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r362: bugfix - occasionally wrong TLEN 

Use the 0.7.2 way to compute TLEN
This commit is contained in:
Heng Li 2013-03-12 00:14:36 -04:00
parent aa7cdf4bb3
commit c29b176cb6
2 changed files with 5 additions and 4 deletions
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7
bwamem.c
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@ -657,9 +657,10 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
kputc('\t', str);
kputl(m->pos + 1, str); kputc('\t', str);
if (p->rid == m->rid) {
int64_t p0 = p->pos + (p->is_rev? get_rlen(p->n_cigar, p->cigar) : 0);
int64_t p1 = m->pos + (m->is_rev? get_rlen(m->n_cigar, m->cigar) : 0);
kputw(m->n_cigar && p->n_cigar? p1 - p0 : 0, str); // compute TLEN if both ends mapped; otherwise, set to zero
int64_t p0 = p->pos + (p->is_rev? get_rlen(p->n_cigar, p->cigar) - 1 : 0);
int64_t p1 = m->pos + (m->is_rev? get_rlen(m->n_cigar, m->cigar) - 1 : 0);
if (m->n_cigar == 0 || p->n_cigar == 0) kputc('0', str);
else kputl(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
} else kputc('0', str);
} else kputsn("*\t0\t0", 5, str);
kputc('\t', str);

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.2-r361-beta"
#define PACKAGE_VERSION "0.7.2-r362-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);