Release minimap2-2.14 (r883)

resolves #252
resolves #255

NEWS.md

@@ -1,3 +1,29 @@
+Release 2.14-r883 (5 November 2018)
+-----------------------------------
+
+Notable changes:
+
+ * Fixed two minor bugs caused by typos (#254 and #266).
+
+ * Fixed a bug that made minimap2 abort when --eqx was used together with --MD
+   or --cs (#257).
+
+ * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may
+   take a lot of memory in the splicing mode. This may lead to issues when we
+   run minimap2 on a cluster with a hard memory limit. The new option avoids
+   unlimited memory usage at the cost of missing a few long introns.
+
+ * Conforming to C99 and C11 when possible (#261).
+
+ * Warn about malformatted FASTA or FASTQ (#252 and #255).
+
+This release occasionally produces base alignments different from v2.13. The
+overall alignment accuracy remain similar.
+
+(2.14: 5 November 2018, r883)
+
+
+
 Release 2.13-r850 (11 October 2018)
 -----------------------------------
 

README.md

@@ -71,8 +71,8 @@ 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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.13_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.14_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
@@ -355,6 +355,8 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
   billion bases or longer (2,147,483,647 to be exact). The total length of all
   sequences can well exceed this threshold.
 
+* Minimap2 often misses small exons.
+
 
 
 [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md

align.c

@@ -300,7 +300,10 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
 		for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
 		fputc('\n', stderr);
 	}
-	if (opt->flag & MM_F_SPLICE)
+	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, flag, 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);
@@ -414,7 +417,7 @@ static void mm_filter_bad_seeds_alt(void *km, int as1, int cnt1, mm128_t *a, int
 			gap2 = ((int32_t)a[as1 + j].y - (int32_t)a[as1 + j - 1].y) - (int32_t)(a[as1 + j].x - a[as1 + j - 1].x);
 			q_span_pre = a[as1 + j - 1].y >> 32 & 0xff;
 			rs2 = (int32_t)a[as1 + j - 1].x + q_span_pre;
-			qs2 = (int32_t)a[as1 + j - 1].x + q_span_pre;
+			qs2 = (int32_t)a[as1 + j - 1].y + q_span_pre;
 			m = rs2 - re1 < qs2 - qe1? rs2 - re1 : qs2 - qe1;
 			gap2 = gap2 > 0? gap2 : -gap2;
 			if (m > gap1 + gap2) break;
@@ -591,11 +594,9 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 		qs0 = 0, qe0 = qlen;
 		l = qs;
 		l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
-		l = l < opt->bw? l : opt->bw;
 		rs0 = rs - l > 0? rs - l : 0;
 		l = qlen - qe;
 		l += l * opt->a + opt->end_bonus > opt->q? (l * opt->a + opt->end_bonus - opt->q) / opt->e : 0;
-		l = l < opt->bw? l : opt->bw;
 		re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len;
 	} else {
 		// compute rs0 and qs0

bseq.c

@@ -39,7 +39,7 @@ mm_bseq_file_t *mm_bseq_open(const char *fn)
 {
 	mm_bseq_file_t *fp;
 	gzFile f;
-	f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	f = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(0, "r");
 	if (f == 0) return 0;
 	fp = (mm_bseq_file_t*)calloc(1, sizeof(mm_bseq_file_t));
 	fp->fp = f;
@@ -65,6 +65,8 @@ static inline char *kstrdup(const kstring_t *s)
 static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_comment)
 {
 	int i;
+	if (ks->name.l == 0)
+		fprintf(stderr, "[WARNING]\033[1;31m empty sequence name in the input.\033[0m\n");
 	s->name = kstrdup(&ks->name);
 	s->seq = kstrdup(&ks->seq);
 	for (i = 0; i < (int)ks->seq.l; ++i) // convert U to T
@@ -78,6 +80,7 @@ static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual, int with_
 mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int with_comment, int frag_mode, int *n_)
 {
 	int64_t size = 0;
+	int ret;
 	kvec_t(mm_bseq1_t) a = {0,0,0};
 	kseq_t *ks = fp->ks;
 	*n_ = 0;
@@ -87,7 +90,7 @@ mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
 		size = fp->s.l_seq;
 		memset(&fp->s, 0, sizeof(mm_bseq1_t));
 	}
-	while (kseq_read(ks) >= 0) {
+	while ((ret = kseq_read(ks)) >= 0) {
 		mm_bseq1_t *s;
 		assert(ks->seq.l <= INT32_MAX);
 		if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
@@ -107,6 +110,8 @@ mm_bseq1_t *mm_bseq_read3(mm_bseq_file_t *fp, int chunk_size, int with_qual, int
 			break;
 		}
 	}
+	if (ret < -1)
+		fprintf(stderr, "[WARNING]\033[1;31m wrong FASTA/FASTQ record. Continue anyway.\033[0m\n");
 	*n_ = a.n;
 	return a.a;
 }

