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Port lh3#48 to the dev branch
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lh3 committed Feb 23, 2016
1 parent 9a82834 commit 11437a1
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29 changes: 29 additions & 0 deletions NEWS.md
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@@ -1,3 +1,32 @@
Release 0.7.13 (23 Feburary 2016)
---------------------------------

This release fixes a few minor bugs in the previous version and adds a few
minor features. All BWA algorithms should produce identical output to 0.7.12
when there are no ALT contigs.

Detailed changes:

* Fixed a bug in "bwa-postalt.js". The old version may produce 0.5% of wrong
bases for reads mapped to the ALT contigs.

* Fixed a potential bug in the multithreading mode. It may occur when mapping
is much faster than file reading, which should almost never happen in
practice.

* Changed the download URL of GRCh38.

* Removed the read overlap mode. It is not working well.

* Added the ropebwt2 algorithm as an alternative to index large genomes.
Ropebwt2 is slower than the "bwtsw" algorithm, but it has a permissive
license. This allows us to create an Apache2-licensed BWA (in the "Apache2"
branch) for commercial users who are concerned with GPL.

(0.7.13: 23 Feburary 2016, r1118)



Release 0.7.12 (28 December 2014)
---------------------------------

2 changes: 1 addition & 1 deletion 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;
q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len + q->ref_shift, &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]->n_multi = n_multi;
1 change: 1 addition & 0 deletions 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;
int is_rev;
*strand = 0;
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;
pos_f = bns_depos(bns, pos_f, &is_rev); // position on the forward strand; this may be the first base or the last base

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