Release minimap2-2.25 (r1173)

I can never remember the operator priority of & and &&

.travis.yml

@@ -1,24 +0,0 @@
-matrix:
-  include:
-    - language: c
-      compiler: gcc
-      script: make
-    - language: c
-      compiler: clang
-      script: make
-    - arch: arm64
-      language: c
-      compiler: gcc
-      script: make arm_neon=1 aarch64=1
-    - language: python
-      python: "2.7"
-      before_install: pip install cython
-      script: python setup.py build_ext
-    - language: python
-      python: "3.5"
-      before_install: pip install cython
-      script: python setup.py build_ext
-    - language: python
-      python: "3.9"
-      before_install: pip install cython
-      script: python setup.py build_ext

Makefile

@@ -8,6 +8,10 @@ PROG=		minimap2
 PROG_EXTRA=	sdust minimap2-lite
 LIBS=		-lm -lz -lpthread
 
+ifneq ($(aarch64),)
+	arm_neon=1
+endif
+
 ifeq ($(arm_neon),) # if arm_neon is not defined
 ifeq ($(sse2only),) # if sse2only is not defined
 	OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
@@ -26,12 +30,12 @@ endif
 
 ifneq ($(asan),)
 	CFLAGS+=-fsanitize=address
-	LIBS+=-fsanitize=address
+	LIBS+=-fsanitize=address -ldl
 endif
 
 ifneq ($(tsan),)
 	CFLAGS+=-fsanitize=thread
-	LIBS+=-fsanitize=thread
+	LIBS+=-fsanitize=thread -ldl
 endif
 
 .PHONY:all extra clean depend

NEWS.md

@@ -1,3 +1,55 @@
+Release 2.25-r1173 (25 April 2023)
+----------------------------------
+
+Notable changes:
+
+ * Improvement: use the miniprot splice model for RNA-seq alignment by default.
+   This model considers non-GT-AG splice sites and leads to slightly higher
+   (<0.1%) accuracy and sensitivity on real human data.
+
+ * Change: increased the default `-I` to `8G` such that minimap2 would create a
+   uni-part index for a pair of mammalian genomes. This change may increase the
+   memory for all-vs-all read overlap alignment given large datasets.
+
+ * New feature: output the sequences in secondary alignments with option
+   `--secondary-seq` (#687).
+
+ * Bugfix: --rmq was not parsed correctly (#1010)
+
+ * Bugfix: possibly incorrect coordinate when applying end bonus to the target
+   sequence (#1025). This is a ksw2 bug. It does not affect minimap2 as
+   minimap2 is not using the affected feature.
+
+ * Improvement: incorporated several changes for better compatibility with
+   Windows (#1051) and for minimap2 integration at Oxford Nanopore Technologies
+   (#1048 and #1033).
+
+ * Improvement: output the HD-line in SAM output (#1019).
+
+ * Improvement: check minimap2 index file in mappy to prevent segmentation
+   fault for certain indices (#1008).
+
+For genomic sequences, minimap2 should give identical output to v2.24.
+Long-read RNA-seq alignment may occasionally differ from previous versions.
+
+(2.25: 25 April 2023, r1173)
+
+
+
+Release 2.24-r1122 (26 December 2021)
+-------------------------------------
+
+This release improves alignment around long poorly aligned regions. Older
+minimap2 may chain through such regions in rare cases which may result in
+missing alignments later. The issue has become worse since the the change of
+the chaining algorithm in v2.19. v2.23 implements an incomplete remedy. This
+release provides a better solution with a X-drop-like heuristic and by enabling
+two-bandwidth chaining in the assembly mode.
+
+(2.24: 26 December 2021, r1122)
+
+
+
 Release 2.23-r1111 (18 November 2021)
 -------------------------------------
 

README.md

@@ -74,8 +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/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.23_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.25/minimap2-2.25_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.25_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
@@ -350,6 +350,11 @@ If you use minimap2 in your work, please cite:
 > Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.
 > *Bioinformatics*, **34**:3094-3100. [doi:10.1093/bioinformatics/bty191][doi]
 
+and/or:
+
+> Li, H. (2021). New strategies to improve minimap2 alignment accuracy.
+> *Bioinformatics*, **37**:4572-4574. [doi:10.1093/bioinformatics/btab705][doi2]
+
 ## <a name="dguide"></a>Developers' Guide
 
 Minimap2 is not only a command line tool, but also a programming library.
@@ -399,5 +404,6 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
 [manpage]: https://lh3.github.io/minimap2/minimap2.html
 [manpage-cs]: https://lh3.github.io/minimap2/minimap2.html#10
 [doi]: https://doi.org/10.1093/bioinformatics/bty191
-[smide]: https://github.com/nemequ/simde
+[doi2]: https://doi.org/10.1093/bioinformatics/btab705
+[simde]: https://github.com/nemequ/simde
 [unimap]: https://github.com/lh3/unimap

align.c

@@ -326,9 +326,11 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 	if (opt->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
 		ksw_reset_extz(ez);
 		ez->zdropped = 1;
-	} else if (opt->flag & MM_F_SPLICE)
-		ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag, junc, ez);
-	else if (opt->q == opt->q2 && opt->e == opt->e2)
+	} else if (opt->flag & MM_F_SPLICE) {
+		int flag_tmp = flag;
+		if (!(opt->flag & MM_F_SPLICE_OLD)) flag_tmp |= KSW_EZ_SPLICE_CMPLX;
+		ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag_tmp, junc, ez);
+	} else if (opt->q == opt->q2 && opt->e == opt->e2)
 		ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
 	else
 		ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);

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/v2.23/minimap2-2.23_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.23_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.25/minimap2-2.25_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.25_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 -

format.c

@@ -119,6 +119,7 @@ int mm_write_sam_hdr(const mm_idx_t *idx, const char *rg, const char *ver, int a
 {
 	kstring_t str = {0,0,0};
 	int ret = 0;
+	mm_sprintf_lite(&str, "@HD\tVN:1.6\tSO:unsorted\tGO:query\n");
 	if (idx) {
 		uint32_t i;
 		for (i = 0; i < idx->n_seq; ++i)
@@ -369,14 +370,16 @@ static void write_sam_cigar(kstring_t *s, int sam_flag, int in_tag, int qlen, co
 		clip_len[0] = r->rev? qlen - r->qe : r->qs;
 		clip_len[1] = r->rev? r->qs : qlen - r->qe;
 		if (in_tag) {
-			int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 5 : 4;
+			int clip_char = (((sam_flag&0x800) || ((sam_flag&0x100) && (opt_flag&MM_F_SECONDARY_SEQ))) &&
+							 !(opt_flag&MM_F_SOFTCLIP)) ? 5 : 4;
 			mm_sprintf_lite(s, "\tCG:B:I");
 			if (clip_len[0]) mm_sprintf_lite(s, ",%u", clip_len[0]<<4|clip_char);
 			for (k = 0; k < r->p->n_cigar; ++k)
 				mm_sprintf_lite(s, ",%u", r->p->cigar[k]);
 			if (clip_len[1]) mm_sprintf_lite(s, ",%u", clip_len[1]<<4|clip_char);
 		} else {
-			int clip_char = (sam_flag&0x800) && !(opt_flag&MM_F_SOFTCLIP)? 'H' : 'S';
+			int clip_char = (((sam_flag&0x800) || ((sam_flag&0x100) && (opt_flag&MM_F_SECONDARY_SEQ))) &&
+							 !(opt_flag&MM_F_SOFTCLIP)) ? 'H' : 'S';
 			assert(clip_len[0] < qlen && clip_len[1] < qlen);
 			if (clip_len[0]) mm_sprintf_lite(s, "%d%c", clip_len[0], clip_char);
 			for (k = 0; k < r->p->n_cigar; ++k)
@@ -451,7 +454,7 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 		if (cigar_in_tag) {
 			int slen;
 			if ((flag & 0x900) == 0 || (opt_flag & MM_F_SOFTCLIP)) slen = t->l_seq;
-			else if (flag & 0x100) slen = 0;
+			else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)) slen = 0;
 			else slen = r->qe - r->qs;
 			mm_sprintf_lite(s, "%dS%dN", slen, r->re - r->rs);
 		} else write_sam_cigar(s, flag, 0, t->l_seq, r, opt_flag);
@@ -492,7 +495,7 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
 			mm_sprintf_lite(s, "\t");
 			if (t->qual) sam_write_sq(s, t->qual, t->l_seq, r->rev, 0);
 			else mm_sprintf_lite(s, "*");
-		} else if (flag & 0x100) {
+		} else if ((flag & 0x100) && !(opt_flag & MM_F_SECONDARY_SEQ)){
 			mm_sprintf_lite(s, "*\t*");
 		} else {
 			sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);

hit.c

@@ -279,7 +279,7 @@ int mm_filter_strand_retained(int n_regs, mm_reg1_t *r)
 	int i, k;
 	for (i = k = 0; i < n_regs; ++i) {
 		int p = r[i].parent;
-		if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f) {
+		if (!r[i].strand_retained || r[i].div < r[p].div * 5.0f || r[i].div < 0.01f) {
 			if (k < i) r[k++] = r[i];
 			else ++k;
 		}

kalloc.c

@@ -40,7 +40,8 @@ void *km_init2(void *km_par, size_t min_core_size)
 	kmem_t *km;
 	km = (kmem_t*)kcalloc(km_par, 1, sizeof(kmem_t));
 	km->par = km_par;
-	km->min_core_size = min_core_size > 0? min_core_size : 0x80000;
+	if (km_par) km->min_core_size = min_core_size > 0? min_core_size : ((kmem_t*)km_par)->min_core_size - 2;
+	else km->min_core_size = min_core_size > 0? min_core_size : 0x80000;
 	return (void*)km;
 }
 