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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.13_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.14_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

@@ -92,7 +92,8 @@ static void sam_write_rg_line(kstring_t *str, const char *s)
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n");
 		goto err_set_rg;
 	}
-	rg_line = strdup(s);
+	rg_line = (char*)malloc(strlen(s) + 1);
+	strcpy(rg_line, s);
 	mm_escape(rg_line);
 	if ((p = strstr(rg_line, "\tID:")) == 0) {
 		if (mm_verbose >= 1) fprintf(stderr, "[ERROR] no ID within the read group line\n");
@@ -139,8 +140,8 @@ 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);
-		if (op == 0) { // match
+		assert((op >= 0 && op <= 3) || op == 7 || op == 8);
+		if (op == 0 || op == 7 || op == 8) { // match
 			int l_tmp = 0;
 			for (j = 0; j < len; ++j) {
 				if (qseq[q_off + j] != tseq[t_off + j]) {
@@ -187,8 +188,8 @@ 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);
-		if (op == 0) { // match
+		assert((op >= 0 && op <= 3) || op == 7 || op == 8);
+		if (op == 0 || op == 7 || op == 8) { // match
 			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]]);

ksw2_dispatch.c

@@ -17,18 +17,20 @@
 void __cpuidex(int cpuid[4], int func_id, int subfunc_id)
 {
 #if defined(__x86_64__)
-	asm volatile ("cpuid"
+	__asm__ volatile ("cpuid"
 			: "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
 			: "0" (func_id), "2" (subfunc_id));
 #else // on 32bit, ebx can NOT be used as PIC code
-	asm volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"
+	__asm__ volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"
 			: "=a" (cpuid[0]), "=r" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])
 			: "0" (func_id), "2" (subfunc_id));
 #endif
 }
 #endif
 
-int x86_simd(void)
+static int ksw_simd = -1;
+
+static int x86_simd(void)
 {
 	int flag = 0, cpuid[4], max_id;
 	__cpuidex(cpuid, 0, 0);
@@ -54,11 +56,10 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 {
 	extern void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 	extern void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
 		ksw_extz2_sse41(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, end_bonus, flag, ez);
-	else if (simd & SIMD_SSE2)
+	else if (ksw_simd & SIMD_SSE2)
 		ksw_extz2_sse2(km, qlen, query, tlen, target, m, mat, q, e, w, zdrop, end_bonus, flag, ez);
 	else abort();
 }
@@ -70,11 +71,10 @@ void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
 	extern void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
 				   int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
 		ksw_extd2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
-	else if (simd & SIMD_SSE2)
+	else if (ksw_simd & SIMD_SSE2)
 		ksw_extd2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, e2, w, zdrop, end_bonus, flag, ez);
 	else abort();
 }
@@ -86,11 +86,10 @@ void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
 				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
 	extern void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
 				   int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez);
-	unsigned simd;
-	simd = x86_simd();
-	if (simd & SIMD_SSE4_1)
+	if (ksw_simd < 0) ksw_simd = x86_simd();
+	if (ksw_simd & SIMD_SSE4_1)
 		ksw_exts2_sse41(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
-	else if (simd & SIMD_SSE2)
+	else if (ksw_simd & SIMD_SSE2)
 		ksw_exts2_sse2(km, qlen, query, tlen, target, m, mat, q, e, q2, noncan, zdrop, flag, ez);
 	else abort();
 }

