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Commits on Jan 12, 2015

• Fix up usage string to be more clear about stdin/stdout usage

  bolosky

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Commits on Dec 1, 2014

• 1.0beta.17: fix bug for very short FASTQ files

  bolosky

  committed
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Commits on Nov 7, 2014

• 1.0beta.16: fix BAM cigar string generation for trailing I fixup

  bolosky

  committed
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Commits on Nov 6, 2014

• 1.0beta.15: Init headerBuffer flag when adding buffers

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  rnpandya

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Commits on Oct 28, 2014

• 1.0beta.14: Resize queue to prevent deadlock

  rnpandya

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Commits on Oct 24, 2014

• Size queue based on MaxImbalance

  rnpandya

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Commits on Oct 18, 2014

• 1.0beta.13: Increase supplier queue size to avoid deadlock

  rnpandya

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Commits on Oct 16, 2014

• Build unit tests on Windows

  bolosky

  committed
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Commits on Oct 14, 2014

• Major update: 64 bit genome locations, better tuning, lot of bugfixes, etc.

  bolosky

  committed
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• 1.0dev.51: merge in changes from master, fix deadlock

  bolosky

  committed
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Commits on Oct 13, 2014

• delete dead code

  bolosky

  committed
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Commits on Oct 8, 2014

• 1.0dev.50: add -omax flag

  bolosky

  committed
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Commits on Oct 4, 2014

• 1.0dev.49: tweak default parameters for paired-end alignment

  bolosky

  committed
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Commits on Oct 1, 2014

• One more tweek for very large header SAM files

  bolosky

  committed
  6cffe2f

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• Linux build

  bolosky

  committed
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• Fix usage message for paired end aligner

  bolosky

  committed
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Commits on Sep 30, 2014

• Merge branch 'dev' of https://github.com/amplab/snap into dev

  bolosky

  committed
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• 1.0dev.48: Support for giant headers, change defaults, etc.

  bolosky

  committed
  6826670

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• Add null check

  rnpandya

  committed
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Commits on Sep 26, 2014

• Support for giant headers (i.e., files with lots of contigs). Doesn't work, committing to allow merge

  bolosky

  committed
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Commits on Sep 15, 2014

• Merge branch 'dev' of https://github.com/amplab/snap into dev

  rnpandya

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• 1.0dev.47: replace leading D in CIGAR with soft clipping

  rnpandya

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Commits on Sep 12, 2014

• 1.0dev.46: what I said with 1.0dev.45, but merged with Ravi's 1.0dev.45 @RG changes

  bolosky

  committed
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• Merge branch 'dev' of https://github.com/amplab/snap into dev

  bolosky

  committed
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• 1.0dev.45: Allow loading indices with keysize > 4, add -nt switch for perf measurements

  bolosky

  committed
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• Merge branch 'dev' of https://github.com/amplab/snap into dev

  rnpandya

  committed
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• Merge remote-tracking branch 'origin/dev' into dev

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  rnpandya

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• 1.0dev.45: add some @RG fields into read for GATK

  rnpandya

  committed
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Commits on Sep 8, 2014

• 1.0dev.44: fix up index sizing, make -exact work for big genomes, add more -hg19 bias tables

  bolosky

  committed
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Commits on Sep 5, 2014

• Turn off printf in index build

  bolosky

  committed
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• Linux build

  bolosky

  committed
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• 1.0dev.43: add -pre option for using fread to prefetch a file before mapping it

  bolosky

  committed
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Commits on Sep 4, 2014

• Merge branch 'dev' of https://github.com/amplab/snap into dev

  bolosky

  committed
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• 1.0dev.42: add option to use file mapping to get the index rather than reading it

  bolosky

  committed
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• Merge

  rnpandya

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