fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-01 22:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r934: --junc-bed to read BED12

Browse Source
This commit is contained in:
Heng Li
2019-04-28 20:12:28 -04:00
parent f64e426a5a
commit 49c6d83a8e
4 changed files with 45 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files
index.c
+37 -11
View File
@@ -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;
int32_t i, id = -1;
char *p, *q, *bl, *bs;
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) {
r->m = r->m? r->m + (r->m>>1) : 16;
r->a = (mm_idx_intv1_t*)realloc(r->a, sizeof(*r->a) * r->m);
if (i >= 11 && read_junc) { // BED12
int32_t st, sz, en;
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);