rbamtools-package	rbamtools-package
addReadGroup	headerReadGroup-class
addReadGroup,headerReadGroup-method	headerReadGroup-class
addReadGroup-methods	headerReadGroup-class
addSeq	refSeqDict-class
addSeq,refSeqDict-method	refSeqDict-class
aldRatio	exonAlignDepth-class
aldRatio,exonAlignDepth-method	exonAlignDepth-class
aldRatio-methods	exonAlignDepth-class
alignDepth	alignDepth-class
alignDepth,bamRange-method	alignDepth-class
alignDepth-class	alignDepth-class
alignDepth-methods	alignDepth-class
alignQual	bamAlign-class
alignQual,bamAlign-method	bamAlign-class
alignQual-methods	bamAlign-class
alignQualVal	bamAlign-class
alignQualVal,bamAlign-method	bamAlign-class
alignQualVal-methods	bamAlign-class
alignSeq	bamAlign-class
alignSeq,bamAlign-method	bamAlign-class
alignSeq-methods	bamAlign-class
as.character	bamHeader-class
as.character,bamHeader-method	bamHeader-class
as.data.frame,refSeqDict-method	refSeqDict-class
as.data.frame-methods	as.data.frame-methods
as.data.frame.bamGapList	bamGapList-class
as.data.frame.bamRange	bamRange-class
as.data.frame.gapList	gapList-class
as.data.frame.gapSiteList	gapSiteList-class
as.data.frame.rangeSegCount	rangeSegCount-class
as.data.frame.refSeqDict	refSeqDict-class
as.list,headerLine-method	headerLine-class
as.list,headerProgram-method	headerProgram-class
as.list,headerReadGroup-method	headerReadGroup-class
bamAlign	bamAlign
bamAlign-class	bamAlign-class
bamClose	bamClose-methods
bamClose,bamReader-method	bamReader-class
bamClose,bamWriter-method	bamWriter-class
bamClose-methods	bamClose-methods
bamCopy	bamReader-class
bamCopy,bamReader,bamWriter-method	bamReader-class
bamCopy-methods	bamReader-class
bamCount	bamCount
bamCount,bamReader-method	bamCount
bamCount-methods	bamCount
bamCountAll	bamCountAll
bamCountAll,bamReader,ANY-method	bamCountAll
bamCountAll,sampleBamFiles,logical-method	sampleBamFiles-class
bamCountAll,sampleBamFiles,missing-method	sampleBamFiles-class
bamCountAll-methods	bamCountAll
bamFiles	sampleBamFiles-class
bamFiles,sampleBamFiles-method	sampleBamFiles-class
bamFiles-methods	sampleBamFiles-class
bamFiles<-	sampleBamFiles-class
bamFiles<-,sampleBamFiles,character,logical-method	sampleBamFiles-class
bamFiles<-,sampleBamFiles,character-method	sampleBamFiles-class
bamFiles<--methods	sampleBamFiles-class
bamGapList	bamGapList-class
bamGapList,bamReader-method	bamGapList-class
bamGapList-class	bamGapList-class
bamGapList-methods	bamGapList-class
bamHeader	bamHeader-class
bamHeader,bamHeaderText-method	bamHeaderText-class
bamHeader-class	bamHeader-class
bamHeaderText	bamHeaderText-class
bamHeaderText-class	bamHeaderText-class
bamIdxFiles	sampleBamFiles-class
bamIdxFiles,sampleBamFiles-method	sampleBamFiles-class
bamIdxFiles-methods	sampleBamFiles-class
bamIdxFiles<-	sampleBamFiles-class
bamIdxFiles<-,sampleBamFiles,character-method	sampleBamFiles-class
bamIdxFiles<--methods	sampleBamFiles-class
bamRange	bamRange
bamRange-class	bamRange-class
bamReader	bamReader
bamReader-class	bamReader-class
bamSave	bamSave
bamSave,bamReader,ANY,ANY-method	bamSave
bamSave,bamReader,bamWriter,missing-method	bamSave
bamSave,bamWriter,bamAlign,numeric-method	bamSave
bamSave,bamWriter,bamRange,character-method	bamSave
bamSave,bamWriter,bamRange,missing-method	bamSave
bamSave,bamWriter,bamRange,numeric-method	bamSave
bamSave,bamWriter-method	bamWriter-class
