Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
Centromere		Centromere
DotPlots		DotPlots
DrawRegion		DrawRegion
Genotyping		Genotyping
HardStop		HardStop
InvDup		InvDup
Inversions		Inversions
PatchedGenome		PatchedGenome
RepeatMasking		RepeatMasking
RepliSeq		RepliSeq
STR		STR
chip-seq		chip-seq
coverage		coverage
cut		cut
falcon		falcon
one_off		one_off
3		3
Align.py		Align.py
Align.sh		Align.sh
AlignConsensus.py		AlignConsensus.py
AlignmentReaders.py		AlignmentReaders.py
AnnotateAlignments.mak		AnnotateAlignments.mak
AnnotateAlignments.sh		AnnotateAlignments.sh
AnnotateGapBed.mak		AnnotateGapBed.mak
AnnotateGapBed.py		AnnotateGapBed.py
AnnotateGapBedWithCensorMap.py		AnnotateGapBedWithCensorMap.py
AnnotateRepeatUnits.py		AnnotateRepeatUnits.py
AnnotateWithTRF.py		AnnotateWithTRF.py
AnnotationPipeline.mak		AnnotationPipeline.mak
AssembleRegion.sh		AssembleRegion.sh
AssembleRegionFromBAMs.sh		AssembleRegionFromBAMs.sh
AssembleRegions.mak		AssembleRegions.mak
AssembleRegions.sh		AssembleRegions.sh
BedIntervalsToDepth.py		BedIntervalsToDepth.py
BedMerge.py		BedMerge.py
BedMod.py		BedMod.py
BedToRegion.py		BedToRegion.py
BinBPCoords.py		BinBPCoords.py
BinDepth.py		BinDepth.py
BinRegions.cpp		BinRegions.cpp
BlasrSelfAlign.py		BlasrSelfAlign.py
BlasrSelfAlign.sh		BlasrSelfAlign.sh
BreakpointCluster.py		BreakpointCluster.py
BuildConsensus.mak		BuildConsensus.mak
CatSeq.sh		CatSeq.sh
CheckInvTests.py		CheckInvTests.py
ClassifyRepeats.py		ClassifyRepeats.py
ClusterSplitReads.py		ClusterSplitReads.py
ComputeCloneSize.py		ComputeCloneSize.py
CountEvents.py		CountEvents.py
CountRepeatComposition.cpp		CountRepeatComposition.cpp
CountRepeatUnits.py		CountRepeatUnits.py
CountRestrictionSites.py		CountRestrictionSites.py
DetectInversions.mak		DetectInversions.mak
DetectInversions.py		DetectInversions.py
Directory.txt		Directory.txt
DotPlot.py		DotPlot.py
DotPlot.py.bak		DotPlot.py.bak
DotplotRegion.py		DotplotRegion.py
DrawGenotype.R		DrawGenotype.R
ExtractSamSubalignment.py		ExtractSamSubalignment.py
ExtractSeq.py		ExtractSeq.py
FaidxPrep.py		FaidxPrep.py
FastBPCluster.py		FastBPCluster.py
FastBreakpointCluster.py		FastBreakpointCluster.py
FastaToFakeFastq.py		FastaToFakeFastq.py
FastqToSam.py		FastqToSam.py
FilterEventListByAssembledTarget.py		FilterEventListByAssembledTarget.py
FilterGapBedByMaskingContent.py		FilterGapBedByMaskingContent.py
FilterGaps.py		FilterGaps.py
FilterHPGaps.py		FilterHPGaps.py
FilterLowComplexity.cpp		FilterLowComplexity.cpp
FilterScreen.py		FilterScreen.py
FilterSeq.py		FilterSeq.py
FilterSupport.py		FilterSupport.py
FilterUniqueReads.py		FilterUniqueReads.py
FindBasFiles.py		FindBasFiles.py
FindJoined.py		FindJoined.py
FindL1NearAlignments.py		FindL1NearAlignments.py
FindL1NearHardStops.py		FindL1NearHardStops.py
FindPairedSupport.py		FindPairedSupport.py
FindUnique.cpp		FindUnique.cpp
FixCoordinates.py		FixCoordinates.py
FullSamToBed.py		FullSamToBed.py
GC_content_explore.py		GC_content_explore.py
GFFToBed.py		GFFToBed.py
GapBedToFasta.py		GapBedToFasta.py
GapSupportToFasta.py		GapSupportToFasta.py
GetNullDist.sh		GetNullDist.sh
GetRandomDist.sh		GetRandomDist.sh
GetReadsInRegion.sh		GetReadsInRegion.sh
GetRegionFromBed.py		GetRegionFromBed.py
GuaranteeUnique.cpp		GuaranteeUnique.cpp
Ideoplot.R		Ideoplot.R
InSilicoDigest.py		InSilicoDigest.py
InsertionBedToConsensus.py		InsertionBedToConsensus.py
LICENSE		LICENSE
M4Reader.py		M4Reader.py
MakeNameQuery.py		MakeNameQuery.py
Makefile		Makefile

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