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refactored --junc-bed

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This commit is contained in:
Heng Li
2025-04-03 21:02:50 -04:00
parent cbe8d61ca4
commit d9d3c0cc3f
2 changed files with 17 additions and 5 deletions
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17
index.c
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@@ -748,16 +748,16 @@ mm_idx_intv_t *mm_idx_read_bed(const mm_idx_t *mi, const char *fn, int read_junc
return I;
}
int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
static mm_idx_intv_t *mm_idx_bed_read_core(const mm_idx_t *mi, const char *fn, int read_junc)
{
long n = 0, n0 = 0;
int32_t i;
if (mi->h == 0) mm_idx_index_name(mi);
mi->I = mm_idx_read_bed(mi, fn, read_junc);
if (mi->I == 0) return -1;
mm_idx_intv_t *I;
I = mm_idx_read_bed(mi, fn, read_junc);
if (I == 0) return 0;
for (i = 0; i < mi->n_seq; ++i) {
int32_t j, j0, k;
mm_idx_intv_t *intv = &mi->I[i];
mm_idx_intv_t *intv = &I[i];
n0 += intv->n;
radix_sort_bed(intv->a, intv->a + intv->n);
for (j = 1, j0 = 0; j <= intv->n; ++j) {
@@ -777,6 +777,13 @@ int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
}
if (mm_verbose >= 3)
fprintf(stderr, "[%s] read %ld introns, %ld of which are non-redundant\n", __func__, n0, n);
return I;
}
int mm_idx_bed_read(mm_idx_t *mi, const char *fn, int read_junc)
{
if (mi->h == 0) mm_idx_index_name(mi);
mi->I = mm_idx_bed_read_core(mi, fn, read_junc);
return 0;
}

5
mmpriv.h
View File

@@ -52,6 +52,11 @@ typedef struct {
mm128_t *a;
} mm_seg_t;
typedef struct {
int32_t off, off2;
int32_t is_rev;
} mm_jjump1_t;
double cputime(void);
double realtime(void);
long peakrss(void);