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Commits on Sep 16, 2014

• r837: removed BAM support

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  lh3

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Commits on Jul 28, 2014

• adding support for SAM/BAM output using htslib. Please turn on within

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  Nils Homer

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Commits on May 3, 2013

• Removed more dependencies on utils.h

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  Rob Davies

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Commits on May 2, 2013

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

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  Rob Davies

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Commits on Mar 1, 2013

• Merge branch 'master' into master_fixes

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  Rob Davies

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Commits on Feb 6, 2013

• updated to the latest kseq.h

  lh3

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Commits on Jan 3, 2013

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

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  Rob Davies

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Commits on Dec 16, 2012

• Use wrapper functions to catch system errors

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  Rob Davies

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Commits on Nov 24, 2011

• fixed a minor issue in trimming

  

  Heng Li

  committed
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• fixed a long-existing bug in trimming

  

  Heng Li

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Commits on Jul 10, 2011

• Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y

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  RoelKluin

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• Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa"

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  RoelKluin

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Commits on Jul 8, 2011

• In Casava 1.8 the fastq output changed, the name had a space which bwa

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  RoelKluin

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Commits on Jun 9, 2011

• increase maximum barcode length limit to 63bp

  

  Heng Li

  committed
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Commits on Jan 15, 2011

• Added barcode support

  

  Heng Li

  committed
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• Added an option to accept Illumina 1.3+ fastq

  

  Heng Li

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Commits on Jan 14, 2011

• Imported from my local bwa repository, the master repository.

  

  Heng Li

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