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r450: differentiate exact repeats via mapq

This commit is contained in:
Heng Li 2017-09-27 23:51:05 -04:00
parent a13691d00d
commit 935a6e6064
3 changed files with 9 additions and 1 deletions
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1
hit.c
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@ -383,6 +383,7 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc, int match_sc, in
mapq -= (int)(4.343f * logf(r->n_sub + 1) + .499f);
mapq = mapq > 0? mapq : 0;
r->mapq = mapq < 60? mapq : 60;
if (r->p && r->p->dp_max > r->p->dp_max2 && r->mapq == 0) r->mapq = 1;
} else r->mapq = 0;
}
}

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r448-dirty"
#define MM_VERSION "2.2-r450-dirty"
#ifdef __linux__
#include <sys/resource.h>

7
pe.c
View File

@ -135,6 +135,13 @@ void mm_pair(void *km, int max_gap_ref, int pe_bonus, int sub_diff, int match_sc
}
if (r[0]->mapq < mapq_pe) r[0]->mapq = (r[0]->mapq + mapq_pe) / 2;
if (r[1]->mapq < mapq_pe) r[1]->mapq = (r[1]->mapq + mapq_pe) / 2;
if (sc.n == 1) {
if (r[0]->mapq < 2) r[0]->mapq = 2;
if (r[1]->mapq < 2) r[1]->mapq = 2;
} else if (max > sc.a[sc.n - 2]) {
if (r[0]->mapq < 1) r[0]->mapq = 1;
if (r[1]->mapq < 1) r[1]->mapq = 1;
}
}
kfree(km, a);