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reduce mapQ when a read is moved

This commit is contained in:
Heng Li 2013-02-22 12:54:42 -05:00
parent 6a16edc15e
commit 38fc5c8822
1 changed files with 4 additions and 3 deletions
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7
bwamem_pair.c
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@ -268,9 +268,10 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
q_se[1] = q_se[1] > q_pe? q_se[1] : q_pe; q_se[1] = q_se[1] > q_pe? q_se[1] : q_pe;
extra_flag |= 2; extra_flag |= 2;
} else { } else {
if (o > a[0].a[0].score + a[1].a[0].score - opt->pen_unpaired) { // then move the pair int un = a[0].a[0].score + a[1].a[0].score - opt->pen_unpaired;
int tmp[2]; if (o > un) { // then move the pair
q_pe = q_pe > 7? q_pe - 7 : 0; int tmp[2], q_un = (o - un) * 6;
q_pe = q_pe < q_un? q_pe : q_un;
tmp[0] = q_se[0]; tmp[1] = q_se[1]; tmp[0] = q_se[0]; tmp[1] = q_se[1];
q_se[0] = z[0] == 0? q_se[0] : tmp[1] < q_pe? tmp[1] : q_pe; q_se[0] = z[0] == 0? q_se[0] : tmp[1] < q_pe? tmp[1] : q_pe;
q_se[1] = z[1] == 0? q_se[1] : tmp[0] < q_pe? tmp[0] : q_pe; q_se[1] = z[1] == 0? q_se[1] : tmp[0] < q_pe? tmp[0] : q_pe;