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.13-r852-dirty"
+#define MM_VERSION "2.14-r883"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -60,6 +60,7 @@ static ko_longopt_t long_options[] = {
 	{ "split-prefix",   ko_required_argument, 334 },
 	{ "no-end-flt",     ko_no_argument,       335 },
 	{ "hard-mask-level",ko_no_argument,       336 },
+	{ "cap-sw-mem",     ko_required_argument, 337 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
 	{ "version",        ko_no_argument,       'V' },
@@ -122,7 +123,7 @@ int main(int argc, char *argv[])
 			fprintf(stderr, "[ERROR] missing option argument\n");
 			return 1;
 		} else if (c == '?') {
-			fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i]);
+			fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[o.i - 1]);
 			return 1;
 		}
 	}
@@ -190,6 +191,7 @@ int main(int argc, char *argv[])
 		else if (c == 334) opt.split_prefix = o.arg; // --split-prefix
 		else if (c == 335) opt.flag |= MM_F_NO_END_FLT; // --no-end-flt
 		else if (c == 336) opt.flag |= MM_F_HARD_MLEVEL; // --hard-mask-level
+		else if (c == 337) opt.max_sw_mat = mm_parse_num(o.arg); // --cap-sw-mat
 		else if (c == 314) { // --frag
 			yes_or_no(&opt, MM_F_FRAG_MODE, o.longidx, o.arg, 1);
 		} else if (c == 315) { // --secondary

minimap.h

@@ -139,6 +139,7 @@ typedef struct {
 	int32_t mid_occ;     // ignore seeds with occurrences above this threshold
 	int32_t max_occ;
 	int mini_batch_size; // size of a batch of query bases to process in parallel
+	int64_t max_sw_mat;
 
 	const char *split_prefix;
 } mm_mapopt_t;

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "11 October 2018" "minimap2-2.13 (r850)" "Bioinformatics tools"
+.TH minimap2 1 "5 November 2018" "minimap2-2.14 (r883)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -274,6 +274,10 @@ Only map to the reverse complement strand of the reference sequences.
 .BR --heap-sort = no | yes
 If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
 faster for short reads, but slower for long reads. [no]
+.TP
+.B --no-pairing
+Treat two reads in a pair as independent reads. The mate related fields in SAM
+are still properly populated.
 .SS Alignment options
 .TP 10
 .BI -A \ INT
@@ -369,6 +373,11 @@ It helps to avoid tiny terminal exons. [6]
 .B --no-end-flt
 Don't filter seeds towards the ends of chains before performing base-level
 alignment.
+.TP
+.BI --cap-sw-mem \ NUM
+Skip alignment if the DP matrix size is above
+.IR NUM .
+Set 0 to disable [0].
 .SS Input/output options
 .TP 10
 .B -a
@@ -493,7 +502,7 @@ Up to 10% sequence divergence.
 .B asm20
 Long assembly to reference mapping
 .RB ( -k19
-.B -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200
+.B -w10 -A1 -B4 -O6,26 -E2,1 -s200 -z200
 .BR --min-occ-floor=100 ).
 Up to 20% sequence divergence.
 .TP

misc.c

@@ -116,8 +116,7 @@ long peakrss(void)
 double realtime(void)
 {
 	struct timeval tp;
-	struct timezone tzp;
-	gettimeofday(&tp, &tzp);
+	gettimeofday(&tp, NULL);
 	return tp.tv_sec + tp.tv_usec * 1e-6;
 }
 

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.13-r850';
+var paftools_version = '2.14-r883';
 
 /*****************************
  ***** Library functions *****
@@ -564,10 +564,12 @@ function paf_call(args)
 
 function paf_asmstat(args)
 {
-	var c, min_seg_len = 10000, max_diff = 0.01;
-	while ((c = getopt(args, "l:d:")) != null) {
+	var c, min_seg_len = 10000, max_diff = 0.01, bp_flank_len = 0, bp_gap_len = 0;
+	while ((c = getopt(args, "l:d:b:g:")) != null) {
 		if (c == 'l') min_seg_len = parseInt(getopt.arg);
 		else if (c == 'd') max_diff = parseFloat(getopt.arg);
+		else if (c == 'b') bp_flank_len = parseInt(getopt.arg);
+		else if (c == 'g') bp_gap_len = parseInt(getopt.arg);
 	}
 	if (getopt.ind == args.length) {
 		print("Usage: paftools.js asmstat [options] <ref.fa.fai> <asm1.paf> [...]");
@@ -587,7 +589,7 @@ function paf_asmstat(args)
 	}
 	file.close();
 