@@ -183,6 +184,16 @@ void *krealloc(void *_km, void *ap, size_t n_bytes) // TODO: this can be made mo
 	return q;
 }
 
+void *krelocate(void *km, void *ap, size_t n_bytes)
+{
+	void *p;
+	if (km == 0 || ap == 0) return ap;
+	p = kmalloc(km, n_bytes);
+	memcpy(p, ap, n_bytes);
+	kfree(km, ap);
+	return p;
+}
+
 void km_stat(const void *_km, km_stat_t *s)
 {
 	kmem_t *km = (kmem_t*)_km;
@@ -203,3 +214,11 @@ void km_stat(const void *_km, km_stat_t *s)
 		s->largest = s->largest > size? s->largest : size;
 	}
 }
+
+void km_stat_print(const void *km)
+{
+	km_stat_t st;
+	km_stat(km, &st);
+	fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n",
+			st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
+}

kalloc.h

@@ -13,6 +13,7 @@ typedef struct {
 
 void *kmalloc(void *km, size_t size);
 void *krealloc(void *km, void *ptr, size_t size);
+void *krelocate(void *km, void *ap, size_t n_bytes);
 void *kcalloc(void *km, size_t count, size_t size);
 void kfree(void *km, void *ptr);
 
@@ -20,11 +21,21 @@ void *km_init(void);
 void *km_init2(void *km_par, size_t min_core_size);
 void km_destroy(void *km);
 void km_stat(const void *_km, km_stat_t *s);
+void km_stat_print(const void *km);
 
 #ifdef __cplusplus
 }
 #endif
 
+#define Kmalloc(km, type, cnt)       ((type*)kmalloc((km), (cnt) * sizeof(type)))
+#define Kcalloc(km, type, cnt)       ((type*)kcalloc((km), (cnt), sizeof(type)))
+#define Krealloc(km, type, ptr, cnt) ((type*)krealloc((km), (ptr), (cnt) * sizeof(type)))
+
+#define Kexpand(km, type, a, m) do { \
+		(m) = (m) >= 4? (m) + ((m)>>1) : 16; \
+		(a) = Krealloc(km, type, (a), (m)); \
+	} while (0)
+
 #define KMALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))kmalloc((km), (len) * sizeof(*(ptr))))
 #define KCALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))kcalloc((km), (len), sizeof(*(ptr))))
 #define KREALLOC(km, ptr, len) ((ptr) = (__typeof__(ptr))krealloc((km), (ptr), (len) * sizeof(*(ptr))))
@@ -50,7 +61,7 @@ void km_stat(const void *_km, km_stat_t *s);
 	} kmp_##name##_t; \
 	SCOPE kmp_##name##_t *kmp_init_##name(void *km) { \
 		kmp_##name##_t *mp; \
-		KCALLOC(km, mp, 1); \
+		mp = Kcalloc(km, kmp_##name##_t, 1); \
 		mp->km = km; \
 		return mp; \
 	} \
@@ -66,7 +77,7 @@ void km_stat(const void *_km, km_stat_t *s);
 	} \
 	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); \
+		if (mp->n == mp->max) Kexpand(mp->km, kmptype_t*, mp->buf, mp->max); \
 		mp->buf[mp->n++] = p; \
 	}
 

ksw2.h

@@ -15,6 +15,7 @@
 #define KSW_EZ_SPLICE_FOR  0x100
 #define KSW_EZ_SPLICE_REV  0x200
 #define KSW_EZ_SPLICE_FLANK 0x400
+#define KSW_EZ_SPLICE_CMPLX 0x800
 
 // The subset of CIGAR operators used by ksw code.
 // Use MM_CIGAR_* from minimap.h if you need the full list.

ksw2_extd2_sse.c

@@ -358,7 +358,7 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e2)) break;

ksw2_exts2_sse.c

@@ -71,6 +71,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 
 	ksw_reset_extz(ez);
 	if (m <= 1 || qlen <= 0 || tlen <= 0 || q2 <= q + e) return;
+	assert((flag & KSW_EZ_SPLICE_FOR) == 0 || (flag & KSW_EZ_SPLICE_REV) == 0); // can't be both set
 
 	zero_   = _mm_set1_epi8(0);
 	q_      = _mm_set1_epi8(q);
@@ -118,55 +119,93 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 
 	// set the donor and acceptor arrays. TODO: this assumes 0/1/2/3 encoding!
 	if (flag & (KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV)) {
-		int semi_cost = flag&KSW_EZ_SPLICE_FLANK? -noncan/2 : 0; // GTr or yAG is worth 0.5 bit; see PMID:18688272
-		memset(donor, -noncan, tlen_ * 16);
-		memset(acceptor, -noncan, tlen_ * 16);
+		const int sp0[4] = { 8, 15, 21, 30 };
+		int sp[4];
+		if (flag & KSW_EZ_SPLICE_CMPLX) {
+			for (t = 0; t < 4; ++t)
+				sp[t] = (int)((double)sp0[t] / 3. + .499);
+		} else {
+			sp[0] = flag&KSW_EZ_SPLICE_FLANK? noncan / 2 : 0;
+			sp[1] = sp[2] = sp[3] = noncan;
+		}
+		memset(donor,    -sp[3], tlen_ * 16);
+		memset(acceptor, -sp[3], tlen_ * 16);
 		if (!(flag & KSW_EZ_REV_CIGAR)) {
 			for (t = 0; t < tlen - 4; ++t) {
-				int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG
-				if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 3) can_type = 1; // GTr...
-				if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 3) can_type = 1; // CTr...
-				if (can_type && (target[t+3] == 0 || target[t+3] == 2)) can_type = 2;
-				if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost;
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t+1] == 2 && target[t+2] == 3)             // |GT.
+						z = target[t+3] == 0 || target[t+3] == 2? -1 : 0; // |GTr or not
+					else if (target[t+1] == 2 && target[t+2] == 1) z = 1; // |GC.
+					else if (target[t+1] == 0 && target[t+2] == 3) z = 2; // |AT.
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t+1] == 1 && target[t+2] == 3)             // |CT. (revcomp of .AG|)
+						z = target[t+3] == 0 || target[t+3] == 2? -1 : 0;
+					else if (target[t+1] == 2 && target[t+2] == 3) z = 2; // |GT. (revcomp of .AC|)
+				}
+				((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
 			}
-			if (junc)
-				for (t = 0; t < tlen - 1; ++t)
-					if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8)))
-						((int8_t*)donor)[t] += junc_bonus;
 			for (t = 2; t < tlen; ++t) {
-				int can_type = 0;
-				if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 0 && target[t] == 2) can_type = 1; // ...yAG
-				if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 0 && target[t] == 1) can_type = 1; // ...yAC
-				if (can_type && (target[t-2] == 1 || target[t-2] == 3)) can_type = 2;
-				if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost;
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t-1] == 0 && target[t] == 2)               // .AG|
+						z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAG| or not
+					else if (target[t-1] == 0 && target[t] == 1) z = 2;   // .AC|
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t-1] == 0 && target[t] == 1)               // .AC| (revcomp of |GT.)
+						z = target[t-2] == 1 || target[t-2] == 3? -1 : 0; // yAC| or not
+					else if (target[t-1] == 2 && target[t] == 1) z = 1;   // .GC| (revcomp of |GC.)
+					else if (target[t-1] == 0 && target[t] == 3) z = 2;   // .AT| (revcomp of |AT.)
+				}
+				((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
 			}
-			if (junc)
-				for (t = 0; t < tlen; ++t)
-					if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&4)))
-						((int8_t*)acceptor)[t] += junc_bonus;
 		} else {
 			for (t = 0; t < tlen - 4; ++t) {
-				int can_type = 0; // type of canonical site: 0=none, 1=GT/AG only, 2=GTr/yAG
-				if ((flag & KSW_EZ_SPLICE_FOR) && target[t+1] == 2 && target[t+2] == 0) can_type = 1; // GAy...
-				if ((flag & KSW_EZ_SPLICE_REV) && target[t+1] == 1 && target[t+2] == 0) can_type = 1; // CAy...
-				if (can_type && (target[t+3] == 1 || target[t+3] == 3)) can_type = 2;
-				if (can_type) ((int8_t*)donor)[t] = can_type == 2? 0 : semi_cost;
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t+1] == 2 && target[t+2] == 0)             // |GA. (rev of .AG|)
+						z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
+					else if (target[t+1] == 1 && target[t+2] == 0) z = 2; // |CA. (rev of .AC|)
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t+1] == 1 && target[t+2] == 0)             // |CA. (comp of |GT.)
+						z = target[t+3] == 1 || target[t+3] == 3? -1 : 0;
+					else if (target[t+1] == 1 && target[t+2] == 2) z = 1; // |CG. (comp of |GC.)
+					else if (target[t+1] == 3 && target[t+2] == 0) z = 2; // |TA. (comp of |AT.)
+				}
+				((int8_t*)donor)[t] = z < 0? 0 : -sp[z];
 			}
-			if (junc)
-				for (t = 0; t < tlen - 1; ++t)
-					if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&4)))
-						((int8_t*)donor)[t] += junc_bonus;
 			for (t = 2; t < tlen; ++t) {
-				int can_type = 0;
-				if ((flag & KSW_EZ_SPLICE_FOR) && target[t-1] == 3 && target[t] == 2) can_type = 1; // ...rTG
-				if ((flag & KSW_EZ_SPLICE_REV) && target[t-1] == 3 && target[t] == 1) can_type = 1; // ...rTC
-				if (can_type && (target[t-2] == 0 || target[t-2] == 2)) can_type = 2;
-				if (can_type) ((int8_t*)acceptor)[t] = can_type == 2? 0 : semi_cost;
+				int z = 3;
+				if (flag & KSW_EZ_SPLICE_FOR) {
+					if (target[t-1] == 3 && target[t] == 2)               // .TG| (rev of |GT.)
+						z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
+					else if (target[t-1] == 1 && target[t] == 2) z = 1;   // .CG| (rev of |GC.)
+					else if (target[t-1] == 3 && target[t] == 0) z = 2;   // .TA| (rev of |AT.)
+				} else if (flag & KSW_EZ_SPLICE_REV) {
+					if (target[t-1] == 3 && target[t] == 1)               // .TC| (comp of .AG|)
+						z = target[t-2] == 0 || target[t-2] == 2? -1 : 0;
+					else if (target[t-1] == 3 && target[t] == 2) z = 2;   // .TG| (comp of .AC|)
+				}
+				((int8_t*)acceptor)[t] = z < 0? 0 : -sp[z];
 			}
-			if (junc)
-				for (t = 0; t < tlen; ++t)
-					if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
-						((int8_t*)acceptor)[t] += junc_bonus;
+		}
+	}
+
+	if (junc) {
+		if (!(flag & KSW_EZ_REV_CIGAR)) {
+			for (t = 0; t < tlen - 1; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&8)))
+					((int8_t*)donor)[t] += junc_bonus;
+			for (t = 0; t < tlen; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&4)))
+					((int8_t*)acceptor)[t] += junc_bonus;
+		} else {
+			for (t = 0; t < tlen - 1; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t+1]&2)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t+1]&4)))
+					((int8_t*)donor)[t] += junc_bonus;
+			for (t = 0; t < tlen; ++t)
+				if (((flag & KSW_EZ_SPLICE_FOR) && (junc[t]&1)) || ((flag & KSW_EZ_SPLICE_REV) && (junc[t]&8)))
+					((int8_t*)acceptor)[t] += junc_bonus;
 		}
 	}
 
