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implemented in exts; testing is the next

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Heng Li
2019-04-28 16:47:12 -04:00
parent cdc730d573
commit be171aa2dc
8 changed files with 37 additions and 20 deletions
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index.c
+2 -2
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@@ -668,7 +668,7 @@ int mm_idx_bed_read(mm_idx_t *mi, const char *fn)
return mi->I? 0 : -1;
}
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, int32_t strand, int8_t *s)
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uint8_t *s)
{
int32_t i, left, right;
mm_idx_intv_t *r;
@@ -682,7 +682,7 @@ int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, int
else left = mid + 1;
}
for (i = left; i < r->n; ++i) {
if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0 && strand * r->a[i].strand >= 0) {
if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
if (r->a[i].strand > 0) {
s[r->a[i].st] |= 1, s[r->a[i].en - 1] |= 2;
} else {