-	function process_query(qblocks, qblock_len, bp) {
+	function process_query(qblocks, qblock_len, bp, qi) {
 		qblocks.sort(function(a,b) { return a[0]-b[0]; });
 		var last_k = null, last_blen = null, st = -1, en = -1, qcov = 0;
 		for (var k = 0; k < qblocks.length; ++k) {
@@ -612,6 +614,7 @@ function paf_asmstat(args)
 				var min = blen < last_blen? blen : last_blen;
 				var flank = k == 0? min : blen;
 				bp.push([flank, gap]);
+				qi.bp.push([flank, gap]);
 			}
 			last_k = k, last_blen = blen;
 		}
@@ -664,16 +667,22 @@ function paf_asmstat(args)
 	for (var i = 0; i < n_asm; ++i) {
 		var n_breaks = 0, qcov = 0;
 		var fn = args[getopt.ind + 1 + i];
-		header.push(fn.replace(/.paf(.gz)?$/, ""));
+		var label = fn.replace(/.paf(.gz)?$/, "");
+		header.push(label);
 		var ref_blocks = [], qblock_len = [], qblocks = [], bp = [];
-		var query = {};
+		var query = {}, qinfo = {};
 		var last_qname = null;
 		file = new File(fn);
 		while (file.readline(buf) >= 0) {
 			var m, line = buf.toString();
 			var t = line.split("\t");
 			t[1] = parseInt(t[1]);
-			if (t.length >= 2) query[t[0]] = t[1];
+			if (t.length >= 2) {
+				query[t[0]] = t[1];
+				if (qinfo[t[0]] == null) qinfo[t[0]] = {};
+				qinfo[t[0]].len = t[1];
+				qinfo[t[0]].bp = [];
+			}
 			if (t.length < 9) continue;
 			if (!/\ttp:A:[PI]/.test(line)) continue;
 			if ((m = /\tcg:Z:(\S+)/.exec(line)) == null) continue;
@@ -690,7 +699,7 @@ function paf_asmstat(args)
 			if (t[3] - t[2] < min_seg_len) continue;
 			if (t[0] != last_qname) {
 				if (last_qname != null)
-					qcov += process_query(qblocks, qblock_len, bp);
+					qcov += process_query(qblocks, qblock_len, bp, qinfo[last_qname]);
 				qblocks = [];
 				last_qname = t[0];
 			}
@@ -698,7 +707,7 @@ function paf_asmstat(args)
 			qblocks.push([t[2], t[3], t[4], t[5], t[7], t[8]]);
 		}
 		if (last_qname != null)
-			qcov += process_query(qblocks, qblock_len, bp);
+			qcov += process_query(qblocks, qblock_len, bp, qinfo[last_qname]);
 		file.close();
 
 		// compute NG50
@@ -733,12 +742,157 @@ function paf_asmstat(args)
 		rst[5][i] = n_breaks;
 		rst[6][i] = count_bp(bp, 500, 0);
 		rst[7][i] = count_bp(bp, 500, 10000);
+
+		// nb-plot
+		var qa = [];
+		for (var qn in qinfo)
+			qa.push([qinfo[qn].len, qinfo[qn].bp]);
+		qa = qa.sort(function(a, b) { return b[0] - a[0] });
+		var sum = 0, n_bp = 0, next_quantile = 0.1;
+		for (var j = 0; j < qa.length; ++j) {
+			sum += qa[j][0];
+			for (var k = 0; k < qa[j][1].length; ++k)
+				if (qa[j][1][k][0] >= bp_flank_len && qa[j][1][k][1] >= bp_gap_len)
+					++n_bp;
+			if (sum >= ref_len * next_quantile) {
+				print(label, Math.floor(next_quantile * 100 + .5), qa[j][0], (sum / n_bp).toFixed(0), n_bp);
+				next_quantile += 0.1;
+				if (next_quantile >= 1.0) break;
+			}
+		}
+	}
+	buf.destroy();
+
+	if (bp_flank_len <= 0) {
+		print(header.join("\t"));
+		for (var i = 0; i < labels.length; ++i)
+			print(labels[i], rst[i].join("\t"));
+	}
+}
+
+function paf_asmgene(args)
+{
+	var c, opt = { min_cov:0.99, min_iden:0.99 }, print_err = false;
+	while ((c = getopt(args, "i:c:e")) != null)
+		if (c == 'i') opt.min_iden = parseFloat(getopt.arg);
+		else if (c == 'c') opt.min_cov = parseFloat(getopt.arg);
+		else if (c == 'e') print_err = true;
+
+	var n_fn = args.length - getopt.ind;
+	if (n_fn < 2) {
+		print("Usage: paftools.js asmgene [options] <ref-splice.paf> <asm-splice.paf> [...]");
+		print("Options:");
+		print("  -i FLOAT     min identity [" + opt.min_iden + "]");
+		print("  -c FLOAT     min coverage [" + opt.min_cov + "]");
+		print("  -e           print fragmented/missing genes");
+		exit(1);
 	}
 