@@ -376,7 +415,7 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, 0)) break;

ksw2_extz2_sse.c

@@ -269,7 +269,7 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 			} else H[0] = v8[0] - qe - qe, max_H = H[0], max_t = 0; // special casing r==0
 			// update ez
 			if (en0 == tlen - 1 && H[en0] > ez->mte)
-				ez->mte = H[en0], ez->mte_q = r - en;
+				ez->mte = H[en0], ez->mte_q = r - en0;
 			if (r - st0 == qlen - 1 && H[st0] > ez->mqe)
 				ez->mqe = H[st0], ez->mqe_t = st0;
 			if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e)) break;

lchain.c

@@ -6,7 +6,25 @@
 #include "kalloc.h"
 #include "krmq.h"
 
-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_)
+static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
+{
+	int64_t i = z[k].y, end_i = -1, max_i = i;
+	int32_t max_s = 0;
+	if (i < 0 || t[i] != 0) return i;
+	do {
+		int32_t s;
+		t[i] = 2;
+		end_i = i = p[i];
+		s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+		if (s > max_s) max_s = s, max_i = i;
+		else if (max_s - s > max_drop) break;
+	} while (i >= 0 && t[i] == 0);
+	for (i = z[k].y; i >= 0 && i != end_i; i = p[i]) // reset modified t[]
+		t[i] = 0;
+	return max_i;
+}
+
+uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t max_drop, int32_t *n_u_, int32_t *n_v_)
 {
 	mm128_t *z;
 	uint64_t *u;
@@ -17,33 +35,39 @@ uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_
 	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);
+	z = Kmalloc(km, mm128_t, n_z);
 	for (i = 0, k = 0; i < n; ++i) // populate z[]
 		if (f[i] >= min_sc) z[k].x = f[i], z[k++].y = i;
 	radix_sort_128x(z, z + n_z);
 
 	memset(t, 0, n * 4);
 	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // precompute n_u
-		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;
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				++n_v, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				++n_u;
+			else n_v = n_v0;
+		}
 	}
-	KMALLOC(km, u, n_u);
+	u = Kmalloc(km, uint64_t, n_u);
 	memset(t, 0, n * 4);
 	for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
-		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;
+		if (t[z[k].y] == 0) {
+			int64_t n_v0 = n_v, end_i;
+			int32_t sc;
+			end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
+			for (i = z[k].y; i != end_i; i = p[i])
+				v[n_v++] = i, t[i] = 1;
+			sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
+			if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
+				u[n_u++] = (uint64_t)sc << 32 | (n_v - n_v0);
+			else n_v = n_v0;
+		}
 	}
 	kfree(km, z);
 	assert(n_v < INT32_MAX);
@@ -58,7 +82,7 @@ static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32
 	int64_t i, j, k;
 
 	// write the result to b[]
-	KMALLOC(km, b, n_v);
+	b = Kmalloc(km, mm128_t, n_v);
 	for (i = 0, k = 0; i < n_u; ++i) {
 		int32_t k0 = k, ni = (int32_t)u[i];
 		for (j = 0; j < ni; ++j)
@@ -67,13 +91,13 @@ static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32
 	kfree(km, v);
 
 	// sort u[] and a[] by the target position, such that adjacent chains may be joined
-	KMALLOC(km, w, n_u);
+	w = Kmalloc(km, mm128_t, n_u);
 	for (i = k = 0; i < n_u; ++i) {
 		w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
 		k += (int32_t)u[i];
 	}
 	radix_sort_128x(w, w + n_u);
-	KMALLOC(km, u2, n_u);
+	u2 = Kmalloc(km, uint64_t, n_u);
 	for (i = k = 0; i < n_u; ++i) {
 		int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
 		u2[i] = u[j];
@@ -114,7 +138,7 @@ static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t ma
 }
 
 /* Input:
- *   a[].x: tid<<33 | rev<<32 | tpos
+ *   a[].x: rev<<63 | tid<<32 | tpos
  *   a[].y: flags<<40 | q_span<<32 | q_pos
  * Output:
  *   n_u: #chains
@@ -124,7 +148,7 @@ static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t ma
 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;
+	int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
 	int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
 	uint64_t *u;
 
@@ -135,10 +159,11 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 	}
 	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);
+	if (is_cdna) max_drop = INT32_MAX;
+	p = Kmalloc(km, int64_t, n);
+	f = Kmalloc(km, int32_t, n);
+	v = Kmalloc(km, int32_t, n);
+	t = Kcalloc(km, int32_t, n);
 
 	// fill the score and backtrack arrays
 	for (i = 0, max_ii = -1; i < n; ++i) {
@@ -181,7 +206,7 @@ mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int
 		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);
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
 	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
 	kfree(km, p); kfree(km, f); kfree(km, t);
 	if (n_u == 0) {
@@ -225,8 +250,8 @@ static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, flo
 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;
+	int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
+	int64_t *p, i, i0, st = 0, st_inner = 0;
 	uint64_t *u;
 	lc_elem_t *root = 0, *root_inner = 0;
 	void *mem_mp = 0;
@@ -239,10 +264,10 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 	}
 	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);
+	p = Kmalloc(km, int64_t, n);
+	f = Kmalloc(km, int32_t, n);
+	t = Kcalloc(km, int32_t, n);
+	v = Kmalloc(km, int32_t, n);
 	mem_mp = km_init2(km, 0x10000);
 	mp = kmp_init_rmq(mem_mp);
 
@@ -320,7 +345,6 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 						}
 						if (!krmq_itr_prev(lc_elem, &itr)) break;
 					}
-					n_iter += n_rmq_iter;
 				}
 			}
 		}
@@ -333,7 +357,7 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
 	}
 	km_destroy(mem_mp);
 
-	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, &n_u, &n_v);
+	u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
 	*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
 	kfree(km, p); kfree(km, f); kfree(km, t);
 	if (n_u == 0) {

main.c

@@ -7,8 +7,6 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.23-r1111"
-
 #ifdef __linux__
 #include <sys/resource.h>
 #include <sys/time.h>
@@ -76,6 +74,9 @@ static ko_longopt_t long_options[] = {
 	{ "cap-kalloc",     ko_required_argument, 349 },
 	{ "q-occ-frac",     ko_required_argument, 350 },
 	{ "chain-skip-scale",ko_required_argument,351 },
+	{ "print-chains",   ko_no_argument,       352 },
+	{ "no-hash-name",   ko_no_argument,       353 },
+	{ "secondary-seq",  ko_no_argument,       354 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -119,7 +120,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int64_t flag, int long_idx, const
 