bamSave-methods	bamSave
bamSort	bamSort
bamSort,bamReader,ANY,ANY,ANY-method	bamSort
bamSort,bamReader-method	bamReader-class
bamSort,sampleBamFiles,ANY,ANY,ANY-method	bamSort
bamSort,sampleBamFiles-method	bamSort
bamSort-methods	bamSort
bamWriter	bamWriter
bamWriter,bamHeader-method	bamHeader-class
bamWriter-class	bamWriter-class
checkBamFiles	sampleBamFiles-class
checkBamFiles,sampleBamFiles-method	sampleBamFiles-class
checkBamFiles-methods	sampleBamFiles-class
checkPartition	GenomePartition-class
checkPartition,GenomePartition,data.frame-method	GenomePartition-class
checkPartition-methods	GenomePartition-class
cigarData	bamAlign-class
cigarData,bamAlign-method	bamAlign-class
cigarData-methods	bamAlign-class
coerce, rangeSegCount, data.frame-method	rangeSegCount-class
coerce,bamGapList,data.frame-method	bamGapList-class
coerce,bamRange,data.frame-method	bamRange-class
coerce,gapList,data.frame-method	gapList-class
coerce,gapSiteList,data.frame-method	gapSiteList-class
coerce,refSeqDict,data.frame-method	refSeqDict-class
countNucs	countNucs
countNucs,bamAlign-method	countNucs
countNucs,bamRange-method	countNucs
countNucs-methods	countNucs
countPartition	GenomePartition-class
countPartition,GenomePartition,bamReader-method	GenomePartition-class
countPartition,GenomePartition,data.frame-method	GenomePartition-class
countPartition-methods	GenomePartition-class
countTextLines	countTextLines
createIdxBatch	createIdxBatch
createIndex	bamReader-class
createIndex,bamReader,character-method	bamReader-class
createIndex,bamReader,missing-method	bamReader-class
createIndex,sampleBamFiles,character-method	sampleBamFiles-class
createIndex,sampleBamFiles,missing-method	sampleBamFiles-class
createIndex-methods	bamReader-class
cutFlatAlignDepth	exonAlignDepth-class
cutFlatAlignDepth,exonAlignDepth-method	exonAlignDepth-class
cutFlatAlignDepth,exonLoessModel-method	exonLoessModel-class
cutFlatAlignDepth-methods	exonAlignDepth-class
dim,refSeqDict-method	refSeqDict-class
exonAlignDepth	exonAlignDepth-class
exonAlignDepth,geneAlignDepth-method	exonAlignDepth-class
exonAlignDepth-class	exonAlignDepth-class
exonAlignDepth-methods	exonAlignDepth-class
exonLoessModel	exonLoessModel-class
exonLoessModel,exonAlignDepth-method	exonLoessModel-class
exonLoessModel-class	exonLoessModel-class
exonLoessModel-methods	exonLoessModel-class
extractBamRegions	extractBamRegions
extractGeneRegions	extractGeneRegions
extractGeneRegions,bamReader,bamWriter,geneList-method	extractGeneRegions
extractGeneRegions,bamReader,character,geneList-method	extractGeneRegions
extractGeneRegions,sampleBamFiles,sampleBamFiles,geneList-method	extractGeneRegions
extractGeneRegions-methods	extractGeneRegions
extractRanges	extractRanges
extractRanges,bamReader-method	extractRanges
extractRanges-methods	extractRanges
failedQC	bamAlign-class
failedQC,bamAlign-method	bamAlign-class
failedQC-methods	bamAlign-class
failedQC<-	bamAlign-class
failedQC<-,bamAlign-method	bamAlign-class
failedQC<--methods	bamAlign-class
filename	filename-methods
filename,bamReader-method	bamReader-class
filename,bamWriter-method	bamWriter-class
filename-methods	filename-methods
firstInPair	bamAlign-class
firstInPair,bamAlign-method	bamAlign-class
firstInPair-methods	bamAlign-class
firstInPair<-	bamAlign-class
firstInPair<-,bamAlign-method	bamAlign-class
