ChangeLog
LICENSE
MANIFEST.in
README.md
make_docker_base.sh
pyproject.toml
requirements.txt
setup.cfg
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/callvar2_cmd.py
MACS3/Commands/callvar_cmd.py
MACS3/Commands/cmbreps_cmd.py
MACS3/Commands/diffpeak_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.pyx
MACS3/IO/BedGraphIO.pyx
MACS3/IO/GenericAlignmentParser.pyx
MACS3/IO/HMMRStates.pyx
MACS3/IO/OutputWriter.py
MACS3/IO/Parser.pyx
MACS3/IO/PeakIO.pyx
MACS3/IO/__init__.py
MACS3/Signal/BedGraph.pyx
MACS3/Signal/BedGraphV2.pyx
MACS3/Signal/CallPeakUnit.pyx
MACS3/Signal/Clipper.pyx
MACS3/Signal/FixWidthTrack.pyx
MACS3/Signal/HMMR_EM.pyx
MACS3/Signal/HMMR_HMM.pyx
MACS3/Signal/HMMR_Signal_Processing.pyx
MACS3/Signal/PairedEndTrack.pyx
MACS3/Signal/PeakDetect.pyx
MACS3/Signal/PeakModel.pyx
MACS3/Signal/PeakVariants.pyx
MACS3/Signal/Pileup.pyx
MACS3/Signal/PileupV2.pyx
MACS3/Signal/PosReadsInfo.pyx
MACS3/Signal/Prob.pyx
MACS3/Signal/RACollection.pyx
MACS3/Signal/ReadAlignment.pyx
MACS3/Signal/Region.pyx
MACS3/Signal/ScoreTrack.pyx
MACS3/Signal/SignalProcessing.pyx
MACS3/Signal/SimpleData.pyx
MACS3/Signal/UnitigRACollection.pyx
MACS3/Signal/VariantStat.pyx
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/Signal/test.py
MACS3/Utilities/Constants.py
MACS3/Utilities/Logger.py
MACS3/Utilities/Math.pyx
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
MACS3/fermi-lite/lib/check.h
MACS3/fermi-lite/lib/debug-trap.h
MACS3/fermi-lite/lib/hedley.h
MACS3/fermi-lite/lib/simde-align.h
MACS3/fermi-lite/lib/simde-arch.h
MACS3/fermi-lite/lib/simde-common.h
MACS3/fermi-lite/lib/simde-constify.h
MACS3/fermi-lite/lib/simde-detect-clang.h
MACS3/fermi-lite/lib/simde-diagnostic.h
MACS3/fermi-lite/lib/simde-features.h
MACS3/fermi-lite/lib/simde-math.h
MACS3/fermi-lite/lib/arm/neon.h
MACS3/fermi-lite/lib/arm/neon/aba.h
MACS3/fermi-lite/lib/arm/neon/abd.h
MACS3/fermi-lite/lib/arm/neon/abdl.h
MACS3/fermi-lite/lib/arm/neon/abs.h
MACS3/fermi-lite/lib/arm/neon/add.h
MACS3/fermi-lite/lib/arm/neon/addl.h
MACS3/fermi-lite/lib/arm/neon/addl_high.h
MACS3/fermi-lite/lib/arm/neon/addlv.h
MACS3/fermi-lite/lib/arm/neon/addv.h
MACS3/fermi-lite/lib/arm/neon/addw.h
MACS3/fermi-lite/lib/arm/neon/addw_high.h
MACS3/fermi-lite/lib/arm/neon/and.h
MACS3/fermi-lite/lib/arm/neon/bic.h
MACS3/fermi-lite/lib/arm/neon/bsl.h
MACS3/fermi-lite/lib/arm/neon/cagt.h
MACS3/fermi-lite/lib/arm/neon/ceq.h
MACS3/fermi-lite/lib/arm/neon/ceqz.h
MACS3/fermi-lite/lib/arm/neon/cge.h
MACS3/fermi-lite/lib/arm/neon/cgez.h
MACS3/fermi-lite/lib/arm/neon/cgt.h
MACS3/fermi-lite/lib/arm/neon/cgtz.h
MACS3/fermi-lite/lib/arm/neon/cle.h
MACS3/fermi-lite/lib/arm/neon/clez.h
