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incorrect mate pos in BWA-SW SE mode

This commit is contained in:
Heng Li 2011-11-23 23:18:51 -05:00
parent dec584d50b
commit 107a9870ef
1 changed files with 2 additions and 1 deletions
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3
bwtsw2_aux.c
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@ -496,7 +496,8 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
for (k = 0; k < q->n_cigar; ++k)
ksprintf(&str, "%d%c", q->cigar[k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[q->cigar[k]&0xf]);
} else ksprintf(&str, "\t0\t*");
ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
if (!is_pe) kputs("\t*\t0\t0\t", &str);
else ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
// get the sequence begin and end
beg = 0; end = ks->l;
if (opt->hard_clip) {