firstInPair<--methods	bamAlign-class
flag	bamAlign-class
flag,bamAlign-method	bamAlign-class
flag-methods	bamAlign-class
flag<-	bamAlign-class
flag<-,bamAlign-method	bamAlign-class
flag<--methods	bamAlign-class
gapList	gapList-class
gapList,bamReader,numeric-method	gapList-class
gapList-class	gapList-class
gapSiteList-class	gapSiteList-class
geneAlignDepth	geneAlignDepth-class
geneAlignDepth,sampleBamFiles,geneModel-method	geneAlignDepth-class
geneAlignDepth-class	geneAlignDepth-class
geneAlignDepth-methods	geneAlignDepth-class
genomePartition	GenomePartition-class
genomePartition,bamReader,data.frame-method	GenomePartition-class
GenomePartition-class	GenomePartition-class
genomePartition-methods	GenomePartition-class
getAlignCounts	GenomePartition-class
getAlignCounts,GenomePartition-method	GenomePartition-class
getAlignCounts-methods	GenomePartition-class
getAlignRange	bamRange-class
getAlignRange,bamRange-method	bamRange-class
getAlignRange-methods	bamRange-class
getCoords	bamRange-class
getCoords,bamRange-method	bamRange-class
getCoords-methods	bamRange-class
getDepth	alignDepth-class
getDepth,alignDepth-method	alignDepth-class
getDepth-methods	alignDepth-class
getFileTable	GenomePartition-class
getFileTable,GenomePartition-method	GenomePartition-class
getFileTable-methods	GenomePartition-class
getGridAlignCounts	GenomePartition-class
getGridAlignCounts,GenomePartition-method	GenomePartition-class
getGridAlignCounts-methods	GenomePartition-class
getHeader	bamHeaderText-class
getHeader,bamHeaderText-method	bamHeaderText-class
getHeader,bamReader-method	bamReader-class
getHeaderText	getHeaderText-methods
getHeaderText,bamHeader-method	bamHeader-class
getHeaderText,bamHeaderText-method	bamHeaderText-class
getHeaderText,bamReader-method	bamReader-class
getHeaderText,headerLine-method	headerLine-class
getHeaderText,headerProgram-method	headerProgram-class
getHeaderText,headerReadGroup-method	headerReadGroup-class
getHeaderText,refSeqDict-method	refSeqDict-class
getHeaderText-methods	getHeaderText-methods
getNextAlign	getNextAlign-methods
getNextAlign,bamRange-method	bamRange-class
getNextAlign,bamReader-method	bamReader-class
getNextAlign-methods	getNextAlign-methods
getNormFactor	exonAlignDepth-class
getNormFactor,exonAlignDepth-method	exonAlignDepth-class
getNormFactor-methods	exonAlignDepth-class
getParams	bamRange-class
getParams,alignDepth-method	alignDepth-class
getParams,bamRange-method	bamRange-class
getParams-methods	bamRange-class
getPos	alignDepth-class
getPos,alignDepth-method	alignDepth-class
getPos-methods	alignDepth-class
getPrevAlign	bamRange-class
getPrevAlign,bamRange-method	bamRange-class
getPrevAlign-methods	bamRange-class
getQualDf	getQualDf
getQualDf,bamRange,logical-method	getQualDf
getQualDf,bamRange,missing-method	getQualDf
getQualDf-methods	getQualDf
getQualQuantiles	getQualDf
getQualQuantiles,bamRange,numeric-method	getQualDf
getQualQuantiles-methods	getQualDf
getRefCoords	getRefData
getRefCoords,bamReader,character-method	getRefData
getRefCoords,bamReader,factor-method	getRefData
getRefCoords-methods	getRefData
getRefCount	getRefData
getRefCount,bamReader-method	getRefData
getRefCount-methods	getRefData
getRefData	getRefData
getRefData,bamReader-method	getRefData
getRefData,bamWriter-method	getRefData
getRefData,GenomePartition-method	GenomePartition-class
