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r219: fixed a bug caused by skipping tandem seeds

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This commit is contained in:
Heng Li
2017-07-28 14:06:56 -04:00
parent c672690564
commit ebbe9c1eb8
3 changed files with 3 additions and 3 deletions
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2
align.c
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@@ -298,7 +298,7 @@ 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 & (MM_SEED_IGNORE|MM_SEED_TANDEM)) continue;
if ((a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) && i != cnt1 - 1) continue;
mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || (qe - qs >= opt->min_ksw_len && re - rs >= opt->min_ksw_len)) {

2
main.c
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@@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r218-dirty"
#define MM_VERSION "2.0-r219-dirty"
void liftrlimit()
{

2
misc/mapstat.js
View File

@@ -144,7 +144,7 @@ while (file.readline(buf) >= 0) {
}
if (n_cigar > 65535) ++n_cigar_64k;
if (ql + sclip != aqlen)
warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno);
warn("WARNING: aligned query length is inconsistent with CIGAR at line " + lineno + " (" + (ql+sclip) + " != " + aqlen + ")");
if (atlen != null && atlen != tl)
warn("WARNING: aligned reference length is inconsistent with CIGAR at line " + lineno);
if (is_sam) {