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support ALT mapping

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This commit is contained in:
Heng Li
2020-01-21 09:17:50 -05:00
parent d2e14705e7
commit eb3ed6993d
10 changed files with 87 additions and 22 deletions
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index.c
+27
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@@ -316,6 +316,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
} else seq->name = 0;
seq->len = s->seq[i].l_seq;
seq->offset = p->sum_len;
seq->is_alt = 0;
// copy the sequence
if (!(p->mi->flag & MM_I_NO_SEQ)) {
for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
@@ -414,6 +415,7 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
}
p->offset = sum_len;
p->len = strlen(s);
p->is_alt = 0;
for (j = 0; j < p->len; ++j) {
int c = seq_nt4_table[(uint8_t)s[j]];
uint64_t o = sum_len + j;
@@ -500,6 +502,7 @@ mm_idx_t *mm_idx_load(FILE *fp)
}
fread(&s->len, 4, 1, fp);
s->offset = sum_len;
s->is_alt = 0;
sum_len += s->len;
}
for (i = 0; i < 1<<mi->b; ++i) {
@@ -607,6 +610,30 @@ int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases
#include "kseq.h"
KSTREAM_DECLARE(gzFile, gzread)
int mm_idx_alt_read(mm_idx_t *mi, const char *fn)
{
int n_alt = 0;
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
fp = fn && strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return -1;
ks = ks_init(fp);
if (mi->h == 0) mm_idx_index_name(mi);
while (ks_getuntil(ks, KS_SEP_LINE, &str, 0) >= 0) {
char *p;
int id;
for (p = str.s; *p && !isspace(*p); ++p) { }
*p = 0;
id = mm_idx_name2id(mi, str.s);
if (id >= 0) mi->seq[id].is_alt = 1, ++n_alt;
}
mi->n_alt = n_alt;
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s] found %d ALT contigs\n", __func__, n_alt);
return n_alt;
}
#define sort_key_bed(a) ((a).st)
KRADIX_SORT_INIT(bed, mm_idx_intv1_t, sort_key_bed, 4)