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r382: similar treatment in bwa-sw (see r381)

This commit is contained in:
Heng Li 2013-04-19 17:52:06 -04:00
parent 3f8caef33c
commit f6ae0d4d0f
2 changed files with 8 additions and 2 deletions
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8
bwtsw2_pair.c
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@ -46,7 +46,7 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
p75 = isize[(int)(.75 * k + .499)]; p75 = isize[(int)(.75 * k + .499)];
ksprintf(msg, "[%s] infer the insert size distribution from %d high-quality pairs.\n", __func__, k); ksprintf(msg, "[%s] infer the insert size distribution from %d high-quality pairs.\n", __func__, k);
if (k < 8) { if (k < 8) {
ksprintf(msg, "[%s] fail to infer the insert size distribution.\n", __func__); ksprintf(msg, "[%s] fail to infer the insert size distribution: too few good pairs.\n", __func__);
free(isize); free(isize);
r.failed = 1; r.failed = 1;
return r; return r;
@ -55,6 +55,12 @@ bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
r.low = tmp > max_len? tmp : max_len; r.low = tmp > max_len? tmp : max_len;
if (r.low < 1) r.low = 1; if (r.low < 1) r.low = 1;
r.high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499); r.high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
if (r.low > r.high) {
ksprintf(msg, "[%s] fail to infer the insert size distribution: upper bound is smaller than max read length.\n", __func__);
free(isize);
r.failed = 1;
return r;
}
ksprintf(msg, "[%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75); ksprintf(msg, "[%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
ksprintf(msg, "[%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r.low, r.high); ksprintf(msg, "[%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r.low, r.high);
for (i = x = 0, r.avg = 0; i < k; ++i) for (i = x = 0, r.avg = 0; i < k; ++i)

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r381-beta" #define PACKAGE_VERSION "0.7.3-r382-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);