getRefData-methods	getRefData
getRefId	getRefData
getRefId,bamReader,character-method	getRefData
getRefId,bamReader,factor-method	getRefData
getRefId,bamWriter,character-method	getRefData
getRefId,bamWriter,factor-method	getRefData
getRefId-methods	getRefData
getRefName	bamRange-class
getRefName,bamRange-method	bamRange-class
getRefName-methods	bamRange-class
getSeqLen	bamRange-class
getSeqLen,bamRange-method	bamRange-class
getSeqLen-methods	bamRange-class
getSeqNr	GenomePartition-class
getSeqNr,GenomePartition-method	GenomePartition-class
getSeqNr-methods	GenomePartition-class
getVal	getVal
getVal,headerLine-method	headerLine-class
getVal,headerProgram-method	headerProgram-class
getVal,headerReadGroup-method	headerReadGroup-class
groupAldMatrix	exonAlignDepth-class
groupAldMatrix,exonAlignDepth-method	exonAlignDepth-class
groupAldMatrix-methods	exonAlignDepth-class
groupAldTable	exonAlignDepth-class
groupAldTable,exonAlignDepth-method	exonAlignDepth-class
groupAldTable-methods	exonAlignDepth-class
groupRatio	groupRatio
groupRatio,exonLoessModel-method	groupRatio
groupRatio-methods	groupRatio
groupTable	sampleBamFiles-class
groupTable,sampleBamFiles-method	sampleBamFiles-class
groupTable-methods	sampleBamFiles-class
groupTable<-	sampleBamFiles-class
groupTable<-,sampleBamFiles,character-method	sampleBamFiles-class
groupTable<-,sampleBamFiles,data.frame-method	sampleBamFiles-class
groupTable<--methods	sampleBamFiles-class
head	refSeqDict-class
head,refSeqDict-method	refSeqDict-class
headerLine	bamHeaderText-class
headerLine,bamHeaderText-method	bamHeaderText-class
headerLine-class	headerLine-class
headerLine<-	bamHeaderText-class
headerLine<-,bamHeaderText-method	bamHeaderText-class
headerProgram	bamHeaderText-class
headerProgram,bamHeaderText-method	bamHeaderText-class
headerProgram-class	headerProgram-class
headerProgram<-	bamHeaderText-class
headerProgram<-,bamHeaderText-method	bamHeaderText-class
headerReadGroup	bamHeaderText-class
headerReadGroup,bamHeaderText-method	bamHeaderText-class
headerReadGroup-class	headerReadGroup-class
headerReadGroup<-	bamHeaderText-class
headerReadGroup<-,bamHeaderText-method	bamHeaderText-class
indexInitialized	bamReader-class
indexInitialized,bamReader-method	bamReader-class
indexInitialized-methods	bamReader-class
initialize, exonAlignDepth	exonAlignDepth-class
initialize, exonLoessModel	exonLoessModel-class
initialize, geneAlignDepth	geneAlignDepth-class
initialize, rangeSegCount-method	rangeSegCount-class
initialize, sampleBamFiles	sampleBamFiles-class
initialize,bamAlign-method	bamAlign-class
initialize,bamGapList-method	bamGapList-class
initialize,bamHeader-method	bamHeader-class
initialize,bamHeaderText-method	bamHeaderText-class
initialize,bamRange-method	bamRange-class
initialize,bamWriter-method	bamWriter-class
initialize,gapList-method	gapList-class
initialize,gapSiteList-method	gapSiteList-class
initialize,headerLine-method	headerLine-class
initialize,headerProgram-method	headerProgram-class
initialize,headerReadGroup-method	headerReadGroup-class
initialize,refSeqDict-method	refSeqDict-class
insertPastCurrent	bamRange-class
insertPastCurrent,bamRange-method	bamRange-class
insertPastCurrent-methods	bamRange-class
insertPreCurrent	bamRange-class
insertPreCurrent,bamRange-method	bamRange-class
