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r464: fixed a bug in pairing, due to randomization

This commit is contained in:
Heng Li 2017-10-04 13:37:40 -04:00
parent 2581c44a21
commit 19c39e704f
2 changed files with 4 additions and 4 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-r463-dirty"
#define MM_VERSION "2.2-r464-dirty"
#ifdef __linux__
#include <sys/resource.h>

6
pe.c
View File

@ -99,7 +99,7 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
q = a[j].r;
if (r->rid != q->rid || r->rs - q->re > max_gap_ref) break;
if (r->p->dp_max + q->p->dp_max < dp_thres) continue;
score = (int64_t)(r->p->dp_max + q->p->dp_max) | (r->hash + q->hash);
score = (int64_t)(r->p->dp_max + q->p->dp_max) << 32 | (r->hash + q->hash);
if (score > max)
max = score, max_idx[a[j].s] = j, max_idx[a[i].s] = i;
kv_push(uint64_t, km, sc, score);
@ -126,11 +126,11 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
}
mapq_pe = r[0]->mapq > r[1]->mapq? r[0]->mapq : r[1]->mapq;
for (i = 0; i < sc.n; ++i)
if (sc.a[i] + sub_diff >= max)
if ((sc.a[i]>>32) + sub_diff >= max>>32)
++n_sub;
if (sc.n > 1) {
int mapq_pe_alt;
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_alt = (int)(6.02f * ((max>>32) - (sc.a[sc.n - 2]>>32)) / 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;