 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:e:U:";
+	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:J:";
 	ketopt_t o = KETOPT_INIT;
 	mm_mapopt_t opt;
 	mm_idxopt_t ipt;
@@ -185,7 +186,12 @@ int main(int argc, char *argv[])
 		else if (c == 'R') rg = o.arg;
 		else if (c == 'h') fp_help = stdout;
 		else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
-		else if (c == 'o') {
+		else if (c == 'J') {
+			int t;
+			t = atoi(o.arg);
+			if (t == 0) opt.flag |= MM_F_SPLICE_OLD;
+			else if (t == 1) opt.flag &= ~MM_F_SPLICE_OLD;
+		} else if (c == 'o') {
 			if (strcmp(o.arg, "-") != 0) {
 				if (freopen(o.arg, "wb", stdout) == NULL) {
 					fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", o.arg, strerror(errno));
@@ -233,6 +239,9 @@ int main(int argc, char *argv[])
 		else if (c == 348) opt.flag |= MM_F_QSTRAND | MM_F_NO_INV; // --qstrand
 		else if (c == 349) opt.cap_kalloc = mm_parse_num(o.arg); // --cap-kalloc
 		else if (c == 350) opt.q_occ_frac = atof(o.arg); // --q-occ-frac
+		else if (c == 352) mm_dbg_flag |= MM_DBG_PRINT_CHAIN; // --print-chains
+		else if (c == 353) opt.flag |= MM_F_NO_HASH_NAME; // --no-hash-name
+		else if (c == 354) opt.flag |= MM_F_SECONDARY_SEQ; // --secondary-seq
 		else if (c == 330) {
 			fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
 		} else if (c == 314) { // --frag
@@ -257,7 +266,8 @@ int main(int argc, char *argv[])
 		} 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);
+			if (o.arg) yes_or_no(&opt, MM_F_RMQ, o.longidx, o.arg, 1);
+			else opt.flag |= MM_F_RMQ;
 		} else if (c == 'S') {
 			opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
 			if (mm_verbose >= 2)
@@ -318,7 +328,7 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -H           use homopolymer-compressed k-mer (preferrable for PacBio)\n");
 		fprintf(fp_help, "    -k INT       k-mer size (no larger than 28) [%d]\n", ipt.k);
 		fprintf(fp_help, "    -w INT       minimizer window size [%d]\n", ipt.w);
-		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [4G]\n");
+		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [8G]\n");
 		fprintf(fp_help, "    -d FILE      dump index to FILE []\n");
 		fprintf(fp_help, "  Mapping:\n");
 		fprintf(fp_help, "    -f FLOAT     filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);
@@ -340,6 +350,7 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -z INT[,INT] Z-drop score and inversion Z-drop score [%d,%d]\n", opt.zdrop, opt.zdrop_inv);
 		fprintf(fp_help, "    -s INT       minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(fp_help, "    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
+		fprintf(fp_help, "    -J INT       splice mode. 0: original minimap2 model; 1: miniprot model [1]\n");
 		fprintf(fp_help, "  Input/Output:\n");
 		fprintf(fp_help, "    -a           output in the SAM format (PAF by default)\n");
 		fprintf(fp_help, "    -o FILE      output alignments to FILE [stdout]\n");

map.c

@@ -10,11 +10,6 @@
 #include "bseq.h"
 #include "khash.h"
 
-struct mm_tbuf_s {
-	void *km;
-	int rep_len, frag_gap;
-};
-
 mm_tbuf_t *mm_tbuf_init(void)
 {
 	mm_tbuf_t *b;
@@ -248,7 +243,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 	if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
 	if (opt->max_qlen > 0 && qlen_sum > opt->max_qlen) return;
 
-	hash  = qname? __ac_X31_hash_string(qname) : 0;
+	hash  = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
 	hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
 	hash  = __ac_Wang_hash(hash);
 
@@ -328,7 +323,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 		mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
 	}
 
-	if (mm_dbg_flag & MM_DBG_PRINT_SEED)
+	if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
 		for (j = 0; j < n_regs0; ++j)
 			for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
 				fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),

minimap.h

@@ -5,40 +5,45 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_F_NO_DIAG       0x001 // no exact diagonal hit
-#define MM_F_NO_DUAL       0x002 // skip pairs where query name is lexicographically larger than target name
-#define MM_F_CIGAR         0x004
-#define MM_F_OUT_SAM       0x008
-#define MM_F_NO_QUAL       0x010
-#define MM_F_OUT_CG        0x020
-#define MM_F_OUT_CS        0x040
-#define MM_F_SPLICE        0x080 // splice mode
-#define MM_F_SPLICE_FOR    0x100 // match GT-AG
-#define MM_F_SPLICE_REV    0x200 // match CT-AC, the reverse complement of GT-AG
-#define MM_F_NO_LJOIN      0x400
-#define MM_F_OUT_CS_LONG   0x800
-#define MM_F_SR            0x1000
-#define MM_F_FRAG_MODE     0x2000
-#define MM_F_NO_PRINT_2ND  0x4000
-#define MM_F_2_IO_THREADS  0x8000
-#define MM_F_LONG_CIGAR    0x10000
-#define MM_F_INDEPEND_SEG  0x20000
-#define MM_F_SPLICE_FLANK  0x40000
-#define MM_F_SOFTCLIP      0x80000
-#define MM_F_FOR_ONLY      0x100000
-#define MM_F_REV_ONLY      0x200000
-#define MM_F_HEAP_SORT     0x400000
-#define MM_F_ALL_CHAINS    0x800000
-#define MM_F_OUT_MD        0x1000000
-#define MM_F_COPY_COMMENT  0x2000000
-#define MM_F_EQX           0x4000000 // use =/X instead of M
-#define MM_F_PAF_NO_HIT    0x8000000 // output unmapped reads to PAF
-#define MM_F_NO_END_FLT    0x10000000
-#define MM_F_HARD_MLEVEL   0x20000000
-#define MM_F_SAM_HIT_ONLY  0x40000000
+#define MM_VERSION "2.25-r1173"
+
+#define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
+#define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name
+#define MM_F_CIGAR         (0x004LL)
+#define MM_F_OUT_SAM       (0x008LL)
+#define MM_F_NO_QUAL       (0x010LL)
+#define MM_F_OUT_CG        (0x020LL)
+#define MM_F_OUT_CS        (0x040LL)
+#define MM_F_SPLICE        (0x080LL) // splice mode
+#define MM_F_SPLICE_FOR    (0x100LL) // match GT-AG
+#define MM_F_SPLICE_REV    (0x200LL) // match CT-AC, the reverse complement of GT-AG
+#define MM_F_NO_LJOIN      (0x400LL)
+#define MM_F_OUT_CS_LONG   (0x800LL)
+#define MM_F_SR            (0x1000LL)
+#define MM_F_FRAG_MODE     (0x2000LL)
+#define MM_F_NO_PRINT_2ND  (0x4000LL)
+#define MM_F_2_IO_THREADS  (0x8000LL)
+#define MM_F_LONG_CIGAR    (0x10000LL)
+#define MM_F_INDEPEND_SEG  (0x20000LL)
+#define MM_F_SPLICE_FLANK  (0x40000LL)
+#define MM_F_SOFTCLIP      (0x80000LL)
+#define MM_F_FOR_ONLY      (0x100000LL)
+#define MM_F_REV_ONLY      (0x200000LL)
+#define MM_F_HEAP_SORT     (0x400000LL)
+#define MM_F_ALL_CHAINS    (0x800000LL)
+#define MM_F_OUT_MD        (0x1000000LL)
+#define MM_F_COPY_COMMENT  (0x2000000LL)
+#define MM_F_EQX           (0x4000000LL) // use =/X instead of M
+#define MM_F_PAF_NO_HIT    (0x8000000LL) // output unmapped reads to PAF
+#define MM_F_NO_END_FLT    (0x10000000LL)
+#define MM_F_HARD_MLEVEL   (0x20000000LL)
+#define MM_F_SAM_HIT_ONLY  (0x40000000LL)
 #define MM_F_RMQ           (0x80000000LL)
 #define MM_F_QSTRAND       (0x100000000LL)
 #define MM_F_NO_INV        (0x200000000LL)
+#define MM_F_NO_HASH_NAME  (0x400000000LL)
+#define MM_F_SPLICE_OLD    (0x800000000LL)
+#define MM_F_SECONDARY_SEQ (0x1000000000LL)	//output SEQ field for seqondary alignments using hard clipping
 
 #define MM_I_HPC          0x1
 #define MM_I_NO_SEQ       0x2
@@ -188,6 +193,11 @@ typedef struct {
 } mm_idx_reader_t;
 
 // memory buffer for thread-local storage during mapping
+struct mm_tbuf_s {
+	void *km;
+	int rep_len, frag_gap;
+};
+
 typedef struct mm_tbuf_s mm_tbuf_t;
 