insertPreCurrent-methods	bamRange-class
insertSize	bamAlign-class
insertSize,bamAlign-method	bamAlign-class
insertSize-methods	bamAlign-class
isOpen	isOpen-methods
isOpen,bamReader-method	bamReader-class
isOpen,bamWriter-method	bamWriter-class
isOpen-methods	isOpen-methods
junctionSites	exonAlignDepth-class
junctionSites,exonAlignDepth-method	exonAlignDepth-class
junctionSites-methods	exonAlignDepth-class
length,exonAlignDepth-method	exonAlignDepth-class
length,exonLoessModel-method	exonLoessModel-class
length,geneAlignDepth-method	geneAlignDepth-class
length,sampleBamFiles-method	sampleBamFiles-class
loadIndex	bamReader-class
loadIndex,bamReader-method	bamReader-class
loadIndex-methods	bamReader-class
mapQuality	bamAlign-class
mapQuality,bamAlign-method	bamAlign-class
mapQuality-methods	bamAlign-class
matePosition	bamAlign-class
matePosition,bamAlign-method	bamAlign-class
matePosition-methods	bamAlign-class
mateRefID	bamAlign-class
mateRefID,bamAlign-method	bamAlign-class
mateRefID-methods	bamAlign-class
mateReverseStrand	bamAlign-class
mateReverseStrand,bamAlign-method	bamAlign-class
mateReverseStrand-methods	bamAlign-class
mateReverseStrand<-	bamAlign-class
mateReverseStrand<-,bamAlign-method	bamAlign-class
mateReverseStrand<--methods	bamAlign-class
mateUnmapped	bamAlign-class
mateUnmapped,bamAlign-method	bamAlign-class
mateUnmapped-methods	bamAlign-class
mateUnmapped<-	bamAlign-class
mateUnmapped<-,bamAlign-method	bamAlign-class
mateUnmapped<--methods	bamAlign-class
meltDownSegments	rangeSegCount-class
meltDownSegments,rangeSegCount-method	rangeSegCount-class
meltDownSegments-methods	rangeSegCount-class
merge.bamGapList	bamGapList-class
merge.gapSiteList	gapSiteList-class
moveCurrentAlign	bamRange-class
moveCurrentAlign,bamRange-method	bamRange-class
moveCurrentAlign-methods	bamRange-class
multSeq	multseq
nAlignGaps	gapList-class
nAlignGaps,bamGapList-method	bamGapList-class
nAlignGaps,gapList-method	gapList-class
nAlignGaps,gapSiteList-method	gapSiteList-class
nAlignGaps-methods	gapList-class
nAligns	gapList-class
nAligns,bamGapList-method	bamGapList-class
nAligns,gapList-method	gapList-class
nAligns,gapSiteList-method	gapSiteList-class
nAligns,sampleBamFiles-method	sampleBamFiles-class
nAligns-methods	gapList-class
nAligns<-	sampleBamFiles-class
nAligns<-,sampleBamFiles,character,numeric-method	sampleBamFiles-class
nAligns<-,sampleBamFiles,integer-method	sampleBamFiles-class
nAligns<-,sampleBamFiles,numeric-method	sampleBamFiles-class
nAligns<--methods	sampleBamFiles-class
name	bamAlign-class
name,bamAlign-method	bamAlign-class
name-methods	bamAlign-class
nCigar	bamAlign-class
nCigar,bamAlign-method	bamAlign-class
nCigar-methods	bamAlign-class
nucStats	nucStats
nucStats,bamRange-method	nucStats
nucStats,bamReader-method	nucStats
nucStats,character-method	nucStats
nucStats-methods	nucStats
paired	bamAlign-class
paired,bamAlign-method	bamAlign-class
paired-methods	bamAlign-class
paired<-	bamAlign-class
paired<-,bamAlign-method	bamAlign-class
paired<--methods	bamAlign-class
pcrORopt_duplicate	bamAlign-class
pcrORopt_duplicate,bamAlign-method	bamAlign-class
pcrORopt_duplicate-methods	bamAlign-class
pcrORopt_duplicate<-	bamAlign-class
pcrORopt_duplicate<-,bamAlign-method	bamAlign-class
pcrORopt_duplicate<--methods	bamAlign-class
plotAlignDepth	alignDepth-class
