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Update bwape.c to allow equal reads in pair to be mapped as mapped in proper pair #259

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Update bwape.c to allow equal reads in pair to be mapped as mapped in proper pair #259

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2 changes: 1 addition & 1 deletion bwape.c
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ static int pairing(bwa_seq_t *p[2], pe_data_t *d, const pe_opt_t *opt, int s_mm,
// here v>=u. When ii is set, we check insert size with ii; otherwise with opt->max_isize
#define __pairing_aux(u,v) do { \
bwtint_t l = (v).x + p[(v).y&1]->len - ((u).x); \
if ((u).x != (uint64_t)-1 && (v).x > (u).x && l >= max_len \
if ((u).x != (uint64_t)-1 && (v).x >= (u).x && l >= max_len \
&& ((ii->high && l <= ii->high_bayesian) || (ii->high == 0 && l <= opt->max_isize))) \
{ \
uint64_t s = d->aln[(v).y&1].a[(v).y>>2].score + d->aln[(u).y&1].a[(u).y>>2].score; \
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