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r826: improved alt mapping for PE

This commit is contained in:
Heng Li 2014-09-15 12:13:04 -04:00
parent aee53f1334
commit bd85af08ab
2 changed files with 4 additions and 4 deletions
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6
bwamem_pair.c
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@ -276,9 +276,9 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
char **XA[2]; char **XA[2];
// check if an end has multiple hits even after mate-SW // check if an end has multiple hits even after mate-SW
for (i = 0; i < 2; ++i) { for (i = 0; i < 2; ++i) {
for (j = 1; j < a[i].n; ++j) for (j = 1; j < n_pri[i]; ++j)
if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break; if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break;
is_multi[i] = j < a[i].n? 1 : 0; is_multi[i] = j < n_pri[i]? 1 : 0;
} }
if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score
// compute mapQ for the best SE hit // compute mapQ for the best SE hit
@ -316,7 +316,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
int k = a[i].a[z[i]].secondary; int k = a[i].a[z[i]].secondary;
if (k >= 0) { // switch secondary and primary if (k >= 0) { // switch secondary and primary
assert(a[i].a[k].secondary < 0); assert(a[i].a[k].secondary < 0);
for (j = 0; j < a[i].n; ++j) for (j = 0; j < n_pri[i]; ++j)
if (a[i].a[j].secondary == k || j == k) if (a[i].a[j].secondary == k || j == k)
a[i].a[j].secondary = z[i]; a[i].a[j].secondary = z[i];
a[i].a[z[i]].secondary = -1; a[i].a[z[i]].secondary = -1;

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r824-dirty" #define PACKAGE_VERSION "0.7.10-r826-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);