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r448: fixed a bug when computing PE quality

This commit is contained in:
Heng Li 2017-09-27 21:54:07 -04:00
parent 9541052564
commit 8301222174
2 changed files with 4 additions and 3 deletions
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2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r446-dirty"
#define MM_VERSION "2.2-r448-dirty"
#ifdef __linux__
#include <sys/resource.h>

5
pe.c
View File

@ -108,7 +108,8 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
last[a[i].rev] = i;
}
}
radix_sort_64(sc.a, sc.a + sc.n);
if (sc.n > 1)
radix_sort_64(sc.a, sc.a + sc.n);
if (sc.n > 0 && max > 0) { // found at least one pair
int n_sub = 0, mapq_pe;
@ -129,7 +130,7 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
++n_sub;
if (sc.n > 1) {
int mapq_pe_alt;
mapq_pe_alt = (int)(6.02f * (max - sc.a[1]) / match_sc - 4.343f * logf(n_sub)); // n_sub > 0 because it counts the optimal, too
mapq_pe_alt = (int)(6.02f * (max - sc.a[sc.n - 2]) / match_sc - 4.343f * logf(n_sub)); // n_sub > 0 because it counts the optimal, too
mapq_pe = mapq_pe < mapq_pe_alt? mapq_pe : mapq_pe_alt;
}
if (r[0]->mapq < mapq_pe) r[0]->mapq = (r[0]->mapq + mapq_pe) / 2;