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mappy to support BED

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This commit is contained in:
Heng Li
2018-09-17 14:54:44 -04:00
parent a3e223f17b
commit b4b70db126
6 changed files with 63 additions and 10 deletions
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index.c
+5 -5
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@@ -611,7 +611,7 @@ KSTREAM_DECLARE(gzFile, gzread)
#define sort_key_bed(a) ((a).x)
KRADIX_SORT_INIT(bed, mm_idx_bed_t, sort_key_bed, 8)
mm_idx_bed_t *mm_idx_read_bed_list(const mm_idx_t *mi, const char *fn, uint32_t *n_)
mm_idx_bed_t *mm_idx_bed_read_list(const mm_idx_t *mi, const char *fn, uint32_t *n_)
{
gzFile fp;
kstream_t *ks;
@@ -656,20 +656,20 @@ mm_idx_bed_t *mm_idx_read_bed_list(const mm_idx_t *mi, const char *fn, uint32_t
return r;
}
int mm_idx_attach_bed(mm_idx_t *mi, uint32_t n, mm_idx_bed_t *r) // TODO: check errors
int mm_idx_bed_attach(mm_idx_t *mi, uint32_t n, mm_idx_bed_t *r) // TODO: check errors
{
radix_sort_bed(r, r + n);
mi->R = r, mi->n_R = n;
return 0;
}
int mm_idx_read_bed(mm_idx_t *mi, const char *fn)
int mm_idx_bed_read(mm_idx_t *mi, const char *fn)
{
mm_idx_bed_t *r;
uint32_t n;
if (mi->h == 0) mm_idx_index_name(mi);
r = mm_idx_read_bed_list(mi, fn, &n);
return mm_idx_attach_bed(mi, n, r);
r = mm_idx_bed_read_list(mi, fn, &n);
return mm_idx_bed_attach(mi, n, r);
}
int mm_idx_bed_query(const mm_idx_t *mi, uint64_t x)