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Merge branch 'master' of github.com:lh3/bwa

This commit is contained in:
Heng Li 2016-02-23 11:05:47 -05:00
parent 4820d8fc32 f9a7869079
commit 5ecdc66e46
2 changed files with 2 additions and 1 deletions
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2
bwape.c
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@ -379,7 +379,7 @@ int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bw
bwt_multi1_t *q = p[j]->multi + k; bwt_multi1_t *q = p[j]->multi + k;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand); q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &strand);
q->strand = strand; q->strand = strand;
if (q->pos != p[j]->pos) if (q->pos != p[j]->pos && q->pos != (bwtint_t)-1)
p[j]->multi[n_multi++] = *q; p[j]->multi[n_multi++] = *q;
} }
p[j]->n_multi = n_multi; p[j]->n_multi = n_multi;

1
bwase.c
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@ -113,6 +113,7 @@ bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int r
{ {
bwtint_t pos_f; bwtint_t pos_f;
int is_rev; int is_rev;
*strand = 0; // initialise strand to 0 otherwise we could return without setting it
pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate pos_f = bwt_sa(bwt, sapos); // position on the forward-reverse coordinate
if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1; if (pos_f < bns->l_pac && bns->l_pac < pos_f + ref_len) return (bwtint_t)-1;
pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base