 // global variables

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "18 November 2021" "minimap2-2.23 (r1111)" "Bioinformatics tools"
+.TH minimap2 1 "25 April 2023" "minimap2-2.25 (r1173)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -77,8 +77,21 @@ SAM format.
 Minimizer k-mer length [15]
 .TP
 .BI -w \ INT
-Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
+Minimizer window size [10]. A minimizer is the smallest k-mer
 in a window of w consecutive k-mers.
+.TP
+.BI -j \ INT
+Syncmer submer size [10]. Option
+.B -j
+and
+.B -w
+will override each: if
+.B -w
+is applied after
+.BR -j ,
+.B -j
+will have no effect, and vice versa.
+
 .TP
 .B -H
 Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
@@ -88,16 +101,17 @@ on the HPC sequence.
 .BI -I \ NUM
 Load at most
 .I NUM
-target bases into RAM for indexing [4G]. If there are more than
+target bases into RAM for indexing [8G]. If there are more than
 .I NUM
 bases in
 .IR target.fa ,
 minimap2 needs to read
 .I query.fa
-multiple times to map it against each batch of target sequences.
+multiple times to map it against each batch of target sequences. This would create a multi-part index.
 .I NUM
 may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
-multi-part index.
+multi-part index. See also option
+.BR --split-prefix .
 .TP
 .B --idx-no-seq
 Don't store target sequences in the index. It saves disk space and memory but
@@ -318,6 +332,9 @@ faster for short reads, but slower for long reads. [no]
 .B --no-pairing
 Treat two reads in a pair as independent reads. The mate related fields in SAM
 are still properly populated.
+.TP
+.B --no-hash-name
+Produce the same alignment for identical sequences regardless of their sequence names.
 .SS Alignment options
 .TP 10
 .BI -A \ INT
@@ -562,7 +579,7 @@ Align older PacBio continuous long (CLR) reads to a reference genome
 .B asm5
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -g10k -A1 -B19 -O39,81 -E3,1 -s200 -z200
 .BR -N50 ).
 Typically, the alignment will not extend to regions with 5% or higher sequence
 divergence. Only use this preset if the average divergence is far below 5%.
@@ -570,21 +587,21 @@ divergence. Only use this preset if the average divergence is far below 5%.
 .B asm10
 Long assembly to reference mapping
 .RB ( -k19
-.B -w19 -U50,500 --rmq -r100k -g10k -A1 -B9 -O16,41 -E2,1 -s200 -z200
+.B -w19 -U50,500 --rmq -r1k,100k -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 -U50,500 --rmq -r100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
+.B -w10 -U50,500 --rmq -r1k,100k -g10k -A1 -B4 -O6,26 -E2,1 -s200 -z200
 .BR -N50 ).
 Up to 20% sequence divergence.
 .TP
 .B splice
 Long-read spliced alignment
 .RB ( -k15
-.B -w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0
+.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
@@ -603,7 +620,7 @@ 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 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20
+.B -w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m25
 .B -s40 -g100 -2K50m --heap-sort=yes
 .BR --secondary=no ).
 .TP

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.23-r1111';
+var paftools_version = '2.25-r1173';
 
 /*****************************
  ***** Library functions *****
@@ -1532,22 +1532,24 @@ function paf_view(args)
 
 function paf_gff2bed(args)
 {
-	var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false, output_gene = false;
-	while ((c = getopt(args, "u:sgjG")) != null) {
+	var c, fn_ucsc_fai = null, is_short = false, keep_gff = false, print_junc = false, output_gene = false, ens_canon_only = false;
+	while ((c = getopt(args, "u:sgjGe")) != null) {
 		if (c == 'u') fn_ucsc_fai = getopt.arg;
 		else if (c == 's') is_short = true;
 		else if (c == 'g') keep_gff = true;
 		else if (c == 'j') print_junc = true;
 		else if (c == 'G') output_gene = true;
+		else if (c == 'e') ens_canon_only = true;
 	}
 
 	if (getopt.ind == args.length) {
 		print("Usage: paftools.js gff2bed [options] <in.gff>");
 		print("Options:");
-		print("  -j       Output junction BED");
-		print("  -s       Print names in the short form");
+		print("  -j       output junction BED");
+		print("  -s       print names in the short form");
 		print("  -u FILE  hg38.fa.fai for chr name conversion");
-		print("  -g       Output GFF (used with -u)");
+		print("  -e       only show transcript tagged with 'Ensembl_canonical'");
+		print("  -g       output GFF (used with -u)");
 		exit(1);
 	}
 
@@ -1606,7 +1608,7 @@ function paf_gff2bed(args)
 		print(a[0][0], st, en, name, 1000, a[0][3], cds_st, cds_en, color, a.length, sizes.join(",") + ",", starts.join(",") + ",");
 	}
 
-	var re_gtf  = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name) "([^"]+)";/g;
+	var re_gtf  = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name|tag) "([^"]+)";/g;
 	var re_gff3 = /\b(transcript_id|transcript_type|transcript_biotype|gene_name|gene_id|gbkey|transcript_name)=([^;]+)/g;
 	var re_gtf_gene  = /\b(gene_id|gene_type|gene_name) "([^;]+)";/g;
 	var re_gff3_gene = /\b(gene_id|gene_type|source_gene|gene_biotype|gene_name)=([^;]+);/g;
@@ -1646,13 +1648,14 @@ function paf_gff2bed(args)
 		if (t[2] != "CDS" && t[2] != "exon") continue;
 		t[3] = parseInt(t[3]) - 1;
 		t[4] = parseInt(t[4]);
-		var id = null, type = "", name = "N/A", biotype = "", m, tname = "N/A";
+		var id = null, type = "", name = "N/A", biotype = "", m, tname = "N/A", ens_canonical = false;
 		while ((m = re_gtf.exec(t[8])) != null) {
 			if (m[1] == "transcript_id") id = m[2];
 			else if (m[1] == "transcript_type") type = m[2];
 			else if (m[1] == "transcript_biotype" || m[1] == "gbkey") biotype = m[2];
 			else if (m[1] == "gene_name" || m[1] == "gene_id") name = m[2];
 			else if (m[1] == "transcript_name") tname = m[2];
+			else if (m[1] == "tag" && m[2] == "Ensembl_canonical") ens_canonical = true;
 		}
 		while ((m = re_gff3.exec(t[8])) != null) {
 			if (m[1] == "transcript_id") id = m[2];
@@ -1661,6 +1664,7 @@ function paf_gff2bed(args)
 			else if (m[1] == "gene_name" || m[1] == "gene_id") name = m[2];
 			else if (m[1] == "transcript_name") tname = m[2];
 		}
+		if (ens_canon_only && !ens_canonical) continue;
 		if (type == "" && biotype != "") type = biotype;
 		if (id == null) throw Error("No transcript_id");
 		if (id != last_id) {
@@ -2341,12 +2345,15 @@ function paf_pbsim2fq(args)
 
 function paf_junceval(args)
 {
-	var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false;
-	while ((c = getopt(args, "l:epc")) != null) {
+	var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false, is_bed = false;
+	while ((c = getopt(args, "l:epcab1")) != null) {
 		if (c == 'l') l_fuzzy = parseInt(getopt.arg);
 		else if (c == 'e') print_err_only = print_ovlp = true;
 		else if (c == 'p') print_ovlp = true;
 		else if (c == 'c') chr_only = true;
+		else if (c == 'a') aa = true;
+		else if (c == 'b') is_bed = true;
+		else if (c == '1') first_only = true;
 	}
 
 	if (args.length - getopt.ind < 1) {
@@ -2356,6 +2363,9 @@ function paf_junceval(args)
 		print("  -p        print overlapping introns");
 		print("  -e        print erroreous overlapping introns");
 		print("  -c        only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
+		print("  -a        miniprot PAF as input");
+		print("  -b        BED as input");
+		print("  -1        only process the first alignment of each query");
 		exit(1);
 	}
 
@@ -2409,13 +2419,17 @@ 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+)([MIDNSHP=X])/g;
+	var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g;
 	while (file.readline(buf) >= 0) {
 		var m, t = buf.toString().split("\t");
-		var ctg_name = null, cigar = null, pos = null, qname = t[0];
+		var ctg_name = null, cigar = null, pos = null, qname;
 
 		if (t[0].charAt(0) == '@') continue;
-		if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
+		if (t[0] == "##PAF") t.shift();
+		qname = t[0];
+		if (is_bed) {
+			ctg_name = t[0], pos = parseInt(t[1]), cigar == null;
+		} else 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) {
@@ -2445,12 +2459,43 @@ function paf_junceval(args)
 		}
 
 		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]);
-				pos += len;
-			} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
+		if (is_bed) {
+			intron.push([pos, parseInt(t[2])]);
+		} else if (aa) {
+			var tmp_junc = [], tmp = 0;
+			while ((m = re_cigar.exec(cigar)) != null) {
+				var len = parseInt(m[1]), op = m[2];
+				if (op == 'N') {
+					tmp_junc.push([tmp, tmp + len]);
+					tmp += len;
+				} else if (op == 'U') {
+					tmp_junc.push([tmp + 1, tmp + len - 2]);
+					tmp += len;
+				} else if (op == 'V') {
+					tmp_junc.push([tmp + 2, tmp + len - 1]);
+					tmp += len;
+				} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') {
+					tmp += len * 3;
+				} else if (op == 'F' || op == 'G') {
+					tmp += len;
+				}
+			}
+			if (t[4] == '+') {
+				for (var i = 0; i < tmp_junc.length; ++i)
+					intron.push([pos + tmp_junc[i][0], pos + tmp_junc[i][1]]);
+			} else if (t[4] == '-') {
+				var glen = parseInt(t[8]) - parseInt(t[7]);
+				for (var i = tmp_junc.length - 1; i >= 0; --i)
+					intron.push([pos + (glen - tmp_junc[i][1]), pos + (glen - tmp_junc[i][0])]);
+			}
+		} else {
+			while ((m = re_cigar.exec(cigar)) != null) {
+				var len = parseInt(m[1]), op = m[2];
+				if (op == 'N') {
+					intron.push([pos, pos + len]);
+					pos += len;
+				} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
+			}
 		}
 		if (intron.length == 0) {
 			++n_sgl;
@@ -2509,6 +2554,276 @@ function paf_junceval(args)
 	}
 }
 
