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r926: prepare to move -g to bwa-postalt.js

This commit is contained in:
Heng Li 2014-10-19 20:43:53 -04:00
parent 6e13694721
commit 3370ae9e35
3 changed files with 9 additions and 6 deletions
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5
bwa-postalt.js
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@ -490,13 +490,16 @@ function bwa_postalt(args)
while ((m = re_cigar.exec(t[5])) != null) while ((m = re_cigar.exec(t[5])) != null)
if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N') if (m[2] == 'M' || m[2] == 'D' || m[2] == 'N')
end += parseInt(m[1]); end += parseInt(m[1]);
if (start < l[3] && l[2] < end) {
var om = -1; var om = -1;
for (var j = 11; j < s.length; ++j) for (var j = 11; j < s.length; ++j)
if ((m = /^om:i:(\d+)/.exec(s[j])) != null) if ((m = /^om:i:(\d+)/.exec(s[j])) != null)
om = parseInt(m[1]); om = parseInt(m[1]);
if (start < l[3] && l[2] < end) {
if (om > 0) s[4] = om; if (om > 0) s[4] = om;
s[4] = s[4] < mapQ? s[4] : mapQ; s[4] = s[4] < mapQ? s[4] : mapQ;
} else {
if (om < 0) s.push("om:i:" + s[4]);
s[4] = 0;
} }
} }
} }

2
bwamem.c
View File

@ -79,7 +79,7 @@ mem_opt_t *mem_opt_init()
o->min_chain_weight = 0; o->min_chain_weight = 0;
o->max_chain_extend = 1<<30; o->max_chain_extend = 1<<30;
o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len); o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len);
o->min_pa_ratio = 0.8; o->min_pa_ratio = 0;
bwa_fill_scmat(o->a, o->b, o->mat); bwa_fill_scmat(o->a, o->b, o->mat);
return o; return o;
} }

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r915-dirty" #define PACKAGE_VERSION "0.7.10-r926-dirty"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);