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r942: ignore ALT hits when counting n_sub for ... 

non-ALT hits. Counting leads to underestimated mapQ.
This commit is contained in:
Heng Li 2014-10-22 10:24:16 -04:00
parent 60b728487a
commit 4177d6c2c7
2 changed files with 3 additions and 2 deletions
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3
bwamem.c
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@ -514,7 +514,8 @@ static void mem_mark_primary_se_core(const mem_opt_t *opt, int n, mem_alnreg_t *
int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb; int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
if (a[j].sub == 0) a[j].sub = a[i].score; if (a[j].sub == 0) a[j].sub = a[i].score;
if (a[j].score - a[i].score <= tmp) ++a[j].sub_n; if (a[j].score - a[i].score <= tmp && (a[j].is_alt || !a[i].is_alt))
++a[j].sub_n;
break; break;
} }
} }

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-r941-dirty" #define PACKAGE_VERSION "0.7.10-r942-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);