alphabetFrequencyFromBam	stackStringsFromBam
as.data.frame,GAlignments-method	GAlignments-class
as.data.frame,OverlapEncodings-method	OverlapEncodings-class
as.data.frame.OverlapEncodings	OverlapEncodings-class
c,GAlignmentPairs-method	GAlignmentPairs-class
c,GAlignments-method	GAlignments-class
c,GAlignmentsList-method	GAlignmentsList-class
c,GappedReads-method	GappedReads-class
cigar	GAlignments-class
cigar,GAlignments-method	GAlignments-class
cigar,GAlignmentsList-method	GAlignmentsList-class
cigar-utils	cigar-utils
cigarNarrow	cigar-utils
cigarOpTable	cigar-utils
cigarQNarrow	cigar-utils
cigarRangesAlongPairwiseSpace	cigar-utils
cigarRangesAlongQuerySpace	cigar-utils
cigarRangesAlongReferenceSpace	cigar-utils
cigarToRleList	cigar-utils
cigarWidthAlongPairwiseSpace	cigar-utils
cigarWidthAlongQuerySpace	cigar-utils
cigarWidthAlongReferenceSpace	cigar-utils
CIGAR_OPS	cigar-utils
class:GAlignmentPairs	GAlignmentPairs-class
class:GAlignments	GAlignments-class
class:GAlignmentsList	GAlignmentsList-class
class:GappedReads	GappedReads-class
class:OverlapEncodings	OverlapEncodings-class
coerce,GAlignmentPairs,GAlignments-method	GAlignmentPairs-class
coerce,GAlignmentPairs,GAlignmentsList-method	GAlignmentsList-class
coerce,GAlignmentPairs,GRanges-method	GAlignmentPairs-class
coerce,GAlignmentPairs,GRangesList-method	GAlignmentPairs-class
coerce,GAlignments,GRanges-method	GAlignments-class
coerce,GAlignments,GRangesList-method	GAlignments-class
coerce,GAlignments,Ranges-method	GAlignments-class
coerce,GAlignments,RangesList-method	GAlignments-class
coerce,GAlignmentsList,GRanges-method	GAlignmentsList-class
coerce,GAlignmentsList,GRangesList-method	GAlignmentsList-class
coerce,GAlignmentsList,Ranges-method	GAlignmentsList-class
coerce,GAlignmentsList,RangesList-method	GAlignmentsList-class
coerce,GenomicRanges,GAlignments-method	GAlignments-class
countCompatibleOverlaps	findCompatibleOverlaps-methods
countDumpedAlignments	findMateAlignment
countOverlaps	findOverlaps-methods
countOverlaps,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
countOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
countOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
countOverlaps,GAlignments,GenomicRanges-method	findOverlaps-methods
countOverlaps,GAlignments,GRangesList-method	findOverlaps-methods
countOverlaps,GAlignments,Vector-method	findOverlaps-methods
countOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
countOverlaps,GAlignmentsList,Vector-method	findOverlaps-methods
countOverlaps,GenomicRanges,GAlignments-method	findOverlaps-methods
countOverlaps,GRangesList,GAlignments-method	findOverlaps-methods
countOverlaps,Vector,GAlignmentPairs-method	findOverlaps-methods
countOverlaps,Vector,GAlignments-method	findOverlaps-methods
countOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
coverage	coverage-methods
coverage,BamFile-method	coverage-methods
coverage,character-method	coverage-methods
coverage,GAlignmentPairs-method	coverage-methods
coverage,GAlignments-method	coverage-methods
coverage-methods	coverage-methods
elementMetadata,GAlignmentsList-method	GAlignmentsList-class
elementMetadata<-,GAlignmentPairs-method	GAlignmentPairs-class
elementMetadata<-,GAlignments-method	GAlignments-class
elementMetadata<-,GAlignmentsList-method	GAlignmentsList-class
encodeOverlaps	encodeOverlaps-methods
encodeOverlaps,GRangesList,GRangesList-method	encodeOverlaps-methods
encodeOverlaps,Ranges,RangesList-method	encodeOverlaps-methods
encodeOverlaps,RangesList,Ranges-method	encodeOverlaps-methods
encodeOverlaps,RangesList,RangesList-method	encodeOverlaps-methods
encodeOverlaps-methods	encodeOverlaps-methods
encodeOverlaps1	encodeOverlaps-methods
