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r216: a bit cleanup; identical output to r215

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Heng Li
2017-07-28 11:54:18 -04:00
parent fc965805f7
commit 254280b8af
5 changed files with 14 additions and 7 deletions
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align.c
+4 -4
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@@ -179,7 +179,7 @@ static void mm_filter_bad_seeds(void *km, int as1, int cnt1, mm128_t *a, int min
if (k == n || k >= max_en) {
if (max_en > 0)
for (i = K[max_st]; i < K[max_en]; ++i)
a[as1 + i].y |= 1ULL << 41;
a[as1 + i].y |= MM_SEED_IGNORE;
max = 0, max_st = max_en = -1;
if (k == n) break;
}
@@ -299,12 +299,12 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < cnt1; ++i) { // gap filling
if (a[as1+i].y>>41&1) continue;
if (a[as1+i].y & MM_SEED_IGNORE) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y>>40&1) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
int bw1 = bw;
if (a[as1+i].y>>40&1)
if (a[as1+i].y & MM_SEED_LONG_JOIN)
bw1 = qe - qs > re - rs? qe - qs : re - rs;
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);