ChangeLog
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
MACS3/__init__.py
MACS3.egg-info/PKG-INFO
MACS3.egg-info/SOURCES.txt
MACS3.egg-info/dependency_links.txt
MACS3.egg-info/requires.txt
MACS3.egg-info/top_level.txt
MACS3/Commands/__init__.py
MACS3/Commands/bdgbroadcall_cmd.py
MACS3/Commands/bdgcmp_cmd.py
MACS3/Commands/bdgdiff_cmd.py
MACS3/Commands/bdgopt_cmd.py
MACS3/Commands/bdgpeakcall_cmd.py
MACS3/Commands/callpeak_cmd.py
MACS3/Commands/callvar_cmd.py
MACS3/Commands/cmbreps_cmd.py
MACS3/Commands/filterdup_cmd.py
MACS3/Commands/hmmratac_cmd.py
MACS3/Commands/pileup_cmd.py
MACS3/Commands/predictd_cmd.py
MACS3/Commands/randsample_cmd.py
MACS3/Commands/refinepeak_cmd.py
MACS3/IO/BAM.py
MACS3/IO/BedGraphIO.py
MACS3/IO/OutputWriter.py
MACS3/IO/Parser.py
MACS3/IO/PeakIO.py
MACS3/IO/__init__.py
MACS3/Signal/BedGraph.py
MACS3/Signal/CallPeakUnit.py
MACS3/Signal/FixWidthTrack.py
MACS3/Signal/HMMR_EM.py
MACS3/Signal/HMMR_HMM.py
MACS3/Signal/HMMR_Signal_Processing.py
MACS3/Signal/PairedEndTrack.py
MACS3/Signal/PeakDetect.py
MACS3/Signal/PeakModel.py
MACS3/Signal/PeakVariants.py
MACS3/Signal/Pileup.py
MACS3/Signal/PileupV2.py
MACS3/Signal/PosReadsInfo.py
MACS3/Signal/Prob.py
MACS3/Signal/RACollection.pxd
MACS3/Signal/RACollection.py
MACS3/Signal/ReadAlignment.py
MACS3/Signal/Region.py
MACS3/Signal/ScoreTrack.py
MACS3/Signal/SignalProcessing.py
MACS3/Signal/UnitigRACollection.py
MACS3/Signal/VariantStat.py
MACS3/Signal/__init__.py
MACS3/Signal/cPosValCalculation.c
MACS3/Signal/cPosValCalculation.h
MACS3/Signal/cPosValCalculation.pxd
MACS3/Signal/swalign.c
MACS3/Signal/swalign.h
MACS3/Utilities/Constants.py
MACS3/Utilities/Logger.py
MACS3/Utilities/OptValidator.py
MACS3/Utilities/__init__.py
MACS3/fermi-lite/bfc.c
MACS3/fermi-lite/bseq.c
MACS3/fermi-lite/bubble.c
MACS3/fermi-lite/example.c
MACS3/fermi-lite/fml.h
MACS3/fermi-lite/htab.c
MACS3/fermi-lite/htab.h
MACS3/fermi-lite/internal.h
MACS3/fermi-lite/khash.h
MACS3/fermi-lite/kmer.h
MACS3/fermi-lite/kseq.h
MACS3/fermi-lite/ksort.h
MACS3/fermi-lite/kstring.h
MACS3/fermi-lite/ksw.c
MACS3/fermi-lite/ksw.h
MACS3/fermi-lite/kthread.c
MACS3/fermi-lite/kvec.h
MACS3/fermi-lite/mag.c
MACS3/fermi-lite/mag.h
MACS3/fermi-lite/misc.c
MACS3/fermi-lite/mrope.c
MACS3/fermi-lite/mrope.h
MACS3/fermi-lite/rld0.c
MACS3/fermi-lite/rld0.h
MACS3/fermi-lite/rle.c
MACS3/fermi-lite/rle.h
MACS3/fermi-lite/rope.c
MACS3/fermi-lite/rope.h
MACS3/fermi-lite/unitig.c
bin/macs3
docs/source/CODE_OF_CONDUCT.md
docs/source/CONTRIBUTING.md
docs/source/index.md
docs/source/docs/Advanced_Step-by-step_Peak_Calling.md
docs/source/docs/BED.md
docs/source/docs/BEDPE.md
docs/source/docs/FRAG.md
docs/source/docs/INSTALL.md
docs/source/docs/SAMBAMBAMPE.md
docs/source/docs/bdgbroadcall.md
docs/source/docs/bdgcmp.md
docs/source/docs/bdgdiff.md
docs/source/docs/bdgopt.md
docs/source/docs/bdgpeakcall.md
docs/source/docs/bedGraph.md
docs/source/docs/broadPeak.md
docs/source/docs/callpeak.md
docs/source/docs/callpeakxls.md
docs/source/docs/callvar.md
docs/source/docs/cmbreps.md
docs/source/docs/cutoffanalysis.md
docs/source/docs/fileformats_index.md
docs/source/docs/filterdup.md
docs/source/docs/gappedPeak.md
docs/source/docs/hmmratac.md
docs/source/docs/hmmratacModel.md
docs/source/docs/narrowPeak.md
docs/source/docs/pileup.md
docs/source/docs/predictd.md
docs/source/docs/qa.md
docs/source/docs/randsample.md
docs/source/docs/refinepeak.md
docs/source/docs/subcommands_index.md
docs/source/docs/tutorial.md
docs/source/docs/vcf.md