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Commits on May 31, 2016

• r1142: added option -5 for Hi-C data

  lh3

  committed
  f123871

Commits on May 20, 2016

• r1138: fixed typo in insert size estimate (lh3#65)

  Show description for 58bcc25
  lh3

  committed
  58bcc25

Commits on Dec 24, 2014

• r1038: wrong 0x100|0x800 flags in PE mode

  lh3

  committed
  e746a3e

• r1037: wrong read number flag

  lh3

  committed
  3ae8d4b

• r1036: PE ALT mapping incorrect

  Show description for b9bbf2d
  lh3

  committed
  b9bbf2d

Commits on Nov 10, 2014

• r983: bugfix - wrong mate info

  Show description for 7eabcf4
  lh3

  committed
  7eabcf4

Commits on Oct 28, 2014

• r960: merge changes from the master branch

  lh3

  committed
  6db2fd9

Commits on Oct 21, 2014

• r939: fixed a memory leak (issue lh3#35)

  lh3

  committed
  5e00d08

Commits on Sep 18, 2014

• These files were committed on a wrong branch

  lh3

  committed
  a41afe4

• r855: show ALT hits in the PE mode, too

  Show description for a32d44d
  lh3

  committed
  a32d44d

Commits on Sep 15, 2014

• r826: improved alt mapping for PE

  lh3

  committed
  bd85af0

Commits on Sep 14, 2014

• r823: towards ALT support

  lh3

  committed
  015ab3f

Commits on Aug 29, 2014

• r815: optionally output ref fasta header

  Show description for 35ac99b
  lh3

  committed
  35ac99b

Commits on May 19, 2014

• 0.7.9a-r786: fixed a segfault in a rare case

  Show description for 3efc331
  lh3

  committed
  3efc331

Commits on May 16, 2014

• r779: fixed a memory leak in SE

  lh3

  committed
  f00cc94

Commits on May 9, 2014

• r759: bugfix - frac_rep not working

  Show description for 43b498a
  lh3

  committed
  43b498a

Commits on May 1, 2014

• r739: output suboptimal hits in the PE mode

  Show description for 5aedc97
  lh3

  committed
  5aedc97

Commits on Apr 30, 2014

• r738: output multi-map in the XA tag (SE only)

  Show description for c6c943f
  lh3

  committed
  c6c943f

Commits on Apr 24, 2014

• Merge branch '0.7.7-softclip' into layout

  Show description for b92bbb4
  lh3

  committed
  b92bbb4

• r725: optionally disable hard clipping

  Show description for 8c12ec4
  lh3

  committed
  8c12ec4

Commits on Apr 16, 2014

• r723: merge adjacent hits

  lh3

  committed
  b93fca2

Commits on Apr 15, 2014

• r721: merge overlapping hits by default

  lh3

  committed
  00a07f6

Commits on Apr 11, 2014

• r705: pairing performed on one chr only

  Show description for 6fda935
  lh3

  committed
  6fda935

• dev-472: get rid of bwa_fix_xref()

  Show description for 8638cfa
  lh3

  committed
  8638cfa

Commits on Mar 31, 2014

• dev-453: change of -A scales -TdBOELU

  Show description for b27bdf1
  lh3

  committed
  b27bdf1

• dev-r451: fixed a few bugs when -A!=1

  Show description for 417c6d6
  lh3

  committed
  417c6d6

Commits on Mar 28, 2014

• dev-450: support diff ins/del penalties. NO TEST!!

  lh3

  committed
  9ce50a4

Commits on Jan 29, 2014

• r430: fix a bug producing incorrect alignment

  Show description for ea3dc2f
  lh3

  committed
  ea3dc2f

Commits on Nov 23, 2013

• r423: bugfix - SE hits not random

  lh3

  committed
  4219e58

Commits on Nov 21, 2013

• r422: matesw hits not sorted

  lh3

  committed
  29aa855

Commits on Jun 14, 2013

• Check that paired reads have the same QNAME

  Show description for 20dc9dd
  jmarshall

  committed
  20dc9dd

Commits on May 2, 2013

• Reduce dependency on utils.h - new malloc wrapping scheme.

  Show description for 96e445d
  

  Rob Davies

  committed
  96e445d

Commits on Apr 11, 2013

• Merge branch 'master' into master_fixes. Merged up to master r375.

  Show description for 90ecd34
  

  Rob Davies

  committed
  90ecd34

Commits on Apr 9, 2013

• r373: optionally distable mate rescue

  lh3

  committed
  53bb846

Commits on Mar 18, 2013

• Merge branch 'master' into master_fixes

  

  Rob Davies

  committed
  c862a1a

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