+function paf_exoneval(args) // adapted from paf_junceval()
+{
+	var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false, is_bed = false, use_cds = false, eval_base = false;
+	while ((c = getopt(args, "l:epcab1ds")) != null) {
+		if (c == 'l') l_fuzzy = parseInt(getopt.arg);
+		else if (c == 'e') print_err_only = print_ovlp = true;
+		else if (c == 'p') print_ovlp = true;
+		else if (c == 'c') chr_only = true;
+		else if (c == 'a') aa = true, use_cds = true;
+		else if (c == 'b') is_bed = true;
+		else if (c == '1') first_only = true;
+		else if (c == 'd') use_cds = true;
+		else if (c == 's') eval_base = true;
+	}
+
+	if (args.length - getopt.ind < 1) {
+		print("Usage: paftools.js exoneval [options] <gene.gtf> <aln.sam>");
+		print("Options:");
+		print("  -l INT    tolerance of junction positions (0 for exact) [0]");
+		print("  -d        evaluate coding regions only (exon regions by default)");
+		print("  -a        miniprot PAF as input (force -d)");
+		print("  -p        print overlapping exons");
+		print("  -e        print erroreous overlapping exons");
+		print("  -c        only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
+		print("  -1        only process the first alignment of each query");
+		print("  -b        BED as input");
+		print("  -s        compute base Sn and Sp (more memory)");
+		exit(1);
+	}
+
+	var file, buf = new Bytes();
+
+	warn("Reading reference GTF...");
+	var tr = {};
+	file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
+	while (file.readline(buf) >= 0) {
+		var m, t = buf.toString().split("\t");
+		if (t[0].charAt(0) == '#') continue;
+		if (use_cds) {
+			if (t[2] != "cds" && t[2] != "CDS") continue;
+		} else {
+			if (t[2] != 'exon') continue;
+		}
+		var st = parseInt(t[3]) - 1;
+		var en = parseInt(t[4]);
+		if ((m = /transcript_id "(\S+)"/.exec(t[8])) == null) continue;
+		var tid = m[1];
+		if (tr[tid] == null) tr[tid] = [t[0], t[6], 0, 0, []];
+		tr[tid][4].push([st, en]); // this keeps transcript
+	}
+	file.close();
+
+	var anno = {};
+	for (var tid in tr) { // traverse each transcript
+		var t = tr[tid];
+		Interval.sort(t[4]);
+		t[2] = t[4][0][0];
+		t[3] = t[4][t[4].length - 1][1];
+		if (anno[t[0]] == null) anno[t[0]] = [];
+		var s = t[4];
+		for (var i = 0; i < s.length; ++i) // traverse each exon
+			anno[t[0]].push([s[i][0], s[i][1]]);
+	}
+	tr = null;
+
+	for (var chr in anno) { // index exons
+		var e = anno[chr];
+		if (e.length == 0) continue;
+		Interval.sort(e);
+		var k = 0;
+		for (var i = 1; i < e.length; ++i) // dedup
+			if (e[i][0] != e[k][0] || e[i][1] != e[k][1])
+				e[++k] = e[i].slice(0);
+		e.length = k + 1;
+		Interval.index_end(e);
+	}
+
+	var n_pri = 0, n_unmapped = 0, n_mapped = 0;
+	var n_exon = 0, n_exon_hit = 0, n_exon_novel = 0;
+
+	file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]);
+	var last_qname = null, qexon = {};
+	var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g;
+
+	warn("Evaluating alignments...");
+	while (file.readline(buf) >= 0) {
+		var m, t = buf.toString().split("\t");
+		var ctg_name = null, cigar = null, pos = null, qname;
+
+		if (t[0].charAt(0) == '@') continue;
+		if (t[0] == "##PAF") t.shift();
+		qname = t[0];
+		if (is_bed) {
+			ctg_name = t[0], pos = parseInt(t[1]), cigar == null;
+		} else 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 != qname) {
+				++n_mapped;
+				last_qname = qname;
+			}
+		}
+
+		var exon = [];
+		if (is_bed) { // BED
+			exon.push([pos, parseInt(t[2])]);
+		} else if (aa) {
+			var tmp_exon = [], tmp = 0, tmp_st = 0;
+			while ((m = re_cigar.exec(cigar)) != null) {
+				var len = parseInt(m[1]), op = m[2];
+				if (op == 'N') {
+					tmp_exon.push([tmp_st, tmp]);
+					tmp_st = tmp + len, tmp += len;
+				} else if (op == 'U') {
+					tmp_exon.push([tmp_st, tmp + 1]);
+					tmp_st = tmp + len - 2, tmp += len;
+				} else if (op == 'V') {
+					tmp_exon.push([tmp_st, tmp + 2]);
+					tmp_st = tmp + len - 1, tmp += len;
+				} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') {
+					tmp += len * 3;
+				} else if (op == 'F' || op == 'G') {
+					tmp += len;
+				}
+			}
+			tmp_exon.push([tmp_st, tmp]);
+			if (t[4] == '+') {
+				for (var i = 0; i < tmp_exon.length; ++i)
+					exon.push([pos + tmp_exon[i][0], pos + tmp_exon[i][1]]);
+			} else if (t[4] == '-') { // For protein-to-genome alignment, the coordinates are on the query strand. Need to flip them.
+				var glen = parseInt(t[8]) - parseInt(t[7]);
+				for (var i = tmp_exon.length - 1; i >= 0; --i)
+					exon.push([pos + (glen - tmp_exon[i][1]), pos + (glen - tmp_exon[i][0])]);
+			}
+		} else {
+			var tmp_st = pos;
+			while ((m = re_cigar.exec(cigar)) != null) {
+				var len = parseInt(m[1]), op = m[2];
+				if (op == 'N') {
+					exon.push([tmp_st, pos]);
+					tmp_st = pos + len, pos += len;
+				} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') pos += len;
+			}
+			exon.push([tmp_st, pos]);
+		}
+		n_exon += exon.length;
+
+		var chr = anno[ctg_name];
+		if (chr != null) {
+			for (var i = 0; i < exon.length; ++i) {
+				if (eval_base) {
+					if (qexon[ctg_name] == null) qexon[ctg_name] = [];
+					qexon[ctg_name].push([exon[i][0], exon[i][1]]);
+				}
+				var o = Interval.find_ovlp(chr, exon[i][0], exon[i][1]);
+				if (o.length > 0) {
+					var hit = false;
+					for (var j = 0; j < o.length; ++j) {
+						var st_diff = exon[i][0] - o[j][0];
+						var en_diff = exon[i][1] - o[j][1];
+						if (st_diff < 0) st_diff = -st_diff;
+						if (en_diff < 0) en_diff = -en_diff;
+						if (st_diff <= l_fuzzy && en_diff <= l_fuzzy)
+							++n_exon_hit, hit = true;
+						if (hit) break;
+					}
+					if (print_ovlp) {
+						var type = hit? 'C' : 'P';
+						if (hit && print_err_only) continue;
+						var x = '[';
+						for (var j = 0; j < o.length; ++j) {
+							if (j) x += ', ';
+							x += '(' + o[j][0] + "," + o[j][1] + ')';
+						}
+						x += ']';
+						print(type, qname, i+1, ctg_name, exon[i][0], exon[i][1], x);
+					}
+				} else {
+					++n_exon_novel;
+					if (print_ovlp)
+						print('N',  qname, i+1, ctg_name, exon[i][0], exon[i][1]);
+				}
+			}
+		} else {
+			n_exon_novel += exon.length;
+		}
+	}
+	file.close();
+
+	buf.destroy();
+
+	if (!print_ovlp) {
+		print("# unmapped reads: " + n_unmapped);
+		print("# mapped reads: " + n_mapped);
+		print("# primary alignments: " + n_pri);
+		print("# predicted exons: " + n_exon);
+		print("# non-overlapping exons: " + n_exon_novel);
+		print("# correct exons: " + n_exon_hit + " (" + (n_exon_hit / n_exon * 100).toFixed(2) + "%)");
+	}
+
+	function merge_and_index(ex) {
+		for (var chr in ex) {
+			var a = [];
+			e = ex[chr];
+			Interval.sort(e);
+			var st = e[0][0], en = e[0][1];
+			for (var i = 1; i < e.length; ++i) { // merge
+				if (e[i][0] > en) {
+					a.push([st, en]);
+					st = e[i][0], en = e[i][1];
+				} else {
+					en = en > e[i][1]? en : e[i][1];
+				}
+			}
+			a.push([st, en]);
+			Interval.index_end(a);
+			ex[chr] = a;
+		}
+	}
+
+	function cal_sn(a0, a1) {
+		var tot = 0, cov = 0;
+		for (var chr in a1) {
+			var e0 = a0[chr], e1 = a1[chr];
+			for (var i = 0; i < e1.length; ++i)
+				tot += e1[i][1] - e1[i][0];
+			if (e0 == null) continue;
+			for (var i = 0; i < e1.length; ++i) {
+				var o = Interval.find_ovlp(e0, e1[i][0], e1[i][1]);
+				for (var j = 0; j < o.length; ++j) { // this only works when there are no overlaps between intervals
+					var st = e1[i][0] > o[j][0]? e1[i][0] : o[j][0];
+					var en = e1[i][1] < o[j][1]? e1[i][1] : o[j][1];
+					cov += en - st;
+				}
+			}
+		}
+		return [tot, cov];
+	}
+
+	if (eval_base) {
+		warn("Computing base Sn and Sp...");
+		merge_and_index(qexon);
+		merge_and_index(anno);
+		var sn = cal_sn(qexon, anno);
+		var sp = cal_sn(anno, qexon);
+		print("Base Sn: " + sn[1] + " / " + sn[0] + " = " + (sn[1] / sn[0] * 100).toFixed(2) + "%");
+		print("Base Sp: " + sp[1] + " / " + sp[0] + " = " + (sp[1] / sp[0] * 100).toFixed(2) + "%");
+	}
+}
+
 // evaluate overlap sensitivity
 function paf_ov_eval(args)
 {
@@ -2704,6 +3019,23 @@ function paf_misjoin(args)
 		return len < (en - st) * cen_ratio? false : true;
 	}
 