MACS3/fermi-lite/lib/arm/neon/cls.h
MACS3/fermi-lite/lib/arm/neon/clt.h
MACS3/fermi-lite/lib/arm/neon/cltz.h
MACS3/fermi-lite/lib/arm/neon/clz.h
MACS3/fermi-lite/lib/arm/neon/cnt.h
MACS3/fermi-lite/lib/arm/neon/combine.h
MACS3/fermi-lite/lib/arm/neon/create.h
MACS3/fermi-lite/lib/arm/neon/cvt.h
MACS3/fermi-lite/lib/arm/neon/dot.h
MACS3/fermi-lite/lib/arm/neon/dot_lane.h
MACS3/fermi-lite/lib/arm/neon/dup_lane.h
MACS3/fermi-lite/lib/arm/neon/dup_n.h
MACS3/fermi-lite/lib/arm/neon/eor.h
MACS3/fermi-lite/lib/arm/neon/ext.h
MACS3/fermi-lite/lib/arm/neon/get_high.h
MACS3/fermi-lite/lib/arm/neon/get_lane.h
MACS3/fermi-lite/lib/arm/neon/get_low.h
MACS3/fermi-lite/lib/arm/neon/hadd.h
MACS3/fermi-lite/lib/arm/neon/hsub.h
MACS3/fermi-lite/lib/arm/neon/ld1.h
MACS3/fermi-lite/lib/arm/neon/ld3.h
MACS3/fermi-lite/lib/arm/neon/ld4.h
MACS3/fermi-lite/lib/arm/neon/max.h
MACS3/fermi-lite/lib/arm/neon/maxnm.h
MACS3/fermi-lite/lib/arm/neon/maxv.h
MACS3/fermi-lite/lib/arm/neon/min.h
MACS3/fermi-lite/lib/arm/neon/minnm.h
MACS3/fermi-lite/lib/arm/neon/minv.h
MACS3/fermi-lite/lib/arm/neon/mla.h
MACS3/fermi-lite/lib/arm/neon/mla_n.h
MACS3/fermi-lite/lib/arm/neon/mlal.h
MACS3/fermi-lite/lib/arm/neon/mlal_high.h
MACS3/fermi-lite/lib/arm/neon/mlal_n.h
MACS3/fermi-lite/lib/arm/neon/mls.h
MACS3/fermi-lite/lib/arm/neon/mlsl.h
MACS3/fermi-lite/lib/arm/neon/mlsl_high.h
MACS3/fermi-lite/lib/arm/neon/mlsl_n.h
MACS3/fermi-lite/lib/arm/neon/movl.h
MACS3/fermi-lite/lib/arm/neon/movl_high.h
MACS3/fermi-lite/lib/arm/neon/movn.h
MACS3/fermi-lite/lib/arm/neon/movn_high.h
MACS3/fermi-lite/lib/arm/neon/mul.h
MACS3/fermi-lite/lib/arm/neon/mul_lane.h
MACS3/fermi-lite/lib/arm/neon/mul_n.h
MACS3/fermi-lite/lib/arm/neon/mull.h
MACS3/fermi-lite/lib/arm/neon/mull_high.h
MACS3/fermi-lite/lib/arm/neon/mull_n.h
MACS3/fermi-lite/lib/arm/neon/mvn.h
MACS3/fermi-lite/lib/arm/neon/neg.h
MACS3/fermi-lite/lib/arm/neon/orn.h
MACS3/fermi-lite/lib/arm/neon/orr.h
MACS3/fermi-lite/lib/arm/neon/padal.h
MACS3/fermi-lite/lib/arm/neon/padd.h
MACS3/fermi-lite/lib/arm/neon/paddl.h
MACS3/fermi-lite/lib/arm/neon/pmax.h
MACS3/fermi-lite/lib/arm/neon/pmin.h
MACS3/fermi-lite/lib/arm/neon/qabs.h
MACS3/fermi-lite/lib/arm/neon/qadd.h
MACS3/fermi-lite/lib/arm/neon/qdmulh.h
MACS3/fermi-lite/lib/arm/neon/qdmull.h
MACS3/fermi-lite/lib/arm/neon/qmovn.h
MACS3/fermi-lite/lib/arm/neon/qmovn_high.h
MACS3/fermi-lite/lib/arm/neon/qmovun.h
MACS3/fermi-lite/lib/arm/neon/qneg.h
MACS3/fermi-lite/lib/arm/neon/qrdmulh.h
MACS3/fermi-lite/lib/arm/neon/qrdmulh_n.h
MACS3/fermi-lite/lib/arm/neon/qshl.h
MACS3/fermi-lite/lib/arm/neon/qsub.h
MACS3/fermi-lite/lib/arm/neon/qtbl.h
