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38 Commits
Makefile
Makefile
 
 
README
README
 
 
addFFtomakeUdosDamagePatternHappy.cpp
addFFtomakeUdosDamagePatternHappy.cpp
 
 
addRG.cpp
addRG.cpp
 
 
addRGInReadAndHeader.cpp
addRGInReadAndHeader.cpp
 
 
addRG_CTEAM.cpp
addRG_CTEAM.cpp
 
 
addRGinHeaderHack.cpp
addRGinHeaderHack.cpp
 
 
allFailqc.cpp
allFailqc.cpp
 
 
allNoDUPRM.cpp
allNoDUPRM.cpp
 
 
allPassqc.cpp
allPassqc.cpp
 
 
bamCat.cpp
bamCat.cpp
 
 
baseQualScorePerCycle.cpp
baseQualScorePerCycle.cpp
 
 
compareRG.cpp
compareRG.cpp
 
 
crossSampleStat.cpp
crossSampleStat.cpp
 
 
cutDeaminated.cpp
cutDeaminated.cpp
 
 
cutEndKeepBeginning.cpp
cutEndKeepBeginning.cpp
 
 
cutReadsDistribution.cpp
cutReadsDistribution.cpp
 
 
cutStart.cpp
cutStart.cpp
 
 
cutUMI.cpp
cutUMI.cpp
 
 
decrQualDeaminated.cpp
decrQualDeaminated.cpp
 
 
decrQualDeaminatedDoubleStranded.cpp
decrQualDeaminatedDoubleStranded.cpp
 
 
decrQualNs.cpp
decrQualNs.cpp
 
 
detectUMIvarLength.cpp
detectUMIvarLength.cpp
 
 
dumpLoneMates.cpp
dumpLoneMates.cpp
 
 
editDist.cpp
editDist.cpp
 
 
errorQCScores.cpp
errorQCScores.cpp
 
 
errorRate.cpp
errorRate.cpp
 
 
failQualPair.cpp
failQualPair.cpp
 
 
filterDeaminated.cpp
filterDeaminated.cpp
 
 
filterDeaminatedDouble.cpp
filterDeaminatedDouble.cpp
 
 
filterDeaminatedFasta.cpp
filterDeaminatedFasta.cpp
 
 
filterDeaminatedVCF.cpp
filterDeaminatedVCF.cpp
 
 
filterDeaminatedVCFpreload.cpp
filterDeaminatedVCFpreload.cpp
 
 
filterDeaminatedVCFpreload1000g.cpp
filterDeaminatedVCFpreload1000g.cpp
 
 
filterDeaminatedpreload1000g.cpp
filterDeaminatedpreload1000g.cpp
 
 
filterEditDist.cpp
filterEditDist.cpp
 
 
filterHighEditDistance.cpp
filterHighEditDistance.cpp
 
 
filterNoNonDNAbase.cpp
filterNoNonDNAbase.cpp
 
 
filterOnlyThoseWithRG.cpp
filterOnlyThoseWithRG.cpp
 
 
fixMates.cpp
fixMates.cpp
 
 
insertSize.cpp
insertSize.cpp
 
 
readWhereEitherIsMapped.cpp
readWhereEitherIsMapped.cpp
 
 
removeIndices.cpp
removeIndices.cpp
 
 
removeRG.cpp
removeRG.cpp
 
 
removeTagsMapping.cpp
removeTagsMapping.cpp
 
 
removeThoseWithoutMD.cpp
removeThoseWithoutMD.cpp
 
 
removeUnalignedANDWrongCigar.cpp
removeUnalignedANDWrongCigar.cpp
 
 
replaceRG.cpp
replaceRG.cpp
 
 
retrieveMappedCertainIsize.cpp
retrieveMappedCertainIsize.cpp
 
 
retrieveMapped_single_and_ProperlyPair.cpp
retrieveMapped_single_and_ProperlyPair.cpp
 
 
retrieveMapped_single_and_ProperlyPair_NoPCR.cpp
retrieveMapped_single_and_ProperlyPair_NoPCR.cpp
 
 
retrieveRG.cpp
retrieveRG.cpp
 
 
retrieveReadsWithName.cpp
retrieveReadsWithName.cpp
 
 
setAsUnpaired.cpp
setAsUnpaired.cpp
 
 
singleAndFirstMate.cpp
singleAndFirstMate.cpp
 
 
splitByChr.cpp
splitByChr.cpp
 
 
splitByRG.cpp
splitByRG.cpp
 
 
subSampleBAM.cpp
subSampleBAM.cpp
 
 
subsamplebamFixedNumber.cpp
subsamplebamFixedNumber.cpp
 
 
subsamplebamFixedNumberCollate.cpp
subsamplebamFixedNumberCollate.cpp
 
 
subsamplebamFixedNumberPair.cpp
subsamplebamFixedNumberPair.cpp
 
 
subsamplebamFixedNumberSingleFirstMate.cpp
subsamplebamFixedNumberSingleFirstMate.cpp
 
 
sumBases.cpp
sumBases.cpp
 
 
tallyByRG.cpp
tallyByRG.cpp
 
 
transBAM.cpp
transBAM.cpp
 
 
transBAMperRead.cpp
transBAMperRead.cpp
 
 

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Various programs I wrote with bamtools.

Gabriel Renaud gabriel.reno [at sign here ] gmail.com

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Library of various programs based on bamtools

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