encoding,OverlapEncodings-method	OverlapEncodings-class
end,GAlignments-method	GAlignments-class
end,GAlignmentsList-method	GAlignmentsList-class
explodeCigarOpLengths	cigar-utils
explodeCigarOps	cigar-utils
extractAlignmentRangesOnReference	cigar-utils
extractQueryStartInTranscript	encodeOverlaps-methods
extractSkippedExonRanks	encodeOverlaps-methods
extractSkippedExonRanks,character-method	encodeOverlaps-methods
extractSkippedExonRanks,factor-method	encodeOverlaps-methods
extractSkippedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
extractSpannedExonRanks	encodeOverlaps-methods
extractSpannedExonRanks,character-method	encodeOverlaps-methods
extractSpannedExonRanks,factor-method	encodeOverlaps-methods
extractSpannedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
extractSteppedExonRanks	encodeOverlaps-methods
extractSteppedExonRanks,character-method	encodeOverlaps-methods
extractSteppedExonRanks,factor-method	encodeOverlaps-methods
extractSteppedExonRanks,OverlapEncodings-method	encodeOverlaps-methods
findCompatibleOverlaps	findCompatibleOverlaps-methods
findCompatibleOverlaps,GAlignmentPairs,GRangesList-method	findCompatibleOverlaps-methods
findCompatibleOverlaps,GAlignments,GRangesList-method	findCompatibleOverlaps-methods
findCompatibleOverlaps-methods	findCompatibleOverlaps-methods
findMateAlignment	findMateAlignment
findMateAlignment2	findMateAlignment
findOverlaps	findOverlaps-methods
findOverlaps,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
findOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
findOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
findOverlaps,GAlignments,GRangesList-method	findOverlaps-methods
findOverlaps,GAlignments,Vector-method	findOverlaps-methods
findOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
findOverlaps,GAlignmentsList,Vector-method	findOverlaps-methods
findOverlaps,GRangesList,GAlignments-method	findOverlaps-methods
findOverlaps,Vector,GAlignmentPairs-method	findOverlaps-methods
findOverlaps,Vector,GAlignments-method	findOverlaps-methods
findOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
findSpliceOverlaps	findSpliceOverlaps-methods
findSpliceOverlaps,BamFile,ANY-method	findSpliceOverlaps-methods
findSpliceOverlaps,character,ANY-method	findSpliceOverlaps-methods
findSpliceOverlaps,GAlignmentPairs,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GAlignments,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps,GRangesList,GRangesList-method	findSpliceOverlaps-methods
findSpliceOverlaps-methods	findSpliceOverlaps-methods
first	GAlignmentPairs-class
first,GAlignmentPairs-method	GAlignmentPairs-class
flippedQuery	OverlapEncodings-class
flippedQuery,OverlapEncodings-method	OverlapEncodings-class
flipQuery	encodeOverlaps-methods
flushDumpedAlignments	findMateAlignment
GAlignmentPairs	GAlignmentPairs-class
GAlignmentPairs-class	GAlignmentPairs-class
GAlignments	GAlignments-class
GAlignments-class	GAlignments-class
GAlignmentsList	GAlignmentsList-class
GAlignmentsList-class	GAlignmentsList-class
GappedReads	GappedReads-class
GappedReads-class	GappedReads-class
getDumpedAlignments	findMateAlignment
granges,GAlignmentPairs-method	GAlignmentPairs-class
granges,GAlignments-method	GAlignments-class
granges,GAlignmentsList-method	GAlignmentsList-class
grglist,GAlignmentPairs-method	GAlignmentPairs-class
grglist,GAlignments-method	GAlignments-class
grglist,GAlignmentsList-method	GAlignmentsList-class
IntersectionNotEmpty	summarizeOverlaps-methods
IntersectionStrict	summarizeOverlaps-methods
intra-range-methods	intra-range-methods
introns	junctions-methods
isCompatibleWithSkippedExons	encodeOverlaps-methods