-	print(header.join("\t"));
-	for (var i = 0; i < labels.length; ++i)
-		print(labels[i], rst[i].join("\t"));
+	function process_query(opt, a) {
+		var b = [], cnt = [0, 0, 0];
+		for (var j = 0; j < a.length; ++j) {
+			if (a[j][4] < a[j][5] * opt.min_iden)
+				continue;
+			b.push(a[j].slice(0));
+		}
+		if (b.length == 0) return cnt;
+		// count full
+		var n_full = 0;
+		for (var j = 0; j < b.length; ++j)
+			if (b[j][3] - b[j][2] >= b[j][1] * opt.min_cov)
+				++n_full;
+		cnt[0] = n_full;
+		// compute coverage
+		b = b.sort(function(x, y) { return x[2] - y[2] });
+		var l_cov = 0, st = b[0][2], en = b[0][3];
+		for (var j = 1; j < b.length; ++j) {
+			if (b[j][2] <= en)
+				en = b[j][3] > en? b[j][3] : en;
+			else l_cov += en - st;
+		}
+		l_cov += en - st;
+		cnt[1] = l_cov / b[0][1];
+		cnt[2] = b.length;
+		return cnt;
+	}
 
+	var buf = new Bytes();
+	var gene = {}, header = [], refpos = {};
+	for (var i = getopt.ind; i < args.length; ++i) {
+		var fn = args[i];
+		var label = fn.replace(/.paf(.gz)?$/, "");
+		header.push(label);
+		var file = new File(fn), a = [];
+		while (file.readline(buf) >= 0) {
+			var t = buf.toString().split("\t");
+			var ql = parseInt(t[1]), qs = parseInt(t[2]), qe = parseInt(t[3]), mlen = parseInt(t[9]), blen = parseInt(t[10]), mapq = parseInt(t[11]);
+			if (i == getopt.ind) refpos[t[0]] = [t[0], t[1], t[5], t[7], t[8]];
+			if (gene[t[0]] == null) gene[t[0]] = [];
+			if (a.length && t[0] != a[0][0]) {
+				gene[t[0]][i - getopt.ind] = process_query(opt, a);
+				a = [];
+			}
+			a.push([t[0], ql, qs, qe, mlen, blen]);
+		}
+		if (a.length)
+			gene[t[0]][i - getopt.ind] = process_query(opt, a);
+		file.close();
+	}
+
+	// select the longest genes (not optimal, but should be good enough)
+	var gene_list = [], gene_nr = {};
+	for (var g in refpos)
+		gene_list.push(refpos[g]);
+	gene_list = gene_list.sort(function(a, b) { return a[2] < b[2]? -1 : a[2] > b[2]? 1 : a[3] - b[3] });
+	var last = 0;
+	for (var j = 1; j < gene_list.length; ++j) {
+		if (gene_list[j][2] != gene_list[last][2] || gene_list[j][3] >= gene_list[last][4]) {
+			gene_nr[gene_list[last][0]] = 1;
+			last = j;
+		} else if (gene_list[j][1] > gene_list[last][1]) {
+			last = j;
+		}
+	}
+	gene_nr[gene_list[last][0]] = 1;
+
+	// count and print
+	var col1 = ["full_sgl", "full_dup", "frag", "part50+", "part10+", "part10-"];
+	var rst = [];
+	for (var k = 0; k < col1.length; ++k) {
+		rst[k] = [];
+		for (var i = 0; i < n_fn; ++i)
+			rst[k][i] = 0;
+	}
+	for (var g in gene) {
+		if (gene[g][0] == null || gene[g][0][0] != 1) continue;
+		if (gene_nr[g] == null) continue;
+		for (var i = 0; i < n_fn; ++i) {
+			if (gene[g][i] == null) {
+				rst[4][i]++;
+				if (print_err) print('M', header[i], refpos[g].join("\t"));
+			} else if (gene[g][i][0] == 1) rst[0][i]++;
+			else if (gene[g][i][0] > 1) {
+				rst[1][i]++;
+				if (print_err) print('D', header[i], refpos[g].join("\t"));
+			} else if (gene[g][i][1] >= opt.min_cov) {
+				rst[2][i]++;
+				if (print_err) print('F', header[i], refpos[g].join("\t"));
+			} else if (gene[g][i][1] >= 0.5) {
+				rst[3][i]++;
+				if (print_err) print('5', header[i], refpos[g].join("\t"));
+			} else if (gene[g][i][1] >= 0.1) {
+				rst[4][i]++;
+				if (print_err) print('1', header[i], refpos[g].join("\t"));
+			} else {
+				rst[5][i]++;
+				if (print_err) print('0', header[i], refpos[g].join("\t")); // TODO: reduce code duplicates...
+			}
+		}
+	}
+	print('H', 'Metric', header.join("\t"));
+	for (var k = 0; k < rst.length; ++k) {
+		print('X', col1[k], rst[k].join("\t"));
+	}
 	buf.destroy();
 }
 
