<<30, max_abs_diff = 0;
+	if (svlen != null && svlen != 0)
+		alen = svlen, min_abs_diff = max_abs_diff = svlen > 0? svlen : -svlen;
+	var rlen = t[3].length;
+	for (var i = 0; i < s.length; ++i) {
+		if (/^<\S+>$/.test(s[i])) continue;
+		var diff = s[i].length - rlen;
+		var abs_diff = diff > 0? diff : -diff;
+		min_abs_diff = min_abs_diff < abs_diff? min_abs_diff : abs_diff;
+		if (max_abs_diff < abs_diff)
+			max_abs_diff = abs_diff, alen = diff;
+	}
+	return [alen, min_abs_diff, max_abs_diff];
+}
+
 function paf_sveval(args)
 {
-	var c, min_flt = 30, min_size = 50, max_size = 10000, win_size = 500, print_err = false, bed_fn = null;
-	while ((c = getopt(args, "f:i:x:w:er:")) != null) {
+	var c, min_flt = 30, min_size = 50, max_size = 100000, win_size = 500, print_err = false, print_match = false, bed_fn = null;
+	var len_diff_ratio = 0.5;
+	while ((c = getopt(args, "f:i:x:w:er:pd:")) != null) {
 		if (c == 'f') min_flt = paf_parseNum(getopt.arg);
 		else if (c == 'i') min_size = paf_parseNum(getopt.arg);
 		else if (c == 'x') max_size = paf_parseNum(getopt.arg);
 		else if (c == 'w') win_size = paf_parseNum(getopt.arg);
+		else if (c == 'd') len_diff_ratio = parseFloat(getopt.arg);
 		else if (c == 'r') bed_fn = getopt.arg;
 		else if (c == 'e') print_err = true;
+		else if (c == 'p') print_match = true;
 	}
 	if (args.length - getopt.ind < 2) {
 		print("Usage: paftools.js sveval [options] <base.vcf> <call.vcf>");
@@ -2737,6 +2776,7 @@ function paf_sveval(args)
 		print("  -i INT     min SV length [" + min_size + "]");
 		print("  -x INT     max SV length [" + max_size + "]");
 		print("  -w INT     fuzzy windown size [" + win_size + "]");
+		print("  -d FLOAT   max allele diff if there is a single allele in the window [" + len_diff_ratio + "]");
 		print("  -e         print errors");
 		return;
 	}
@@ -2773,24 +2813,18 @@ function paf_sveval(args)
 			if (t[4] == '<INV>' || t[4] == '<INVDUP>') continue; // no inversion
 			if (/[\[\]]/.test(t[4])) continue; // no break points
 			var st = parseInt(t[1]) - 1, en = st + t[3].length;
-			if ((m = /((;END)|(^END))=(\d+)/.exec(t[7])) != null)
-				en = parseInt(m[4]);
-			if (bed != null && Interval.find_ovlp(bed[t[0]], st, en).length == 0) continue;
-			// determine svlen
-			var s = t[4].split(","), max_del = 0, max_ins = 0;
-			for (var i = 0; i < s.length; ++i) {
-				var l = s[i].length - t[3].length;
-				if (l > 0)
-					max_ins = max_ins > l? max_ins : l;
-				else if (l < 0)
-					max_del = max_del > -l? max_del : -l;
-			}
-			if (max_ins < min_flt && max_del < min_flt) continue;
-			var svlen = max_ins > max_del? max_ins : -max_del;
-			if ((m = /((;SVLEN)|(^SVLEN))=(\d+)/.exec(t[7])) != null)
-				svlen = parseInt(m[4]);
-			var abslen = svlen > 0? svlen : -svlen;
+			// parse svlen
+			var b = _paf_get_alen(t), svlen = b[0];
+			var abslen = svlen == null? 0 : svlen > 0? svlen : -svlen;
 			if (abslen < min_flt || abslen > max_size) continue;
+			// update end
+			if ((m = /(^|;)END=(\d+)/.exec(t[7])) != null)
+				en = parseInt(m[2]);
+			else if (svlen != null && svlen < 0)
+				en = st + (-svlen);
+			if (en < st) en = st;
+			if (st == en) --st, ++en;
+			if (bed != null && Interval.find_ovlp(bed[t[0]], st, en).length == 0) continue;
 			// insert
 			if (v[t[0]] == null) v[t[0]] = [];
 			v[t[0]].push([st, en, svlen, abslen]);
@@ -2812,10 +2846,38 @@ function paf_sveval(args)
 				if (a1[i][3] < min_size) continue;
 				++n;
 				if (a0 == null) continue;
-				var st = a1[i][0] > win_size? a1[i][0] - win_size : 0;
-				b = Interval.find_ovlp(a0, st, a1[i][1] + win_size);
-				if (b.length > 0) ++m;
-				else if (print_err) print(label, x, a1[i].slice(0, 3).join("\t"));
+				var ws = win_size + (a1[i][3]>>1);
+				var st = a1[i][0] > ws? a1[i][0] - ws : 0;
+				b = Interval.find_ovlp(a0, st, a1[i][1] + ws);
+				var n_ins = 0, n_del = 0, sv_del = null, sv_ins = null;
+				for (var j = 0; j < b.length; ++j) {
+					if (b[j][2] < 0) ++n_del, sv_del = -b[j][2];
+					else if (b[j][2] > 0) ++n_ins, sv_ins = b[j][2];
+					if (print_match)
+						print("MA", x, a1[i].slice(0, 3).join("\t"), b[j].slice(0, 3).join("\t"));
+				}
+				var match = false;
+				if (a1[i][2] > 0) { // insertion
+					if (n_ins == 1) {
+						var diff = sv_ins - a1[i][3];
+						if (diff < 0) diff = -diff;
+						if (diff < min_size || diff / a1[i][3] < len_diff_ratio)
+							match = true;
+					} else if (n_ins > 1) match = true; // multiple insertions; ambiguous
+				} else if (a1[i][2] < 0) {
+					if (n_del == 1) { // deletion
+						var diff = sv_del - a1[i][3];
+						if (diff < 0) diff = -diff;
+						if (diff < min_size || diff / a1[i][3] < len_diff_ratio)
+							match = true;
+					} else if (n_del > 1) match = true; // multiple deletions; ambiguous
+				}
+				if (match) ++m;
+				else if (print_err) {
+					if ((a1[i][2] > 0 && n_ins > 0) || (a1[i][2] < 0 && n_del > 0))
+						print("MM", x, a1[i].slice(0, 3).join("\t"));
+					print(label, x, a1[i].slice(0, 3).join("\t"));
+				}
 			}
 		}
 		return [n, m];
@@ -2830,6 +2892,44 @@ function paf_sveval(args)
 	print('F1', ((fn[1] / fn[0] + fp[1] / fp[0]) / 2).toFixed(6));
 }
 