MACS3/fermi-lite/lib/arm/neon/qtbx.h
MACS3/fermi-lite/lib/arm/neon/rbit.h
MACS3/fermi-lite/lib/arm/neon/reinterpret.h
MACS3/fermi-lite/lib/arm/neon/rev16.h
MACS3/fermi-lite/lib/arm/neon/rev32.h
MACS3/fermi-lite/lib/arm/neon/rev64.h
MACS3/fermi-lite/lib/arm/neon/rhadd.h
MACS3/fermi-lite/lib/arm/neon/rnd.h
MACS3/fermi-lite/lib/arm/neon/rshl.h
MACS3/fermi-lite/lib/arm/neon/rshr_n.h
MACS3/fermi-lite/lib/arm/neon/rsra_n.h
MACS3/fermi-lite/lib/arm/neon/set_lane.h
MACS3/fermi-lite/lib/arm/neon/shl.h
MACS3/fermi-lite/lib/arm/neon/shl_n.h
MACS3/fermi-lite/lib/arm/neon/shr_n.h
MACS3/fermi-lite/lib/arm/neon/sra_n.h
MACS3/fermi-lite/lib/arm/neon/st1.h
MACS3/fermi-lite/lib/arm/neon/st1_lane.h
MACS3/fermi-lite/lib/arm/neon/st3.h
MACS3/fermi-lite/lib/arm/neon/st4.h
MACS3/fermi-lite/lib/arm/neon/sub.h
MACS3/fermi-lite/lib/arm/neon/subl.h
MACS3/fermi-lite/lib/arm/neon/subw.h
MACS3/fermi-lite/lib/arm/neon/subw_high.h
MACS3/fermi-lite/lib/arm/neon/tbl.h
MACS3/fermi-lite/lib/arm/neon/tbx.h
MACS3/fermi-lite/lib/arm/neon/trn.h
MACS3/fermi-lite/lib/arm/neon/trn1.h
MACS3/fermi-lite/lib/arm/neon/trn2.h
MACS3/fermi-lite/lib/arm/neon/tst.h
MACS3/fermi-lite/lib/arm/neon/types.h
MACS3/fermi-lite/lib/arm/neon/uqadd.h
MACS3/fermi-lite/lib/arm/neon/uzp.h
MACS3/fermi-lite/lib/arm/neon/uzp1.h
MACS3/fermi-lite/lib/arm/neon/uzp2.h
MACS3/fermi-lite/lib/arm/neon/zip.h
MACS3/fermi-lite/lib/arm/neon/zip1.h
MACS3/fermi-lite/lib/arm/neon/zip2.h
MACS3/fermi-lite/lib/x86/avx.h
MACS3/fermi-lite/lib/x86/avx2.h
MACS3/fermi-lite/lib/x86/avx512.h
MACS3/fermi-lite/lib/x86/clmul.h
MACS3/fermi-lite/lib/x86/fma.h
MACS3/fermi-lite/lib/x86/gfni.h
MACS3/fermi-lite/lib/x86/mmx.h
MACS3/fermi-lite/lib/x86/sse.h
MACS3/fermi-lite/lib/x86/sse2.h
MACS3/fermi-lite/lib/x86/sse3.h
MACS3/fermi-lite/lib/x86/sse4.1.h
MACS3/fermi-lite/lib/x86/sse4.2.h
MACS3/fermi-lite/lib/x86/ssse3.h
MACS3/fermi-lite/lib/x86/svml.h
MACS3/fermi-lite/lib/x86/avx512/2intersect.h
MACS3/fermi-lite/lib/x86/avx512/abs.h
MACS3/fermi-lite/lib/x86/avx512/add.h
MACS3/fermi-lite/lib/x86/avx512/adds.h
MACS3/fermi-lite/lib/x86/avx512/and.h
MACS3/fermi-lite/lib/x86/avx512/andnot.h
MACS3/fermi-lite/lib/x86/avx512/avg.h
MACS3/fermi-lite/lib/x86/avx512/blend.h
MACS3/fermi-lite/lib/x86/avx512/broadcast.h
MACS3/fermi-lite/lib/x86/avx512/cast.h
MACS3/fermi-lite/lib/x86/avx512/cmp.h
MACS3/fermi-lite/lib/x86/avx512/cmpeq.h
MACS3/fermi-lite/lib/x86/avx512/cmpge.h
MACS3/fermi-lite/lib/x86/avx512/cmpgt.h
MACS3/fermi-lite/lib/x86/avx512/cmple.h
MACS3/fermi-lite/lib/x86/avx512/cmplt.h
MACS3/fermi-lite/lib/x86/avx512/copysign.h
MACS3/fermi-lite/lib/x86/avx512/cvt.h
MACS3/fermi-lite/lib/x86/avx512/cvts.h
