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Commits on Apr 4, 2013

• r371: extend overlapping seeds

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  lh3

  committed
  d7ca088

• r370: suppress "D" at the end of a cigar

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  lh3

  committed
  1e118e0

Commits on Mar 19, 2013

• r369: bugfix - segfault caused by the last change

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  lh3

  committed
  8437cd4

• r368: bugfix - wrong CIGAR when bridging 3 contigs

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  lh3

  committed
  1e3cadb

Commits on Mar 16, 2013

• Release bwa-0.7.3a-r367

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  lh3

  committed
  9346acd

Commits on Mar 15, 2013

• Release BWA-0.7.3-r366

  lh3

  committed
  7dec00c

• r365: bugfix - wrong alignment (right mapping)

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  lh3

  committed
  dd51177

• r364: bug in mem pairing (no effect with -A=1)

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  lh3

  committed
  e5355fe

Commits on Mar 12, 2013

• r363: XA=>XP; output mapQ in XP

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  lh3

  committed
  bdf34f6

• r362: bugfix - occasionally wrong TLEN

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  lh3

  committed
  c29b176

• r361: flag proper pair even if multi-primary

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  lh3

  committed
  aa7cdf4

• r360: output alternative primary alignments in XA

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  dab5b17

• r359: identical output to 0.7.2 (without -a)

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  6c66518

• SAM almost identical to 0.7.2

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  0f88103

• drop the old SAM writer

  lh3

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  26f4c70

• replace PE; BUGGY right now!!

  lh3

  committed
  0b0455c

• new code works for SE

  lh3

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  ebb45dc

• to test the new sam writer...

  lh3

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  c7edaa8

• drop an unnecessary member from mem_aln_t

  lh3

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  47952b6

• prepare to replace the SAM printing code

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  lh3

  committed
  8f0d439

Commits on Mar 9, 2013

• Release bwa-0.7.2-r351

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  lh3

  committed
  5581cb9

• Improving 'properly paired' flag.

  Show description for 2d01a29
  lh3

  committed
  2d01a29

• Match to 'N' costs -1, instead of 0.

  Show description for 740d2c1
  lh3

  committed
  740d2c1

• Emergent bugfix: wrong TLEN sign

  Show description for 9ea7f83
  lh3

  committed
  9ea7f83

Commits on Mar 8, 2013

• Release 0.7.1-r347

  lh3

  committed
  1d132a5

• Updated NEWS; added stddef.h for size_t

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  lh3

  committed
  5370bb2

• r345: bugfix in mem - wrong mate strand for unmap

  Show description for 66c9783
  lh3

  committed
  66c9783

• gcc wrongly thinks a variable may be uninitialized

  Show description for af7b4d8
  lh3

  committed
  af7b4d8

• r343: bugfix in mem - wrong mate info for unmap

  Show description for 274c0ac
  lh3

  committed
  274c0ac

• r342: bugfix in bwasw - AS is off by one

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  lh3

  committed
  017be45

• r341: bugfix - wrong mate position

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  lh3

  committed
  b5b50ac

Commits on Mar 7, 2013

• r340: feature freeze; updated the manpage

  Show description for b0a7688
  lh3

  committed
  b0a7688

• r339: pemerge - expose some settings to CLI

  lh3

  committed
  503ca9e

• r338: pemerge - fixed memory leaks; multithreading

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  lh3

  committed
  1cadfa1

• r337: mem - always read even number of reads

  Show description for 3e3236d
  lh3

  committed
  3e3236d

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