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Commits on Jan 11, 2022

• Merge pull request #68 from ahvigil/git-protocol

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  hyunminkang

  authored
  017721c

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• git:// protocol is being deprecated by github

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  ahvigil

  committed
  e2b9409

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Commits on Mar 8, 2021

• Bumps version to v1.0.15.

  jonathonl

  committed
  3ad3980

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Commits on Jun 2, 2020

• Update TrimBam to accept -.ubam, etc. Previously it failed if the input/output filename was -.ubam, etc

  mktrost

  committed
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Commits on Apr 20, 2019

• Update Dedup & Recab to fail and print an error message when stdin is specified. Both require reading the input file twice. Previously they did not work properly, but produced no error messages.

  mktrost

  committed
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Commits on Sep 3, 2018

• ClipOverlap - add option to turn off read name alpha-numeric sort validation

  mktrost

  committed
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Commits on Aug 9, 2017

• MateMapByCoord.h - remove use of unordered_multimap since it does not work with the first() and popFirst() methods

  mktrost

  committed
  16eebf6

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• MateMapByCoord.h - fix use of multimap vs unordered_multimap based on __GXX_EXPERIMENTAL_CXX0X__, it was using unordered for non-CXX0X

  mktrost

  committed
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Commits on Jul 27, 2017

• Mention - for STDOUT in bam stats --help

  pjvandehaar

  authored
  eb54217

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Commits on Sep 6, 2016

• resolve issue of read gourp info of interleaved output (#38)

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  Griffan

  authored
  6ce9665

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Commits on Aug 29, 2016

• Bam2FastQ update interleave (--merge) to work with splitRG option

  mktrost

  committed
  6566422

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Commits on Aug 12, 2016

• Fixes test files.

  jonathonl

  committed
  a79f1ca

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Commits on Aug 10, 2016

• Added custom binning scheme

  hyunminkang

  committed
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Commits on Jun 23, 2016

• Append gz extension to gzipped output.

  jonathonl

  committed
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Commits on Apr 7, 2016

• Merge pull request #25 from statgen/fix-standard-streams

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  jonathonl

  committed
  184fe84

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• Escape percent sign for fprintf.

  jonathonl

  committed
  c4b7989

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• Fix case sensitivity bug.

  jonathonl

  committed
  d2ce674

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• Replace -T flag with -n to support mac version of ln.

  jonathonl

  committed
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• Revert previous commit.

  jonathonl

  committed
  4aeb90b

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• Replace -T flag with -n to support mac version of ln.

  jonathonl

  committed
  05bda55

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• Add usage command for each tool without outputting error.

  jonathonl

  committed
  559dd6c

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Commits on Apr 6, 2016

• Add cmake project file.

  jonathonl

  committed
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Commits on Apr 5, 2016

• Add error message for no args.

  jonathonl

  committed
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Commits on Apr 4, 2016

• Change main usage output stream to stdout.

  jonathonl

  committed
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Commits on Apr 2, 2016

• Initial Travis CI config

  pjvandehaar

  committed
  661a3dc

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• Merge pull request #24 from rleonid/master

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  pjvandehaar

  committed
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Commits on Apr 1, 2016

• Add usage & help command to print dialoge and exit.

  rleonid

  committed
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Commits on Mar 6, 2016

• Add logic to handle Supplementary reads similar to secondary reads

  mktrost

  committed
  cd4036e

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• Dedup - change message about missing mate from ERROR to WARNING

  mktrost

  committed
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Commits on Jan 2, 2016

• Update Makefile.inc to only look for the INCLUDE_MAKE if it is not cloneLib

  mktrost

  committed
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Commits on Dec 2, 2015

• Add Validation test to test that cigar and seq length are not validated if seq is '*'

  mktrost

  committed
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Commits on Nov 18, 2015

• MateMapByCoord - update to use unordered_map if c++11

  mktrost

  committed
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Commits on Oct 16, 2015

• Remove c++0x logic since it is now in the libStatGen Makefile

  mktrost

  committed
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Commits on Sep 12, 2015

• Recab - update to apply maximum quality after binning

  mktrost

  committed
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Commits on Aug 29, 2015

• Merge pull request #13 from pjvandehaar/master

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  mktrost

  committed
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