MACS3/fermi-lite/lib/x86/avx512/div.h
MACS3/fermi-lite/lib/x86/avx512/extract.h
MACS3/fermi-lite/lib/x86/avx512/fmadd.h
MACS3/fermi-lite/lib/x86/avx512/fmsub.h
MACS3/fermi-lite/lib/x86/avx512/fnmadd.h
MACS3/fermi-lite/lib/x86/avx512/fnmsub.h
MACS3/fermi-lite/lib/x86/avx512/insert.h
MACS3/fermi-lite/lib/x86/avx512/kshift.h
MACS3/fermi-lite/lib/x86/avx512/load.h
MACS3/fermi-lite/lib/x86/avx512/loadu.h
MACS3/fermi-lite/lib/x86/avx512/lzcnt.h
MACS3/fermi-lite/lib/x86/avx512/madd.h
MACS3/fermi-lite/lib/x86/avx512/maddubs.h
MACS3/fermi-lite/lib/x86/avx512/max.h
MACS3/fermi-lite/lib/x86/avx512/min.h
MACS3/fermi-lite/lib/x86/avx512/mov.h
MACS3/fermi-lite/lib/x86/avx512/mov_mask.h
MACS3/fermi-lite/lib/x86/avx512/movm.h
MACS3/fermi-lite/lib/x86/avx512/mul.h
MACS3/fermi-lite/lib/x86/avx512/mulhi.h
MACS3/fermi-lite/lib/x86/avx512/mulhrs.h
MACS3/fermi-lite/lib/x86/avx512/mullo.h
MACS3/fermi-lite/lib/x86/avx512/negate.h
MACS3/fermi-lite/lib/x86/avx512/or.h
MACS3/fermi-lite/lib/x86/avx512/packs.h
MACS3/fermi-lite/lib/x86/avx512/packus.h
MACS3/fermi-lite/lib/x86/avx512/permutex2var.h
MACS3/fermi-lite/lib/x86/avx512/permutexvar.h
MACS3/fermi-lite/lib/x86/avx512/sad.h
MACS3/fermi-lite/lib/x86/avx512/set.h
MACS3/fermi-lite/lib/x86/avx512/set1.h
MACS3/fermi-lite/lib/x86/avx512/set4.h
MACS3/fermi-lite/lib/x86/avx512/setone.h
MACS3/fermi-lite/lib/x86/avx512/setr.h
MACS3/fermi-lite/lib/x86/avx512/setr4.h
MACS3/fermi-lite/lib/x86/avx512/setzero.h
MACS3/fermi-lite/lib/x86/avx512/shuffle.h
MACS3/fermi-lite/lib/x86/avx512/sll.h
MACS3/fermi-lite/lib/x86/avx512/slli.h
MACS3/fermi-lite/lib/x86/avx512/sllv.h
MACS3/fermi-lite/lib/x86/avx512/sqrt.h
MACS3/fermi-lite/lib/x86/avx512/sra.h
MACS3/fermi-lite/lib/x86/avx512/srai.h
MACS3/fermi-lite/lib/x86/avx512/srav.h
MACS3/fermi-lite/lib/x86/avx512/srl.h
MACS3/fermi-lite/lib/x86/avx512/srli.h
MACS3/fermi-lite/lib/x86/avx512/srlv.h
MACS3/fermi-lite/lib/x86/avx512/store.h
MACS3/fermi-lite/lib/x86/avx512/storeu.h
MACS3/fermi-lite/lib/x86/avx512/sub.h
MACS3/fermi-lite/lib/x86/avx512/subs.h
MACS3/fermi-lite/lib/x86/avx512/test.h
MACS3/fermi-lite/lib/x86/avx512/types.h
MACS3/fermi-lite/lib/x86/avx512/unpackhi.h
MACS3/fermi-lite/lib/x86/avx512/unpacklo.h
MACS3/fermi-lite/lib/x86/avx512/xor.h
MACS3/fermi-lite/lib/x86/avx512/xorsign.h
bin/macs3
docs/Advanced_Step-by-step_Peak_Calling.md
docs/INSTALL.md
docs/bdgbroadcall.md
docs/bdgcmp.md
docs/bdgdiff.md
docs/bdgopt.md
docs/bdgpeakcall.md
docs/callpeak.md
docs/callvar.md
docs/cmbreps.md
docs/filterdup.md
docs/hmmratac.md
docs/pileup.md
docs/predictd.md
docs/qa.md
docs/randsample.md
docs/refinepeak.md
docs/testing_in_docker.md
docs/tutorial.md