+	function test_cen_point(cen, chr, x) {
+		var b = cen[chr];
+		if (b == null) return false;
+		for (var j = 0; j < b.length; ++j)
+			if (x >= b[j][0] && x < b[j][1])
+				return true;
+		return false;
+	}
+
+	if (show_err || show_long) {
+		print("C\tJ  inter-chromosomal misjoin");
+		print("C\tj  inter-chromosomal misjoin with both breakpoints ending in centromeres");
+		print("C\tG  long gap on the reference genome");
+		print("C\tg  long gap on the reference genome with both breakpoints ending in centromeres");
+		print("C\tM  closed inversion");
+		print("C");
+	}
 	function process(a) {
 		var k = 0;
 		for (var i = 0; i < a.length; ++i) {
@@ -2716,14 +3048,17 @@ function paf_misjoin(args)
 		a = a.sort(function(x,y){return x[2]-y[2]});
 		if (show_long) for (var i = 0; i < a.length; ++i) print(a[i].join("\t"));
 		for (var i = 1; i < a.length; ++i) {
-			var ov = [false, false];
+			var ov = [false, false], end_cen = [false, false];
 			ov[0] = test_cen(cen, a[i-1][5], a[i-1][7], a[i-1][8]);
 			ov[1] = test_cen(cen, a[i][5], a[i][7], a[i][8]);
+			end_cen[0] = test_cen_point(cen, a[i-1][5], a[i-1][4] == '+'? a[i-1][8] : a[i-1][7]);
+			end_cen[1] = test_cen_point(cen, a[i][5],   a[i][4] == '+'?   a[i][7]   : a[i][8]);
 			if (a[i-1][5] != a[i][5]) { // different chr
 				if (ov[0] || ov[1]) ++n_diff[1];
 				else if (show_err) {
-					print("J", a[i-1].slice(0, 12).join("\t"));
-					print("J", a[i].slice(0, 12).join("\t"));
+					var label = end_cen[0] && end_cen[1]? 'j' : 'J';
+					print(label, a[i-1].slice(0, 12).join("\t"));
+					print(label, a[i].slice(0, 12).join("\t"));
 				}
 				++n_diff[0];
 			} else if (a[i-1][4] == a[i][4]) { // a gap
@@ -2733,8 +3068,9 @@ function paf_misjoin(args)
 				if (gap > max_gap) {
 					if (ov[0] || ov[1]) ++n_gap[1];
 					else if (show_err) {
-						print("G", a[i-1].slice(0, 12).join("\t"));
-						print("G", a[i].slice(0, 12).join("\t"));
+						var label = end_cen[0] && end_cen[1]? 'g' : 'G';
+						print(label, a[i-1].slice(0, 12).join("\t"));
+						print(label, a[i].slice(0, 12).join("\t"));
 					}
 					++n_gap[0];
 				}
@@ -3084,6 +3420,183 @@ function paf_pafcmp(args)
 	buf.destroy();
 }
 
+function paf_longcs2seq(args) {
+	var c, opt = { query:false };
+	while ((c = getopt(args, "q")) != null)
+		if (c == 'q') opt.query = true;
+	if (args.length == getopt.ind) {
+		print("Usage: paftools.js longcs2seq [-q] <long-cs.paf>");
+		return;
+	}
+	var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g
+	var buf = new Bytes();
+	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
+	while (file.readline(buf) >= 0) {
+		var m, cs = null, t = buf.toString().split("\t");
+		for (var i = 12; i < t.length; ++i)
+			if ((m = /^cs:Z:(\S+)/.exec(t[i])) != null) {
+				cs = m[1];
+				break;
+			}
+		if (cs == null) continue;
+		var ts = "", qs = "";
+		while ((m = re_cs.exec(cs)) != null) {
+			if (m[1] == "=") ts += m[2], qs += m[2];
+			else if (m[1] == "+") qs += m[2].toUpperCase();
+			else if (m[1] == "-") ts += m[2].toUpperCase();
+			else if (m[1] == "*") ts += m[2][0].toUpperCase(), qs += m[2][1].toUpperCase();
+			else if (m[1] == ":") throw Error("Long cs is required");
+		}
+		if (opt.query) {
+			print(">" + t[0] + "_" + t[2] + "_" + t[3]);
+			print(qs);
+		} else {
+			print(">" + t[5] + "_" + t[7] + "_" + t[8]);
+			print(ts);
+		}
+	}
+	file.close();
+	buf.destroy();
+}
+
+function paf_paf2gff(args) {
+	var c, opt = { aa:false };
+	var re_cigar = /(\d+)([A-Z=])/g;
+	while ((c = getopt(args, "a")) != null) {
+		if (c == 'a') opt.aa = true;
+	}
+	if (args.length == getopt.ind) {
+		print("Usage: paftools.js paf2gff [-a] <in.paf>");
+		return;
+	}
+	var buf = new Bytes();
+	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
+	var hid = 1, last_name = null;
+	while (file.readline(buf) >= 0) {
+		var m, t = buf.toString().split("\t");
+		if (t[5] == '*') continue; // skip unmapped lines
+
+		if (t[0] != last_name) last_name = t[0], hid = 1;
+		else ++hid;
+		for (var i = 1; i <= 3; ++i) t[i] = parseInt(t[i]);
+		for (var i = 6; i <= 11; ++i) t[i] = parseInt(t[i]);
+		var cigar = null, score = null, np = null, dist_stop = null, dist_start = null;
+		for (var i = 12; i < t.length; ++i) {
+			if ((m = /^(cg:Z|AS:i|np:i|da:i|do:i):(\S+)/.exec(t[i])) != null) {
+				if (m[1] == 'cg:Z') cigar = m[2];
+				else if (m[1] == 'AS:i') score = parseInt(m[2]);
+				else if (m[1] == 'np:i') np = parseInt(m[2]);
+				else if (m[1] == 'do:i') dist_stop = parseInt(m[2]);
+				else if (m[1] == 'da:i') dist_start = parseInt(m[2]);
+			}
+		}
+		if (cigar == null) throw Error("failed to find the cg:Z tag");
+		if (score == null) throw Error("failed to find the AS:i tag");
+
+		var st = 0, en = 0, phase = 0, pseudo = false, fs = 0, a = [];
+		if (dist_start != null && dist_start == 0)
+			a.push([t[5], 'paf2gff', 'start_codon', 0, 3, 0, t[4], '.', 0]);
+		while ((m = re_cigar.exec(cigar)) != null) {
+			var len = parseInt(m[1]);
+			if (m[2] == 'M' || m[2] == 'D') {
+				en += opt.aa? len * 3 : len;
+			} else if (m[2] == 'F' || m[2] == 'G' || m[2] == 'R') {
+				en += len, pseudo = true, fs = 1;
+			} else if (m[2] == 'N') {
+				a.push([t[5], 'paf2gff', 'exon', st, en, 0, t[4], phase, fs]);
+				st = en + len, en += len, phase = 0, fs = 0;
+			} else if (m[2] == 'U') { // ...xGT...AGxx...
+				a.push([t[5], 'paf2gff', 'exon', st, en + 1, 0, t[4], phase, fs]);
+				st = en + len - 2, en += len, phase = 2, fs = 0;
+			} else if (m[2] == 'V') { // ...xxGT...AGx...
+				a.push([t[5], 'paf2gff', 'exon', st, en + 2, 0, t[4], phase, fs]);
+				st = en + len - 1, en += len, phase = 1, fs = 0;
+			}
+		}
+		a.push([t[5], 'paf2gff', 'exon', st, en, 0, t[4], phase, fs]);
+		if (en != t[8] - t[7]) throw Error("inconsistent cigar");
+		if (dist_stop != null && dist_stop == 0)
+			a.push([t[5], 'paf2gff', 'stop_codon', en, en + 3, 0, t[4], '.', 0]);
+		var type = pseudo? 'pseudogene' : 'protein_coding';
+		var attr = ['transcript_id=' + t[0] + '#' + hid, 'transcript_type=' + type].join(";");
+		var trans_attr = 'identity=' + (t[9] / t[10]).toFixed(4);
+		if (np != null) trans_attr += ';positive=' + (np * 3 / t[10]).toFixed(4);
+		trans_attr += ';aa_start=' + t[2];
+		trans_attr += ';aa_end=' + (t[1] - t[3]);
+		if (dist_start != null && dist_start >= 0) trans_attr += ';dist_start_codon=' + dist_start;
+		if (dist_stop != null && dist_stop >= 0) trans_attr += ';dist_stop_codon=' + dist_stop;
+		var trans_st = t[7], trans_en = t[8];
+		if (dist_stop != null && dist_stop == 0) {
+			if (t[4] == '-') trans_st -= 3;
+			else trans_en += 3;
+		}
+		print([t[5], 'paf2gff', 'transcript', trans_st + 1, trans_en, score, t[4], '.', attr + ';' + trans_attr].join("\t"));
+		if (opt.aa && t[4] == '-') {
+			var b = [], len = t[8] - t[7];
+			for (var i = a.length - 1; i >= 0; --i) {
+				var x = len - a[i][3];
+				a[i][3] = len - a[i][4];
+				a[i][4] = x;
+				//a[i][7] = a[i][7] == 0? 0 : 3 - a[i][7]; // not sure if this line is needed
+				b.push(a[i]);
+			}
+			a = b;
+		}
+		for (var i = 0; i < a.length; ++i) {
+			if (!pseudo && a[i][2] == "exon") a[i][2] = "CDS";
+			a[i][3] += t[7] + 1;
+			a[i][4] += t[7];
+			a[i][8] = attr + ";frameshift=" + a[i][8];
+			print(a[i].join("\t"));
+		}
+	}
+	file.close();
+	buf.destroy();
+}
+
+function paf_gff2junc(args) {
+	var c, feat = "CDS";
+	while ((c = getopt(args, "f:")) != null) {
+		if (c == 'f') feat = getopt.arg;
+	}
+	if (getopt.ind == args.length) {
+		print("Usage: paftools.js gff2junc [-f feature] <in.gff3>");
+		return;
+	}
+	var buf = new Bytes();
+	var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
+
+	function process_a(a) {
+		if (a.length < 2) return;
+		a = a.sort(function(x, y) { return x[4] - y[4] });
+		for (var i = 1; i < a.length; ++i)
+			print([a[i][1], a[i-1][5], a[i][4], a[i][0], 0, a[i][7]].join("\t"));
+	}
+
+	var a = [];
+	while (file.readline(buf) >= 0) {
+		var m, t = buf.toString().split("\t");
+		if (t[0][0] == '#') continue;
+		if (t[2].toLowerCase() != feat.toLowerCase()) continue;
+		//print(t.join("\t"));
+		if ((m = /\bParent=([^;]+)/.exec(t[8])) == null) {
+			warn("Can't find Parent");
+			continue;
+		}
+		t[3] = parseInt(t[3]) - 1;
+		t[4] = parseInt(t[4]);
+		t.unshift(m[1]);
+		if (a.length > 0 && a[0][0] != m[1]) {
+			process_a(a);
+			a.length = 0;
+			a.push(t);
+		} else a.push(t);
+	}
+	process_a(a);
+	file.close();
+	buf.destroy();
+}
+
 /*************************
  ***** main function *****
  *************************/
@@ -3098,6 +3611,9 @@ function main(args)
 		print("  sam2paf    convert SAM to PAF");
 		print("  delta2paf  convert MUMmer's delta to PAF");
 		print("  gff2bed    convert GTF/GFF3 to BED12");
+		print("  gff2junc   convert GFF3 to junction BED");
+		print("  longcs2seq convert long-cs PAF to sequences");
+//		print("  paf2gff    convert PAF to GFF3 (tested for miniprot only)");
 		print("");
 		print("  stat       collect basic mapping information in PAF/SAM");
 		print("  asmstat    collect basic assembly information");
@@ -3115,6 +3631,7 @@ function main(args)
 		print("  mason2fq   convert mason2-simulated SAM to FASTQ");
 		print("  pbsim2fq   convert PBSIM-simulated MAF to FASTQ");
 		print("  junceval   evaluate splice junction consistency with known annotations");
+		print("  exoneval   evaluate exon-level consistency with known annotations");
 		print("  ov-eval    evaluate read overlap sensitivity using read-to-ref mapping");
 		exit(1);
 	}
@@ -3125,6 +3642,7 @@ function main(args)
 	else if (cmd == 'delta2paf') paf_delta2paf(args);
 	else if (cmd == 'splice2bed') paf_splice2bed(args);
 	else if (cmd == 'gff2bed') paf_gff2bed(args);
+	else if (cmd == 'gff2junc') paf_gff2junc(args);
 	else if (cmd == 'stat') paf_stat(args);
 	else if (cmd == 'asmstat') paf_asmstat(args);
 	else if (cmd == 'asmgene') paf_asmgene(args);
@@ -3138,10 +3656,13 @@ function main(args)
 	else if (cmd == 'mason2fq') paf_mason2fq(args);
 	else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
 	else if (cmd == 'junceval') paf_junceval(args);
+	else if (cmd == 'exoneval') paf_exoneval(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 == 'longcs2seq') paf_longcs2seq(args);
+	else if (cmd == 'paf2gff') paf_paf2gff(args);
 	else if (cmd == 'version') print(paftools_version);
 	else throw Error("unrecognized command: " + cmd);
 }

