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r361: flag proper pair even if multi-primary 

Up to here, all the features in my checklist have been implemented.
This commit is contained in:
Heng Li 2013-03-12 00:00:04 -04:00
parent dab5b17c1a
commit aa7cdf4bb3
2 changed files with 7 additions and 1 deletions
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6
bwamem_pair.c
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@ -305,6 +305,12 @@ no_pairing:
h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]); h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0); else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
} }
if (h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
int64_t dist;
int d;
d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
if (!pes[d].failed && dist >= pes[d].low && dist <= pes[d].high) extra_flag |= 2;
}
mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]); mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]); mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
free(h[0].cigar); free(h[1].cigar); free(h[0].cigar); free(h[1].cigar);

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.2-r360-beta" #define PACKAGE_VERSION "0.7.2-r361-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);