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minor changes

This commit is contained in:
Heng Li 2013-02-21 10:39:17 -05:00
parent 41624fb347
commit a9cae8c9af
1 changed files with 5 additions and 2 deletions
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7
bwamem_pair.c
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@ -268,13 +268,16 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
// the following assumes no split hits
if (z[0] == 0 && z[1] == 0) { // the best hit
q_pe = q_pe > q_se[0] + q_se[1]? q_pe : q_se[0] + q_se[1];
if (q_pe > 60) q_pe = 60;
q_se[0] = is_tandem[0]? q_se[0] : q_pe;
q_se[1] = is_tandem[1]? q_se[1] : q_pe;
extra_flag |= 2;
} else {
if (o > un) { // then move the pair
q_se[0] = z[0] == 0? q_se[0] : 0;
q_se[1] = z[1] == 0? q_se[1] : 0;
int tmp[2];
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[1] = z[1] == 0? q_se[1] : tmp[0] < q_pe? tmp[0] : q_pe;
if (q_se[0] == 0) q_se[0] = q_se[1];
if (q_se[1] == 0) q_se[1] = q_se[0];
} else { // the unpaired alignment is much better