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--junc-bed apparently working

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Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
This commit is contained in:
Heng Li
2019-04-28 16:47:12 -04:00
parent f4c844b143
commit e80759c97a
2 changed files with 48 additions and 24 deletions
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index.c
+2 -3
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@@ -689,11 +689,10 @@ int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, uin
}
for (i = left; i < r->n; ++i) {
if (st <= r->a[i].st && en >= r->a[i].en && r->a[i].strand != 0) {
//fprintf(stderr, "[2] %d\t%d\t%c\n", r->a[i].st, r->a[i].en, r->a[i].strand > 0? '+' : r->a[i].strand < 0? '-' : '.');
if (r->a[i].strand > 0) {
s[r->a[i].st] |= 1, s[r->a[i].en - 1] |= 2;
s[r->a[i].st - st] |= 1, s[r->a[i].en - 1 - st] |= 2;
} else {
s[r->a[i].st] |= 2, s[r->a[i].en - 1] |= 1;
s[r->a[i].st - st] |= 8, s[r->a[i].en - 1 - st] |= 4;
}
}
}