r934: --junc-bed to read BED12

index.c

@@ -610,7 +610,7 @@ KSTREAM_DECLARE(gzFile, gzread)
 #define sort_key_bed(a) ((a).st)
 KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
 
-mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
+mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn, int read_junc)
 {
 	gzFile fp;
 	kstream_t *ks;
@@ -624,8 +624,8 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
 	while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
 		mm_idx_intv_t *r;
 		mm_idx_intv1_t t = {-1,-1,-1,-1,0};
-		char *p, *q;
+		char *p, *q, *bl, *bs;
-		int32_t i, id = -1;
+		int32_t i, id = -1, n_blk = 0;
 		for (p = q = str.s, i = 0;; ++p) {
 			if (*p == 0 || isspace(*p)) {
 				int32_t c = *p;
@@ -639,23 +639,49 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
 				} else if (i == 2) { // end
 					t.en = atol(q);
 					if (t.en < 0) break;
-				} else if (i == 3) { // name; do nothing
 				} else if (i == 4) { // BED score
 					t.score = atol(q);
 				} else if (i == 5) { // strand
 					t.strand = *q == '+'? 1 : *q == '-'? -1 : 0;
-				} else break;
+				} else if (i == 9) {
+					if (!isdigit(*q)) break;
+					n_blk = atol(q);
+				} else if (i == 10) {
+					bl = q;
+				} else if (i == 11) {
+					bs = q;
+					break;
+				}
 				if (c == 0) break;
 				++i, q = p + 1;
 			}
 		}
 		if (id < 0 || t.st < 0 || t.st >= t.en) continue;
 		r = &I[id];
-		if (r->n == r->m) {
+		if (i >= 11 && read_junc) { // BED12
-			r->m = r->m? r->m + (r->m>>1) : 16;
+			int32_t st, sz, en;
-			r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+			st = strtol(bs, &bs, 10); ++bs;
+			sz = strtol(bl, &bl, 10); ++bl;
+			en = t.st + st + sz;
+			for (i = 1; i < n_blk; ++i) {
+				mm_idx_intv1_t s = t;
+				if (r->n == r->m) {
+					r->m = r->m? r->m + (r->m>>1) : 16;
+					r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+				}
+				st = strtol(bs, &bs, 10); ++bs;
+				sz = strtol(bl, &bl, 10); ++bl;
+				s.st = en, s.en = t.st + st;
+				en = t.st + st + sz;
+				if (s.en > s.st) r->a[r->n++] = s;
+			}
+		} else {
+			if (r->n == r->m) {
+				r->m = r->m? r->m + (r->m>>1) : 16;
+				r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
+			}
+			r->a[r->n++] = t;
 		}
-		r->a[r->n++] = t;
 	}
 	free(str.s);
 	ks_destroy(ks);
@@ -663,11 +689,11 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
 	return I;
 }
 
-int mm_idx_bed_read(mm_idx_t *mi, const char *fn)
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
 {
 	int32_t i;
 	if (mi->h == 0) mm_idx_index_name(mi);
-	mi->I = mm_idx_read_bed(mi, fn);
+	mi->I = mm_idx_read_bed(mi, fn, read_junc);
 	if (mi->I == 0) return -1;
 	for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals
 		radix_sort_bed(mi->I[i].a, mi->I[i].a + mi->I[i].n);

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.16-r933-dirty"
+#define MM_VERSION "2.16-r934-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -366,7 +366,7 @@ int main(int argc, char *argv[])
 					__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
 		if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
 		if (mm_verbose >= 3) mm_idx_stat(mi);
-		if (junc_bed) mm_idx_bed_read(mi, junc_bed);
+		if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
 		if (!(opt.flag & MM_F_FRAG_MODE)) {
 			for (i = o.ind + 1; i < argc; ++i)
 				mm_map_file(mi, argv[i], &opt, n_threads);

minimap.h

@@ -367,7 +367,7 @@ int mm_idx_index_name(mm_idx_t *mi);
 int mm_idx_name2id(const mm_idx_t *mi, const char *name);
 int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
 
-int mm_idx_bed_read(mm_idx_t *mi, const char *fn);
+int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
 int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);
 
 // deprecated APIs for backward compatibility

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r933)" "Bioinformatics tools"
+.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r934)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -365,10 +365,10 @@ on SIRV data, please add
 to the command line.
 .TP
 .BR --junc-bed \ FILE
-BED file consisting of annotated introns and their strands. With this option,
+Gene annotations in the BED12 format (aka 12-column BED), or intron positions
-minimap2 prefers splicing in annotations.
+in 5-column BED. With this option, minimap2 prefers splicing in annotations.
-.I FILE
+BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'
-can be generated with `paftools.js gff2bed -j ann.gtf' [].
+[].
 .TP
 .BR --junc-bonus \ INT
 Score bonus for a splice donor or acceptor found in annotation (effective with