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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 10, 2013

• r375: fixed compiling errors by the last change

  lh3

  committed
  4752013

Commits on Mar 11, 2013

• Merge branch 'master' into master_fixes

  Show description for 9228e48
  

  Rob Davies

  committed
  9228e48

Commits on Mar 8, 2013

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

  Show description for 017be45
  lh3

  committed
  017be45

• Merge branch 'master' into master_fixes

  Show description for aabd990
  

  Rob Davies

  committed
  aabd990

Commits on Mar 5, 2013

• bwa-sw: ditch stdaln

  lh3

  committed
  e6c2625

• bwa-sw: use bwa_gen_cigar() for cigar generation

  lh3

  committed
  086c9d0

Commits on Mar 1, 2013

• Merge branch 'master' into master_fixes

  Show description for 3d33ab0
  

  Rob Davies

  committed
  3d33ab0

Commits on Feb 23, 2013

• moved some common code to bwa.{c,h}

  lh3

  committed
  e613195

• removed a few unused variables

  Show description for 904c320
  lh3

  committed
  904c320

Commits on Feb 12, 2013

• merge bseq.{h,c} to utils.{h,c}

  Show description for 95d1844
  lh3

  committed
  95d1844

Commits on Feb 6, 2013

• In bwtsw, replace the batch seq-reader with bseq

  lh3

  committed
  a09db69

• updated to the latest kseq.h

  lh3

  committed
  5a0b32b

Commits on Jan 3, 2013

• New wrapper for gzclose; added err_fflush calls and made it call fsync too.

  Show description for 55f1b36
  

  Rob Davies

  committed
  55f1b36

Commits on Dec 16, 2012

• Use wrapper functions to catch system errors

  Show description for b081ac9
  

  Rob Davies

  committed
  b081ac9

Commits on Oct 26, 2012

• r132: optionally copy FASTA/Q comment to SAM

  lh3

  committed
  292f906

Commits on Jun 28, 2012

• r128: more conservative chaining filter

  lh3

  committed
  f44edd4

• resolve duphits after right extension as well

  lh3

  committed
  0ae318b

Commits on Apr 18, 2012

• r115: added -I and -S to bwasw

  lh3

  committed
  cd81868

Commits on Apr 2, 2012

• commented out debugging code

  lh3

  committed
  cff4733

• updated revision number

  lh3

  committed
  790df95

• bugfix: incorrect bandwidth

  lh3

  committed
  36f2fd6

• debugging; bug persistant

  lh3

  committed
  d316980

• debugging code: bwasw has a rare bug

  lh3

  committed
  173b93d

Commits on Nov 24, 2011

• output the NM tag

  

  Heng Li

  committed
  b5170e0

• optionally mark multi-part hits as secondary

  

  Heng Li

  committed
  196b50d

• removed a useless bwa-sw CMD option

  

  Heng Li

  committed
  b17b657

• incorrect mate pos in BWA-SW SE mode

  

  Heng Li

  committed
  107a987

Commits on Nov 18, 2011

• fixed a segfault when there are too few good bases.

  

  Heng Li

  committed
  8f89f55

Commits on Nov 12, 2011

• multithreading works again

  

  Heng Li

  committed
  8060693

• bugfix: wrong mapping quality

  

  Heng Li

  committed
  fa8cfe5

• proper mate information

  

  Heng Li

  committed
  b42910a

Commits on Nov 7, 2011

• bwa-sw PE seems working (SAM is incorrect)

  

  Heng Li

  committed
  e06685d

Commits on Nov 6, 2011

• mate rescue seems working (not MT)

  

  Heng Li

  committed
  c8c79ef

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