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Commits on Mar 9, 2016

• Remove filtering criteria of bwflag&2048 so PCR/Optical duplicate will

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  taoliu

  committedMar 9, 2016
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Commits on Feb 26, 2016

• Release 2.1.1.

  taoliu

  committedFeb 26, 2016
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Commits on Feb 15, 2016

• A more flexible format, BEDPE, is supported. Related to issue

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  taoliu

  committedFeb 15, 2016
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Commits on Jan 30, 2016

• Replace C FLAG '-Ofast' with more compatible '-O3 -ffast-math' in

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  taoliu

  committedJan 30, 2016
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Commits on Dec 22, 2015

• Fix a bug related to the broad peak calling function in previous

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  taoliu

  committedDec 22, 2015
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Commits on Jul 31, 2015

• Correct time-stamp for 20150731 release.

  taoliu

  committedJul 31, 2015
  a3438e8

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• Update version tag.

  taoliu

  committedJul 31, 2015
  871a984

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Commits on Jul 27, 2015

• Fixed cProb reference in filterdup_cmd.py --> Prob.

  taoliu

  committedJul 27, 2015
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Commits on Jun 3, 2015

• Fixed the issue with multiple input files. Now, call fwtrack.finalize

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  taoliu

  committedJun 3, 2015
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Commits on Apr 20, 2015

• 2015.4.20 release

  taoliu

  committedApr 20, 2015
  7f46b06

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Commits on Mar 12, 2015

• O3 -> Ofast

  taoliu

  committedMar 12, 2015
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Commits on Mar 10, 2015

• Fix setup script. Put back -Ofast...

  taoliu

  committedMar 10, 2015
  782bf5c

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• Optimize model building step. Change compilation option from -Ofast to

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  taoliu

  committedMar 10, 2015
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• Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx;

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  taoliu

  committedMar 10, 2015
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Commits on Jan 21, 2015

• Change version number.

  taoliu

  committedJan 21, 2015
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Commits on Oct 29, 2014

• Change subversion tag 20141030.

  taoliu

  committedOct 29, 2014
  1a2ce10

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Commits on Oct 23, 2014

• Fixed issue macs3-project#51. Set GCC flags to suppress all warning and set

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  taoliu

  committedOct 23, 2014
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• Fixed issue macs3-project#49: switch to setuptools.

  taoliu

  committedOct 23, 2014
  07d09ad

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Commits on Jul 31, 2014

• Add two new commands: cmbreps to combine two replicates; bdgopt to

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  taoliu

  committedJul 31, 2014
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Commits on Jun 17, 2014

• 2.1.0 package. Revised testing scripts.

  taoliu

  committedJun 17, 2014
  b85a265

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• --shift is added and --half-ext and --control-shift are

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  taoliu

  committedJun 17, 2014
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Commits on Apr 14, 2014

• Clean intermediate C codes generated from pyx files. Add --ratio

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  taoliu

  committedApr 14, 2014
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Commits on Dec 16, 2013

• Change license to 3-clauses BSD license.

  taoliu

  committedDec 16, 2013
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• Version 2.0.10 12162013. With bug fixes and some tweaks for gappedPeak output.

  taoliu

  committedDec 16, 2013
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Commits on Oct 28, 2013

• Tag version 2.0.10 20131028

  taoliu

  committedOct 28, 2013
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Commits on Oct 10, 2013

• Fix --outdir options. (testing, try to) Fix call-summits local maxima detection.

  taoliu

  committedOct 10, 2013
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Commits on Sep 18, 2013

• Test revised PeakModel.

  taoliu

  committedSep 18, 2013
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Commits on Sep 16, 2013

• Speed up preparing p-q-table. Add pure c code for calculating poisson

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  taoliu

  committedSep 16, 2013
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• Speed up pqstat.

  taoliu

  committedSep 16, 2013
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Commits on Sep 12, 2013

• Separate codes that need scipy out in cDiffScore.pyx file.

  taoliu

  committedSep 12, 2013
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Commits on Sep 11, 2013

• Fixes for logLR calculation. Add optional buffer_size parameter.

  taoliu

  committedSep 11, 2013
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Commits on Jul 31, 2013

• 1. bdgcmp logLR output is fixed; 2. bdgdiff is fixed; 3. callpeak

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  taoliu

  committedJul 31, 2013
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Commits on Jul 19, 2013

• Update of changelog and version for release 20130713.

  taoliu

  committedJul 19, 2013
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Commits on Jul 13, 2013

• Fixed output of broadPeak and modified bdgcmp option -T & -C

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  taoliu

  committedJul 13, 2013
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Commits on Jul 10, 2013

• label 2.0.10.20130710: with fixes for output format.

  taoliu

  committedJul 10, 2013
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