plotAlignDepth,alignDepth-method	alignDepth-class
plotAlignDepth-methods	alignDepth-class
plotQualQuant	getQualDf
plotQualQuant,bamRange-method	getQualDf
plotQualQuant-methods	getQualDf
pop_back	bamRange-class
pop_back,bamRange-method	bamRange-class
pop_back-methods	bamRange-class
pop_front	bamRange-class
pop_front,bamRange-method	bamRange-class
pop_front-methods	bamRange-class
position	bamAlign-class
position,bamAlign-method	bamAlign-class
position-methods	bamAlign-class
properPair	bamAlign-class
properPair,bamAlign-method	bamAlign-class
properPair-methods	bamAlign-class
properPair<-	bamAlign-class
properPair<-,bamAlign-method	bamAlign-class
properPair<--methods	bamAlign-class
push_back	bamRange-class
push_back,bamRange-method	bamRange-class
push_back-methods	bamRange-class
push_front	bamRange-class
push_front,bamRange-method	bamRange-class
push_front-methods	bamRange-class
rangeSegCount	rangeSegCount-class
rangeSegCount,bamReader-method	bamReader-class
rangeSegCount-class	rangeSegCount-class
rangeSegCount-methods	bamReader-class
rangeToFastq	rangeToFastq
rangeToFastq,bamRange,character-method	rangeToFastq
rangeToFastq-methods	rangeToFastq
rbamtools	rbamtools-package
readerToFastq	readerToFastq
readerToFastq,bamReader-method	readerToFastq
readerToFastq-methods	readerToFastq
readPooledBamGapDf	readPooledBamGapDf
readPooledBamGaps	readPooledBamGaps
readRange	bamRange-class
readRange,bamReader,character,numeric,logical-method	bamRange-class
readRange,bamReader,character,numeric,missing-method	bamRange-class
readRange,bamReader,factor,numeric,logical-method	bamRange-class
readRange,bamReader,factor,numeric,missing-method	bamRange-class
readRange-methods	bamRange-class
refID	bamAlign-class
refID,bamAlign-method	bamAlign-class
refID,gapSiteList-method	gapSiteList-class
refID-methods	bamAlign-class
refID<-	gapSiteList-class
refID<-,gapSiteList,numeric-method	gapSiteList-class
refID<--methods	gapSiteList-class
refSeqDict	bamHeaderText-class
refSeqDict,bamHeaderText-method	bamHeaderText-class
refSeqDict-class	refSeqDict-class
refSeqDict<-	bamHeaderText-class
refSeqDict<-,bamHeaderText-method	bamHeaderText-class
removeSeqs	refSeqDict-class
removeSeqs,refSeqDict-method	refSeqDict-class
reverseStrand	bamAlign-class
reverseStrand,bamAlign-method	bamAlign-class
reverseStrand-methods	bamAlign-class
reverseStrand<-	bamAlign-class
reverseStrand<-,bamAlign-method	bamAlign-class
reverseStrand<--methods	bamAlign-class
rewind	bamReader-class
rewind,bamRange-method	bamRange-class
rewind,bamReader-method	bamReader-class
rewind-methods	bamReader-class
sampleBamFiles	sampleBamFiles-class
sampleBamFiles,character-method	sampleBamFiles-class
sampleBamFiles,factor-method	sampleBamFiles-class
sampleBamFiles,integer-method	sampleBamFiles-class
sampleBamFiles,numeric-method	sampleBamFiles-class
sampleBamFiles-class	sampleBamFiles-class
sampleBamFiles-methods	sampleBamFiles-class
sampleGroups	sampleBamFiles-class
sampleGroups,sampleBamFiles-method	sampleBamFiles-class
sampleGroups-methods	sampleBamFiles-class
sampleGroups<-	sampleBamFiles-class
sampleGroups<-,sampleBamFiles,character-method	sampleBamFiles-class
sampleGroups<-,sampleBamFiles,factor-method	sampleBamFiles-class
sampleGroups<--methods	sampleBamFiles-class
sampleLabels	sampleBamFiles-class
sampleLabels,sampleBamFiles-method	sampleBamFiles-class
