r934: --junc-bed to read BED12
This commit is contained in:
Heng Li
parent
f64e426a5a
commit
49c6d83a8e
48
index.c
48
index.c
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@ -610,7 +610,7 @@ KSTREAM_DECLARE(gzFile, gzread)
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#define sort_key_bed(a) ((a).st)
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KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)
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mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
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mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn, int read_junc)
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{
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gzFile fp;
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kstream_t *ks;
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@ -624,8 +624,8 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
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while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
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mm_idx_intv_t *r;
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mm_idx_intv1_t t = {-1,-1,-1,-1,0};
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char *p, *q;
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int32_t i, id = -1;
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char *p, *q, *bl, *bs;
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int32_t i, id = -1, n_blk = 0;
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for (p = q = str.s, i = 0;; ++p) {
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if (*p == 0 || isspace(*p)) {
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int32_t c = *p;
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@ -639,23 +639,49 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
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} else if (i == 2) { // end
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t.en = atol(q);
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if (t.en < 0) break;
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} else if (i == 3) { // name; do nothing
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} else if (i == 4) { // BED score
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t.score = atol(q);
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} else if (i == 5) { // strand
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t.strand = *q == '+'? 1 : *q == '-'? -1 : 0;
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} else break;
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} else if (i == 9) {
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if (!isdigit(*q)) break;
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n_blk = atol(q);
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} else if (i == 10) {
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bl = q;
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} else if (i == 11) {
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bs = q;
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break;
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}
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if (c == 0) break;
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++i, q = p + 1;
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}
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}
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if (id < 0 || t.st < 0 || t.st >= t.en) continue;
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r = &I[id];
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if (r->n == r->m) {
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r->m = r->m? r->m + (r->m>>1) : 16;
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r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
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if (i >= 11 && read_junc) { // BED12
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int32_t st, sz, en;
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st = strtol(bs, &bs, 10); ++bs;
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sz = strtol(bl, &bl, 10); ++bl;
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en = t.st + st + sz;
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for (i = 1; i < n_blk; ++i) {
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mm_idx_intv1_t s = t;
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if (r->n == r->m) {
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r->m = r->m? r->m + (r->m>>1) : 16;
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r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
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}
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st = strtol(bs, &bs, 10); ++bs;
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sz = strtol(bl, &bl, 10); ++bl;
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s.st = en, s.en = t.st + st;
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en = t.st + st + sz;
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if (s.en > s.st) r->a[r->n++] = s;
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}
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} else {
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if (r->n == r->m) {
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r->m = r->m? r->m + (r->m>>1) : 16;
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r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
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}
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r->a[r->n++] = t;
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}
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r->a[r->n++] = t;
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}
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free(str.s);
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ks_destroy(ks);
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@ -663,11 +689,11 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn)
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return I;
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}
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int mm_idx_bed_read(mm_idx_t *mi, const char *fn)
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int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
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{
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int32_t i;
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if (mi->h == 0) mm_idx_index_name(mi);
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mi->I = mm_idx_read_bed(mi, fn);
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mi->I = mm_idx_read_bed(mi, fn, read_junc);
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if (mi->I == 0) return -1;
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for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals
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radix_sort_bed(mi->I[i].a, mi->I[i].a + mi->I[i].n);
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4
main.c
4
main.c
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@ -6,7 +6,7 @@
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#include "mmpriv.h"
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#include "ketopt.h"
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#define MM_VERSION "2.16-r933-dirty"
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#define MM_VERSION "2.16-r934-dirty"
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#ifdef __linux__
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#include <sys/resource.h>
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@ -366,7 +366,7 @@ int main(int argc, char *argv[])
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
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if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
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if (mm_verbose >= 3) mm_idx_stat(mi);
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if (junc_bed) mm_idx_bed_read(mi, junc_bed);
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if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
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if (!(opt.flag & MM_F_FRAG_MODE)) {
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for (i = o.ind + 1; i < argc; ++i)
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mm_map_file(mi, argv[i], &opt, n_threads);
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@ -367,7 +367,7 @@ int mm_idx_index_name(mm_idx_t *mi);
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int mm_idx_name2id(const mm_idx_t *mi, const char *name);
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int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
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int mm_idx_bed_read(mm_idx_t *mi, const char *fn);
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int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc);
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int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s);
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// deprecated APIs for backward compatibility
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10
minimap2.1
10
minimap2.1
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@ -1,4 +1,4 @@
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.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r933)" "Bioinformatics tools"
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.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r934)" "Bioinformatics tools"
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.SH NAME
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.PP
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minimap2 - mapping and alignment between collections of DNA sequences
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@ -365,10 +365,10 @@ on SIRV data, please add
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to the command line.
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.TP
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.BR --junc-bed \ FILE
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BED file consisting of annotated introns and their strands. With this option,
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minimap2 prefers splicing in annotations.
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.I FILE
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can be generated with `paftools.js gff2bed -j ann.gtf' [].
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Gene annotations in the BED12 format (aka 12-column BED), or intron positions
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in 5-column BED. With this option, minimap2 prefers splicing in annotations.
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BED12 file can be converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'
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[].
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.TP
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.BR --junc-bonus \ INT
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Score bonus for a splice donor or acceptor found in annotation (effective with
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