taoliu Merge pull request #240 from jsh58/master
Added --max-gap, --min-length CL arguments; PE fragment length calculation and other debugs
Latest commit 33187ea May 4, 2018
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IO macs2: fix hash collision failure for p-score calculations Mar 28, 2018
data Fix gfold calculation and txt output. Feb 23, 2012
Constants.py macs2: update version to 2.1.2_dev Apr 2, 2018
OptValidator.py Merge pull request #240 from jsh58/master May 4, 2018
OutputWriter.py Add an extra subcommand to predict fragment size from alignment Oct 2, 2012
PeakDetect.pyx macs2: add --max-gap, --min-length parameters Mar 21, 2018
PeakModel.pyx Merge branch 'master' of https://github.com/taoliu/MACS Mar 9, 2016
Pileup.pyx Related to issue #122. Check ndarray size, then resize it to half size May 19, 2016
Prob.pyx Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
Signal.pyx Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
Statistics.pyx macs2: fix p-score miscalculations for large lambda Mar 29, 2018
__init__.py Modify bdgdiff to use precompiled gfold (general fold change) values. Feb 11, 2012
bdgbroadcall_cmd.py Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
bdgcmp_cmd.py Enable 'max' and 'min' functions for bdgopt; enable 'max' function fo… Feb 12, 2016
bdgdiff_cmd.py Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
bdgopt_cmd.py Enable 'max' and 'min' functions for bdgopt; enable 'max' function fo… Feb 12, 2016
bdgpeakcall_cmd.py Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
cPosValCalculation.c Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
cPosValCalculation.h Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
cPosValCalculation.pxd Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
cStatistics.c Feature added for callpeak and bdgpeakcall: analyze cutoff vs peaks to Aug 22, 2014
cStatistics.h Feature added for callpeak and bdgpeakcall: analyze cutoff vs peaks to Aug 22, 2014
callpeak_cmd.py macs2: fix hash collision failure for p-score calculations Mar 28, 2018
cmbreps_cmd.py Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx; Mar 10, 2015
diffpeak_cmd.py Fixed cProb reference in filterdup_cmd.py --> Prob. Jul 27, 2015
filterdup_cmd.py Fixed cProb reference in filterdup_cmd.py --> Prob. Jul 27, 2015
hashtable.pyx use khash to save p-q-table. Apr 8, 2013
khash.h khash store float as values. bdgcmp using new ScoreTrack class. Jun 1, 2012
khash.pxd khash store float as values. bdgcmp using new ScoreTrack class. Jun 1, 2012
pileup_cmd.py Fixed the issue with multiple input files. Now, call fwtrack.finalize Jun 3, 2015
predictd_cmd.py Fixed the issue with multiple input files. Now, call fwtrack.finalize Jun 3, 2015
randsample_cmd.py Fixed the issue with multiple input files. Now, call fwtrack.finalize Jun 3, 2015
refinepeak_cmd.py Fixed the issue with multiple input files. Now, call fwtrack.finalize Jun 3, 2015