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on039ea20

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Commits on Sep 19, 2014

• r867: fixed a few bugs; added ALT hits to XA

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  committed
  9af3606

Commits on Sep 17, 2014

• r854: improved the calculation of pa

  Show description for c982443
  lh3

  committed
  c982443

Commits on Sep 16, 2014

• r848: tag alignments with primary ALT

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  committed
  6f37c14

Commits on Sep 8, 2014

• code backup

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  committed
  ca61fe3

Commits on Aug 29, 2014

• r815: optionally output ref fasta header

  Show description for 35ac99b
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  committed
  35ac99b

Commits on Aug 25, 2014

• r809: new strategy for the -a mode

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  committed
  b5cba25

Commits on May 11, 2014

• r762: cleanup for the new release; unfinished

  Show description for 39a6cd5
  lh3

  committed
  39a6cd5

Commits on May 9, 2014

• r759: bugfix - frac_rep not working

  Show description for 43b498a
  lh3

  committed
  43b498a

Commits on May 2, 2014

• r746: tuned heuristic for GRCh38

  Show description for 6db761e
  lh3

  committed
  6db761e

Commits on Apr 30, 2014

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

  Show description for c6c943f
  lh3

  committed
  c6c943f

• r736: improved in low-complexity regions

  Show description for 88f89be
  lh3

  committed
  88f89be

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

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  b93fca2

Commits on Apr 15, 2014

• r721: merge overlapping hits by default

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  00a07f6

Commits on Apr 14, 2014

• r718: merge alnregs overlapping on both query/ref

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  committed
  4e22270

Commits on Apr 11, 2014

• dev-472: get rid of bwa_fix_xref()

  Show description for 8638cfa
  lh3

  committed
  8638cfa

Commits on Apr 10, 2014

• dev-470: don't stop on bwa_fix_xref2() failures

  Show description for ccbbe48
  lh3

  committed
  ccbbe48

Commits on Apr 9, 2014

• dev-467: limit the max #chains to extend

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  committed
  99f6f9a

Commits on Apr 8, 2014

• dev-465: a new output format for read overlap

  Show description for f12dfae
  lh3

  committed
  f12dfae

Commits on Apr 4, 2014

• dev-r462: refined setting for PacBio; weight flt

  Show description for 114901b
  lh3

  committed
  114901b

• dev-461: added a heuristic for PacBio data

  Show description for 41f720d
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  committed
  41f720d

Commits on Apr 3, 2014

• dev-458: simplified the smem iterator

  Show description for b322558
  lh3

  committed
  b322558

Commits on Mar 28, 2014

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

  lh3

  committed
  9ce50a4

Commits on Feb 27, 2014

• dev-r442: suppress exact full-length matches

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  committed
  2e9463e

Commits on Nov 23, 2013

• r423: bugfix - SE hits not random

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  4219e58

Commits on Sep 9, 2013

• r413: fixed an issue causing redundant alignment

  Show description for b51a66e
  lh3

  committed
  b51a66e

Commits on Sep 6, 2013

• alternative way to estimate mapQ

  Show description for 623da05
  lh3

  committed
  623da05

Commits on Aug 28, 2013

• r406: allow to use diff clipping penalties

  Show description for 3b84c03
  lh3

  committed
  3b84c03

Commits on May 22, 2013

• conform to the latest (unpublished) SAM spec

  Show description for 9735d7a
  lh3

  committed
  9735d7a

Commits on Apr 26, 2013

• r388: cleanup mem_process_seqs() interface

  Show description for 19cb7cd
  lh3

  committed
  19cb7cd

Commits on Apr 9, 2013

• r373: optionally distable mate rescue

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  committed
  53bb846

Commits on Mar 16, 2013

• Release bwa-0.7.3a-r367

  Show description for 9346acd
  lh3

  committed
  9346acd

Commits on Mar 12, 2013

• drop the old SAM writer

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  committed
  26f4c70

• drop an unnecessary member from mem_aln_t

  lh3

  committed
  47952b6

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