+function paf_vcfsel(args)
+{
+	var c, min_l = 0, max_l = 1<<30;
+	while ((c = getopt(args, "l:L:")) != null) {
+		if (c == 'l') min_l = parseInt(getopt.arg);
+		else if (c == 'L') max_l = parseInt(getopt.arg);
+	}
+
+	var buf = new Bytes();
+	if (getopt.ind == args.length) {
+		print("Usage: paftools.js vcfsel [options] <in.vcf>");
+		return 1;
+	}
+	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
+	while (file.readline(buf) >= 0) {
+		var m, line = buf.toString();
+		if (line[0] == '#') {
+			print(line);
+			continue;
+		}
+		var t = line.split("\t");
+		var st = parseInt(t[1]), en = st + t[3].length - 1;
+		if ((m = /(^|;)END=(\d+)/.exec(t[7])) != null)
+			en = parseInt(m[2]);
+		if (en < st) {
+			warn("END is smaller than POS: " + en + " < " + st);
+			en = st;
+		}
+		var b = _paf_get_alen(t);
+		var alen = b[0], min_abs_diff = b[1], max_abs_diff = b[2];
+		if (max_abs_diff < min_l || min_abs_diff > max_l)
+			continue;
+		print(line);
+	}
+	file.close();
+	buf.destroy();
+}
+
 /*************************
  ***** main function *****
  *************************/
@@ -2885,6 +2985,7 @@ function main(args)
 	else if (cmd == 'ov-eval') paf_ov_eval(args);
 	else if (cmd == 'vcfstat') paf_vcfstat(args);
 	else if (cmd == 'sveval') paf_sveval(args);
+	else if (cmd == 'vcfsel') paf_vcfsel(args);
 	else if (cmd == 'version') print(paftools_version);
 	else throw Error("unrecognized command: " + cmd);
 }

mmpriv.h

@@ -36,6 +36,14 @@
 extern "C" {
 #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;
 	uint64_t *u;
@@ -52,6 +60,8 @@ 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);
 
+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 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_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int rep_len);
@@ -62,9 +72,15 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 void mm_idxopt_init(mm_idxopt_t *opt);
 const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
 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 max_iter, int min_cnt, int min_sc, float gap_scale, 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);
 
+mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float gap_scale,
+					 int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km);
+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);
+
 mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u, mm128_t *a);
 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);
@@ -75,7 +91,6 @@ void mm_set_parent(void *km, float mask_level, int mask_len, int n, mm_reg1_t *r
 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_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(const mm_mapopt_t *opt, int qlen, 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(void *km, int *n_regs, mm_reg1_t *r, float alt_diff_frac);
 void mm_set_mapq(void *km, int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, int rep_len, int is_sr);
 

options.c

@@ -16,27 +16,30 @@ 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->min_cnt = 3;
 	opt->min_chain_score = 40;
-	opt->bw = 500;
+	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->chain_gap_scale = 1.0f;
+	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->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->max_join_long = 20000;
-	opt->max_join_short = 2000;
-	opt->min_join_flank_sc = 1000;
-	opt->min_join_flank_ratio = 0.5f;
-
 	opt->alt_drop = 0.15f;
 
 	opt->a = 2, opt->b = 4, opt->q = 4, opt->e = 2, opt->q2 = 24, opt->e2 = 1;
@@ -48,6 +51,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 	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->pe_ori = 0; // FF
 	opt->pe_bonus = 33;
@@ -57,10 +61,13 @@ 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)
+	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->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 (mm_verbose >= 3)
 		fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
 }
@@ -68,7 +75,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 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;
+		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)
@@ -76,37 +83,44 @@ 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, "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_gap = 10000, mo->max_chain_skip = 25;
-		mo->bw = 2000;
+		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_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) {
+		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, "map-hifi") == 0 || strcmp(preset, "map-ccs") == 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 = mo->zdrop_inv = 200;
-		mo->min_mid_occ = 100;
+		mo->max_gap = 10000;
+		mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1;
+		mo->occ_dist = 500;
+		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
 		mo->min_dp_max = 200;
-		mo->best_n = 50;
-	} else if (strcmp(preset, "asm10") == 0) {
+	} else if (strncmp(preset, "asm", 3) == 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 = mo->zdrop_inv = 200;
-		mo->min_mid_occ = 100;
-		mo->min_dp_max = 200;
-		mo->best_n = 50;
-	} else if (strcmp(preset, "asm20") == 0) {
-		io->flag = 0, io->k = 19, io->w = 10;
-		mo->a = 1, mo->b = 4, mo->q = 6, mo->q2 = 26, mo->e = 2, mo->e2 = 1, mo->zdrop = mo->zdrop_inv = 200;
-		mo->min_mid_occ = 100;
+		mo->bw = 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;
@@ -116,7 +130,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->end_bonus = 10;
 		mo->max_frag_len = 800;
 		mo->max_gap = 100;
-		mo->bw = 100;
+		mo->bw = mo->bw_long = 100;
 		mo->pri_ratio = 0.5f;
 		mo->min_cnt = 2;
 		mo->min_chain_score = 25;
@@ -128,7 +142,8 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 	} else if (strncmp(preset, "splice", 6) == 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->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;
@@ -141,6 +156,16 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 
 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");

python/README.rst

@@ -144,7 +144,7 @@ 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

python/cmappy.pxd

@@ -13,22 +13,27 @@ cdef extern from "minimap.h":
 		int64_t flag
 		int seed
 		int sdust_thres
+
 		int max_qlen
-		int bw
+
+		int bw, bw_long
 		int max_gap, max_gap_ref
 		int max_frag_len
 		int max_chain_skip, max_chain_iter
 		int min_cnt
 		int min_chain_score
 		float chain_gap_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 min_join_flank_ratio
+
 		float alt_drop
+
 		int a, b, q, e, q2, e2
 		int sc_ambi
 		int noncan
@@ -39,13 +44,16 @@ cdef extern from "minimap.h":
 		int min_ksw_len
 		int anchor_ext_len, anchor_ext_shift
 		float max_clip_ratio
+
 		int pe_ori, pe_bonus
+
 		float mid_occ_frac
 		int32_t min_mid_occ
 		int32_t mid_occ
 		int32_t max_occ
 		int64_t mini_batch_size
 		int64_t max_sw_mat
+
 		const char *split_prefix
 
 	int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.18'
+__version__ = '2.21'
 
 cmappy.mm_reset_timer()
 
@@ -82,7 +82,7 @@ cdef class Alignment:
 
 	@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 = '+'

seed.c

@@ -0,0 +1,106 @@
+#include "mmpriv.h"
+#include "kalloc.h"
+#include "ksort.h"
+
+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];
+		//fprintf(stderr, "X\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

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.18',
+	version = '2.21',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -33,7 +33,7 @@ setup(
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
 	ext_modules = [Extension('mappy',
-		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
+		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.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', 'splitidx.c'],
 		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',