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Commits on Feb 25, 2016

• Recompiled binaries.

  alexdobin

  committed
  21a68ed

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• Merge branch 'smoe-bikeshedding'

  alexdobin

  committed
  be1b380

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• Merge branch 'bikeshedding' of https://github.com/smoe/STAR into smoe-bikeshedding

  alexdobin

  committed
  631380a

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• Added Extend5pOfReads12 option to parametersDefault.

  alexdobin

  committed
  3786c8c

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• Final optical treat in sjdbBuildIndex.cpp

  smoe

  committed
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• optics in sjdbInsertJunctions.cpp

  smoe

  committed
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• optics in Genome_insertSequences.cpp

  smoe

  committed
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• More optical refinements - now in loadGTF

  smoe

  committed
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• More optical refinements

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  smoe

  committed
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• Merge pull request #115 from smoe/bikeshedding

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  alexdobin

  committed
  221825d

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• deciding for lower case in status msg

  smoe

  committed
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• deciding for lower case for the sake of consistency

  smoe

  committed
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Commits on Feb 24, 2016

• Implemented --alignEndsType Extend5pOfReads12 option for full extension of 5' ends of both mates.

  alexdobin

  committed
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• Eliminates compilation warnings in ReadAlign_alignBAM.cpp

  alexdobin

  committed
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Commits on Feb 23, 2016

• Increased maximum read length to 650.

  alexdobin

  committed
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Commits on Feb 18, 2016

• Removed trailing white space from all source files.

  alexdobin

  committed
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Commits on Jan 29, 2016

• Fixed a bug that caused output of unmapped mates for single end alignments even with --outSAMunmapped None .

  alexdobin

  committed
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Commits on Jan 22, 2016

• Merge pull request #105 from mschilli87/mschilli87-typo_fix

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  alexdobin

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• Merge pull request #106 from arahuja/patch-1

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  alexdobin

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• 2.5.1b

  alexdobin

  committed
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• Fixed a bug in signal generation with --outWigType introduced in 2.5.1a

  alexdobin

  committed
  2e0d6cc

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• Update README.md

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  arahuja

  committed
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Commits on Jan 21, 2016

• fixed typo in sjdbGTFchrPrefix description

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  mschilli87

  committed
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Commits on Jan 19, 2016

• 2.5.1a

  alexdobin

  committed
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• Updated manual.

  alexdobin

  committed
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Commits on Jan 15, 2016

• Fixed a bug causing crashed introduced in the previous patch.

  alexdobin

  committed
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Commits on Jan 13, 2016

• Fixed a bug in --quantMode TranscriptomeSAM that prevented output to Aligned.toTranscriptome.out.bam of the reads mapped to the very last annotated transcript.

  alexdobin

  committed
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Commits on Jan 8, 2016

• Cleaned up the code to remove compilation warnings.

  alexdobin

  committed
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Commits on Jan 4, 2016

• Implemented --outSAMunmapped Within KeepPairs option to record unmapped mate adjacent to the mapped one, in case single-end alignments are allowed.

  alexdobin

  committed
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Commits on Dec 23, 2015

• Merge branch 'master' of /sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR

  alexdobin

  committed
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• Implementing paired output for single-end alignments.

  alexdobin

  committed
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• 2.5.0c Mac OSX executables.

  alexdobin

  committed
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• 2.5.0c

  alexdobin

  committed
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Commits on Dec 21, 2015

• Merged with master

  alexdobin

  committed
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• Increased speed of the suffix array generation.

  alexdobin

  committed
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