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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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index.c
+12 -5
View File
@@ -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; 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; long n = 0, n0 = 0;
int32_t i; int32_t i;
if (mi->h == 0) mm_idx_index_name(mi); mm_idx_intv_t *I;
mi->I = mm_idx_read_bed(mi, fn, read_junc); I = mm_idx_read_bed(mi, fn, read_junc);
if (mi->I == 0) return -1; if (I == 0) return 0;
for (i = 0; i < mi->n_seq; ++i) { for (i = 0; i < mi->n_seq; ++i) {
int32_t j, j0, k; int32_t j, j0, k;
mm_idx_intv_t *intv = &mi->I[i]; mm_idx_intv_t *intv = &I[i];
n0 += intv->n; n0 += intv->n;
radix_sort_bed(intv->a, intv->a + intv->n); radix_sort_bed(intv->a, intv->a + intv->n);
for (j = 1, j0 = 0; j <= intv->n; ++j) { 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) if (mm_verbose >= 3)
fprintf(stderr, "[%s] read %ld introns, %ld of which are non-redundant\n", __func__, n0, n); 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; return 0;
} }
mmpriv.h
+5
View File
@@ -52,6 +52,11 @@ typedef struct {
mm128_t *a; mm128_t *a;
} mm_seg_t; } mm_seg_t;
typedef struct {
int32_t off, off2;
int32_t is_rev;
} mm_jjump1_t;
double cputime(void); double cputime(void);
double realtime(void); double realtime(void);
long peakrss(void); long peakrss(void);