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r1268: avoid extra small introns

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Heng Li
2025-04-07 23:32:56 -04:00
parent 9c3c4b1ce8
commit bd03d975fc
2 changed files with 3 additions and 1 deletions
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jump.c
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@@ -66,6 +66,7 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
assert(ai->off >= r->rs - extt && ai->off <= r->rs + ext);
if (ts_strand * ai->strand < 0) continue; // wrong strand
if (ai->off2 >= ai->off) continue; // wrong direction
if (ai->off - ai->off2 < 6) continue; // intron too small
if (ai->off2 < clip + ext) continue; // not long enough
if (tseq == 0) {
tseq = Kcalloc(km, uint8_t, (clip + ext) * 2); // tseq and qseq are allocated together
@@ -130,6 +131,7 @@ static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t
assert(ai->off >= r->re - ext && ai->off <= r->re + extt);
if (ts_strand * ai->strand < 0) continue; // wrong strand
if (ai->off2 <= ai->off) continue; // wrong direction
if (ai->off2 - ai->off < 6) continue; // intron too small
if (ai->off2 + clip + ext > mi->seq[r->rid].len) continue; // not long enough
if (tseq == 0) {
tseq = Kcalloc(km, uint8_t, (clip + ext) * 2); // tseq and qseq are allocated together