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Commits on Apr 10, 2013

• r375: fixed compiling errors by the last change

  lh3

  committed
  4752013

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Commits on Mar 8, 2013

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

  Show description for 017be45
  lh3

  committed
  017be45

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Commits on Mar 5, 2013

• bwa-sw: ditch stdaln

  lh3

  committed
  e6c2625

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

  lh3

  committed
  086c9d0

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Commits on Feb 23, 2013

• moved some common code to bwa.{c,h}

  lh3

  committed
  e613195

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• removed a few unused variables

  Show description for 904c320
  lh3

  committed
  904c320

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Commits on Feb 12, 2013

• merge bseq.{h,c} to utils.{h,c}

  Show description for 95d1844
  lh3

  committed
  95d1844

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Commits on Feb 6, 2013

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

  lh3

  committed
  a09db69

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• updated to the latest kseq.h

  lh3

  committed
  5a0b32b

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Commits on Oct 26, 2012

• r132: optionally copy FASTA/Q comment to SAM

  lh3

  committed
  292f906

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Commits on Jun 28, 2012

• r128: more conservative chaining filter

  lh3

  committed
  f44edd4

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• resolve duphits after right extension as well

  lh3

  committed
  0ae318b

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Commits on Apr 18, 2012

• r115: added -I and -S to bwasw

  lh3

  committed
  cd81868

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Commits on Apr 2, 2012

• commented out debugging code

  lh3

  committed
  cff4733

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• updated revision number

  lh3

  committed
  790df95

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• bugfix: incorrect bandwidth

  lh3

  committed
  36f2fd6

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• debugging; bug persistant

  lh3

  committed
  d316980

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• debugging code: bwasw has a rare bug

  lh3

  committed
  173b93d

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Commits on Nov 24, 2011

• output the NM tag

  

  Heng Li

  committed
  b5170e0

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• optionally mark multi-part hits as secondary

  

  Heng Li

  committed
  196b50d

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• removed a useless bwa-sw CMD option

  

  Heng Li

  committed
  b17b657

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• incorrect mate pos in BWA-SW SE mode

  

  Heng Li

  committed
  107a987

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Commits on Nov 18, 2011

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

  

  Heng Li

  committed
  8f89f55

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Commits on Nov 12, 2011

• multithreading works again

  

  Heng Li

  committed
  8060693

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• bugfix: wrong mapping quality

  

  Heng Li

  committed
  fa8cfe5

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• proper mate information

  

  Heng Li

  committed
  b42910a

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Commits on Nov 7, 2011

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

  

  Heng Li

  committed
  e06685d

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Commits on Nov 6, 2011

• mate rescue seems working (not MT)

  

  Heng Li

  committed
  c8c79ef

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• compute insert size distribution

  

  Heng Li

  committed
  17eaac5

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Commits on Nov 5, 2011

• further preparation for pairing

  

  Heng Li

  committed
  a29b179

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• bwasw: read and align two fastq at a time

  

  Heng Li

  committed
  06687a3

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Commits on Oct 24, 2011

• fixed a potential int overflow

  

  Heng Li

  committed
  8f3c780

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• fixed a bug about reverse alignment

  

  Heng Li

  committed
  eed46e8

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• fixed negative mapping quality; still byggy

  

  Heng Li

  committed
  b204437

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• bwasw works on a couple of sequences

  

  Heng Li

  committed
  8512b55

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