@@ -2189,6 +2343,7 @@ function main(args)
 		print("");
 		print("  stat       collect basic mapping information in PAF/SAM");
 		print("  asmstat    collect basic assembly information");
+		print("  asmgene    evaluate gene completeness (EXPERIMENTAL)");
 		print("  liftover   simplistic liftOver");
 		print("  call       call variants from asm-to-ref alignment with the cs tag");
 		print("  bedcov     compute the number of bases covered");
@@ -2210,6 +2365,7 @@ function main(args)
 	else if (cmd == 'gff2bed') paf_gff2bed(args);
 	else if (cmd == 'stat') paf_stat(args);
 	else if (cmd == 'asmstat') paf_asmstat(args);
+	else if (cmd == 'asmgene') paf_asmgene(args);
 	else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
 	else if (cmd == 'call') paf_call(args);
 	else if (cmd == 'mapeval') paf_mapeval(args);

options.c

@@ -159,6 +159,11 @@ int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
 			fprintf(stderr, "[ERROR]\033[1;31m --for-only and --rev-only can't be applied at the same time\033[0m\n");
 		return -3;
 	}
+	if (mo->e <= 0 || mo->q <= 0) {
+		if (mm_verbose >= 1)
+			fprintf(stderr, "[ERROR]\033[1;31m -O and -E must be positive\033[0m\n");
+		return -1;
+	}
 	if ((mo->q != mo->q2 || mo->e != mo->e2) && !(mo->e > mo->e2 && mo->q + mo->e < mo->q2 + mo->e2)) {
 		if (mm_verbose >= 1)
 			fprintf(stderr, "[ERROR]\033[1;31m dual gap penalties violating E1>E2 and O1+E1<O2+E2\033[0m\n");

pe.c

@@ -54,7 +54,7 @@ void mm_set_pe_thru(const int *qlens, int *n_regs, mm_reg1_t **regs)
 	if (n_pri[0] == 1 && n_pri[1] == 1) {
 		mm_reg1_t *p = &regs[0][pri[0]];
 		mm_reg1_t *q = &regs[1][pri[1]];
-		if (p->rid == q->rid && p->rev == q->rev && abs(p->rs - q->rs) < 3 && abs(p->re - p->re) < 3
+		if (p->rid == q->rid && p->rev == q->rev && abs(p->rs - q->rs) < 3 && abs(p->re - q->re) < 3
 			&& ((p->qs == 0 && qlens[1] - q->qe == 0) || (q->qs == 0 && qlens[0] - p->qe == 0)))
 		{
 			p->pe_thru = q->pe_thru = 1;

python/cmappy.pxd

@@ -40,6 +40,7 @@ cdef extern from "minimap.h":
 		int32_t mid_occ
 		int32_t max_occ
 		int 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__ = '2.13'
+__version__ = '2.14'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -33,7 +33,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.13',
+	version = '2.14',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),