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Commits on Oct 28, 2016

• Removed the gccx.x.x directories.

  alexdobin

  committedOct 28, 2016
  6fa1afa

• Fixed a problem with RNEXT field in the Chimeric.out.sam file: RNEXT now always points to the other mate start.

  alexdobin

  committedOct 28, 2016
  d518659

Commits on Sep 29, 2016

• Added static exexutables compiled with gcc 4.7.0 and 5.3.0 .

  alexdobin

  committedSep 29, 2016
  b405dea

Commits on Aug 25, 2016

• Implemented --bamRemoveDuplicatesType UniqueIdenticalNotMulti option, which (unlike the UniqueIdentical optipon) will NOT mark multi-mappers as duplicates. For --bamRemoveDuplicatesType UniqueIdent…

  alexdobin

  committedAug 25, 2016
  3773992

Commits on Aug 19, 2016

• 2.5.2b

  alexdobin

  committedAug 19, 2016
  c00301c

Commits on Aug 18, 2016

• Getting ready for 2.5.2b

  alexdobin

  committedAug 18, 2016
  7e95a81

Commits on Jun 15, 2016

• Fixed a bug with chimeric BAM output for --chimOutType WithinBAM option.

  alexdobin

  committedJun 15, 2016
  30ef216

Commits on Jun 9, 2016

• Fixed a bug that could cause non-stable BAM sorting if the gcc qsort is unstable.

  alexdobin

  committedJun 9, 2016
  4ad2100

Commits on May 25, 2016

• Fixed a bug with causing seg-faults when combining --twopassMode Basic --outSAMorder PairedKeepInputOrder .

  alexdobin

  committedMay 25, 2016
  a7756f5

Commits on May 24, 2016

• Fixed a problem with SAM header in cases where reference sequences are added at the mapping stage.

  alexdobin

  committedMay 24, 2016
  487b836

Commits on May 10, 2016

• 2.5.2a : Fixed the GstrandBit problem. Fixed a bug introduced in 2.5.1a that caused problems with single-end alignments output in some cases.

  alexdobin

  committedMay 10, 2016
  41b5d74

Commits on May 6, 2016

• New sorting routine for inserting sequence into the genome - fixes the problem with sorting long repeat suffixes.

  alexdobin

  committedMay 6, 2016
  d93cd79

Commits on Apr 18, 2016

• Compiled executables

  alexdobin

  committedApr 18, 2016
  216fbc9

Commits on Mar 4, 2016

• More threads safe chunks concatenation for Unmapped Fastx option.

  alexdobin

  committedMar 4, 2016
  61a3622

Commits on Mar 3, 2016

• Implemented --outTmpKeep All option to keep the temporary files. Implemented --alignEndsProtrude option to control output of alignments with protruding ends.

  alexdobin

  committedMar 3, 2016
  1a90fb4

Commits on Feb 25, 2016

• Recompiled binaries.

  alexdobin

  committedFeb 25, 2016
  21a68ed

Commits on Feb 24, 2016

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

  alexdobin

  committedFeb 24, 2016
  f3559f7

• Eliminates compilation warnings in ReadAlign_alignBAM.cpp

  alexdobin

  committedFeb 24, 2016
  f74a811

Commits on Jan 29, 2016

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

  alexdobin

  committedJan 29, 2016
  c708ab0

Commits on Jan 22, 2016

• 2.5.1b

  alexdobin

  committedJan 22, 2016
  9a688c2

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

  alexdobin

  committedJan 22, 2016
  2e0d6cc

Commits on Jan 19, 2016

• 2.5.1a

  alexdobin

  committedJan 19, 2016
  a979f3f

• Updated manual.

  alexdobin

  committedJan 19, 2016
  161761e

Commits on Jan 15, 2016

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

  alexdobin

  committedJan 15, 2016
  c1feaac

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

  committedJan 13, 2016
  e585bd4

Commits on Jan 8, 2016

• Cleaned up the code to remove compilation warnings.

  alexdobin

  committedJan 8, 2016
  c514c69

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

  committedJan 4, 2016
  a5975c2

Commits on Dec 23, 2015

• 2.5.0c Mac OSX executables.

  alexdobin

  committedDec 23, 2015
  7612ef0

• 2.5.0c

  alexdobin

  committedDec 23, 2015
  87d7db7

Commits on Dec 21, 2015

• Increased speed of the suffix array generation.

  alexdobin

  committedDec 21, 2015
  98f8e11

Commits on Dec 9, 2015

• In Aligned.toTranscriptome.out.bam (--quantMode TranscriptomeSAM), non-primary SAM flag is assigned to all but one randomly selected alignment.

  alexdobin

  committedDec 9, 2015
  6dc1798

Commits on Dec 3, 2015

• Fixed a bug that prevented chimeric output for some of the circular configurations.

  alexdobin

  committedDec 3, 2015
  7e15df9

Commits on Nov 30, 2015

• Mac binaries for 2.5.0b from travis.

  alexdobin

  committedNov 30, 2015
  9f9e8b4

• Fixed a problem with non-primary alignment flags with --outSAMmultNmax option.

  alexdobin

  committedNov 30, 2015
  70b6859

Commits on Nov 20, 2015

• Added counting of chimeric reads into Log.final.out .

  alexdobin

  committedNov 20, 2015
  e0ca9bf

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