mmpriv.h

@@ -13,6 +13,7 @@
 #define MM_DBG_PRINT_QNAME   0x2
 #define MM_DBG_PRINT_SEED    0x4
 #define MM_DBG_PRINT_ALN_SEQ 0x8
+#define MM_DBG_PRINT_CHAIN   0x10
 
 #define MM_SEED_LONG_JOIN  (1ULL<<40)
 #define MM_SEED_IGNORE     (1ULL<<41)

options.c

@@ -8,7 +8,7 @@ void mm_idxopt_init(mm_idxopt_t *opt)
 	opt->k = 15, opt->w = 10, opt->flag = 0;
 	opt->bucket_bits = 14;
 	opt->mini_batch_size = 50000000;
-	opt->batch_size = 4000000000ULL;
+	opt->batch_size = 8000000000ULL;
 }
 
 void mm_mapopt_init(mm_mapopt_t *opt)
@@ -74,6 +74,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 		if (opt->max_mid_occ > opt->min_mid_occ && opt->mid_occ > opt->max_mid_occ)
 			opt->mid_occ = opt->max_mid_occ;
 	}
+	if (opt->bw_long < opt->bw) opt->bw_long = opt->bw;
 	if (mm_verbose >= 3)
 		fprintf(stderr, "[M::%s::%.3f*%.2f] mid_occ = %d\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), opt->mid_occ);
 }
@@ -113,7 +114,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		mo->min_dp_max = 200;
 	} else if (strncmp(preset, "asm", 3) == 0) {
 		io->flag = 0, io->k = 19, io->w = 19;
-		mo->bw = mo->bw_long = 100000;
+		mo->bw = 1000, mo->bw_long = 100000;
 		mo->max_gap = 10000;
 		mo->flag |= MM_F_RMQ;
 		mo->min_mid_occ = 50, mo->max_mid_occ = 500;

pyproject.toml

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

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.23'
+__version__ = '2.25'
 
 cmappy.mm_reset_timer()
 
@@ -172,6 +172,7 @@ cdef class Aligner:
 		cdef cmappy.mm_mapopt_t map_opt
 
 		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
 		map_opt = self.map_opt
 		if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
 		if extra_flags is not None: map_opt.flag |= extra_flags
@@ -217,6 +218,7 @@ cdef class Aligner:
 		cdef int l
 		cdef char *s
 		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
 		s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
 		if l == 0: return None
 		r = s[:l] if isinstance(s, str) else s[:l].decode()

seed.c

@@ -7,7 +7,7 @@ void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac)
 	mm128_t *a;
 	size_t i, j, st;
 	if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
-	KMALLOC(km, a, mv->n);
+	a = Kmalloc(km, mm128_t, mv->n);
 	for (i = 0; i < mv->n; ++i)
 		a[i].x = mv->a[i].x, a[i].y = i;
 	radix_sort_128x(a, a + mv->n);

setup.py

@@ -1,29 +1,40 @@
 try:
 	from setuptools import setup, Extension
+	from setuptools.command.build_ext import build_ext
 except ImportError:
 	from distutils.core import setup
 	from distutils.extension import Extension
+	from distutils.command.build_ext import build_ext
 
-import sys, platform
+import sys, platform, subprocess
 
-sys.path.append('python')
-
-extra_compile_args = ['-DHAVE_KALLOC']
-include_dirs = ["."]
-
-if platform.machine() in ["aarch64", "arm64"]:
-	include_dirs.append("sse2neon/")
-	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
-else:
-	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
 
 def readme():
 	with open('python/README.rst') as f:
 		return f.read()
 
+
+class LibMM2Build(build_ext):
+	# Uses Makefile to build library, avoids duplicating logic
+	# determining which objects to compile but does require
+	# end users to have Make (since precompiled wheels are not
+	# distributed on PyPI).
+	def run(self):
+		def compile_libminimap2(*args, **kwargs):
+			cmd = ['make', 'libminimap2.a'] + list(args)
+			subprocess.check_call(cmd)
+		options = []
+		if platform.machine() in ["aarch64", "arm64"]:
+			options = ["arm_neon=1", "aarch64=1"]
+		self.execute(
+			compile_libminimap2, options,
+			'Compiling libminimap2 using Makefile')
+		build_ext.run(self)
+
+
 setup(
 	name = 'mappy',
-	version = '2.23',
+	version = '2.25',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -32,16 +43,15 @@ setup(
 	license = 'MIT',
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
-	ext_modules = [Extension('mappy',
-		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',
-				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
-				   'python/cmappy.h', 'python/cmappy.pxd'],
-		extra_compile_args = extra_compile_args,
-		include_dirs = include_dirs,
-		libraries = ['z', 'm', 'pthread'])],
+	cmdclass = {'build_ext': LibMM2Build},
+	ext_modules = [
+		Extension(
+			'mappy',
+			sources = ['python/mappy.pyx'],
+			depends = ['python/cmappy.h', 'python/cmappy.pxd'],
+			include_dirs = ['.'],
+			extra_objects = ['libminimap2.a'],
+			libraries = ['z', 'm', 'pthread'])],
 	classifiers = [
 		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',