sampleLabels-methods	sampleBamFiles-class
sampleLabels<-	sampleBamFiles-class
sampleLabels<-,sampleBamFiles,character-method	sampleBamFiles-class
sampleLabels<-,sampleBamFiles,factor-method	sampleBamFiles-class
sampleLabels<-,sampleBamFiles,integer-method	sampleBamFiles-class
sampleLabels<--methods	sampleBamFiles-class
saveAldData	saveAldData
saveAldData,sampleBamFiles,geneList-method	saveAldData
saveAldData-methods	saveAldData
secondaryAlign	bamAlign-class
secondaryAlign,bamAlign-method	bamAlign-class
secondaryAlign-methods	bamAlign-class
secondaryAlign<-	bamAlign-class
secondaryAlign<-,bamAlign-method	bamAlign-class
secondaryAlign<--methods	bamAlign-class
secondInPair	bamAlign-class
secondInPair,bamAlign-method	bamAlign-class
secondInPair-methods	bamAlign-class
secondInPair<-	bamAlign-class
secondInPair<-,bamAlign-method	bamAlign-class
secondInPair<--methods	bamAlign-class
segmentize	segmentize
segmentize,ANY-method	segmentize
segmentize,data.frame-method	segmentize
segmentize,matrix-method	segmentize
segmentize-methods	segmentize
setVal	setVal
setVal,headerLine-method	headerLine-class
setVal,headerProgram-method	headerProgram-class
setVal,headerReadGroup-method	headerReadGroup-class
show,alignDepth-method	alignDepth-class
show,bamGapList-method	bamGapList-class
show,bamHeader-method	bamHeader-class
show,exonAlignDepth-method	exonAlignDepth-class
show,exonLoessModel-method	exonLoessModel-class
show,gapList-method	gapList-class
show,gapSiteList-method	gapSiteList-class
show,geneAlignDepth-method	geneAlignDepth-class
show,GenomePartition-method	GenomePartition-class
show,sampleBamFiles-method	sampleBamFiles-class
siteList	gapSiteList-class
siteList,bamRange,missing-method	gapSiteList-class
siteList,bamReader,numeric-method	gapSiteList-class
siteList,missing,missing-method	gapSiteList-class
siteList,numeric,missing-method	gapSiteList-class
size	bamRange-class
size,bamGapList-method	bamGapList-class
size,bamRange-method	bamRange-class
size,gapList-method	gapList-class
size,gapSiteList-method	gapSiteList-class
size,rangeSegCount-method	rangeSegCount-class
size-methods	bamRange-class
stepNextAlign	bamRange-class
stepNextAlign,bamRange-method	bamRange-class
stepNextAlign-methods	bamRange-class
stepPrevAlign	bamRange-class
stepPrevAlign,bamRange-method	bamRange-class
stepPrevAlign-methods	bamRange-class
summary.bamGapList	bamGapList-class
suppAlign	bamAlign-class
suppAlign,bamAlign-method	bamAlign-class
suppAlign-methods	bamAlign-class
suppAlign<-	bamAlign-class
suppAlign<-,bamAlign-method	bamAlign-class
suppAlign<--methods	bamAlign-class
tail	refSeqDict-class
tail,refSeqDict-method	refSeqDict-class
unmapped	bamAlign-class
unmapped,bamAlign-method	bamAlign-class
unmapped-methods	bamAlign-class
unmapped<-	bamAlign-class
unmapped<-,bamAlign-method	bamAlign-class
unmapped<--methods	bamAlign-class
writeCurrentAlign	bamRange-class
writeCurrentAlign,bamRange-method	bamRange-class
writeCurrentAlign-methods	bamRange-class
[,bamRange,ANY,ANY,ANY-method	bamRange-class
[,exonAlignDepth,ANY,ANY,ANY-method	exonAlignDepth-class
[,exonLoessModel,ANY,ANY,ANY-method	exonLoessModel-class
[,geneAlignDepth,ANY,ANY,ANY-method	geneAlignDepth-class
[,refSeqDict,ANY,ANY,ANY-method	refSeqDict-class
[,sampleBamFiles,ANY,ANY,ANY-method	sampleBamFiles-class
[-methods	bamRange-class
[<-,refSeqDict-method	refSeqDict-class