isCompatibleWithSkippedExons,character-method	encodeOverlaps-methods
isCompatibleWithSkippedExons,factor-method	encodeOverlaps-methods
isCompatibleWithSkippedExons,OverlapEncodings-method	encodeOverlaps-methods
isCompatibleWithSplicing	encodeOverlaps-methods
isCompatibleWithSplicing,character-method	encodeOverlaps-methods
isCompatibleWithSplicing,factor-method	encodeOverlaps-methods
isCompatibleWithSplicing,OverlapEncodings-method	encodeOverlaps-methods
isProperPair	GAlignmentPairs-class
isProperPair,GAlignmentPairs-method	GAlignmentPairs-class
junctions	junctions-methods
junctions,GAlignmentPairs-method	junctions-methods
junctions,GAlignments-method	junctions-methods
junctions,GAlignmentsList-method	junctions-methods
junctions-methods	junctions-methods
last	GAlignmentPairs-class
last,GAlignmentPairs-method	GAlignmentPairs-class
left	GAlignmentPairs-class
left,GAlignmentPairs-method	GAlignmentPairs-class
Lencoding	OverlapEncodings-class
Lencoding,character-method	OverlapEncodings-class
Lencoding,factor-method	OverlapEncodings-class
Lencoding,OverlapEncodings-method	OverlapEncodings-class
length,GAlignmentPairs-method	GAlignmentPairs-class
length,GAlignments-method	GAlignments-class
length,OverlapEncodings-method	OverlapEncodings-class
levels,OverlapEncodings-method	OverlapEncodings-class
levels.OverlapEncodings	OverlapEncodings-class
Lngap	OverlapEncodings-class
Lnjunc	OverlapEncodings-class
Lnjunc,character-method	OverlapEncodings-class
Lnjunc,factor-method	OverlapEncodings-class
Lnjunc,OverlapEncodings-method	OverlapEncodings-class
Loffset	OverlapEncodings-class
Loffset,OverlapEncodings-method	OverlapEncodings-class
makeGAlignmentPairs	findMateAlignment
makeGAlignmentsListFromFeatureFragments	GAlignmentsList-class
map,GenomicRanges,GAlignments-method	map-methods
map-methods	map-methods
mapCoords,GenomicRanges,GAlignments-method	mapCoords-methods
mapCoords-methods	mapCoords-methods
names,GAlignmentPairs-method	GAlignmentPairs-class
names,GAlignments-method	GAlignments-class
names,GAlignmentsList-method	GAlignmentsList-class
names<-,GAlignmentPairs-method	GAlignmentPairs-class
names<-,GAlignments-method	GAlignments-class
names<-,GAlignmentsList-method	GAlignmentsList-class
narrow	intra-range-methods
narrow,GAlignments-method	intra-range-methods
narrow,GAlignmentsList-method	intra-range-methods
narrow,GappedReads-method	intra-range-methods
NATURAL_INTRON_MOTIFS	junctions-methods
ngap,character-method	OverlapEncodings-class
ngap,factor-method	OverlapEncodings-class
ngap,GAlignmentPairs-method	GAlignmentPairs-class
ngap,GAlignments-method	GAlignments-class
ngap,GAlignmentsList-method	GAlignmentsList-class
ngap,OverlapEncodings-method	OverlapEncodings-class
njunc	GAlignments-class
njunc,character-method	OverlapEncodings-class
njunc,factor-method	OverlapEncodings-class
njunc,GAlignmentPairs-method	GAlignmentPairs-class
njunc,GAlignments-method	GAlignments-class
njunc,GAlignmentsList-method	GAlignmentsList-class
njunc,OverlapEncodings-method	OverlapEncodings-class
OverlapEncodings	OverlapEncodings-class
OverlapEncodings-class	OverlapEncodings-class
overlapsAny	findOverlaps-methods
overlapsAny,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
overlapsAny,GAlignmentPairs,Vector-method	findOverlaps-methods
overlapsAny,GAlignments,GAlignments-method	findOverlaps-methods
overlapsAny,GAlignments,Vector-method	findOverlaps-methods
overlapsAny,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
overlapsAny,GAlignmentsList,Vector-method	findOverlaps-methods
overlapsAny,Vector,GAlignmentPairs-method	findOverlaps-methods
overlapsAny,Vector,GAlignments-method	findOverlaps-methods
overlapsAny,Vector,GAlignmentsList-method	findOverlaps-methods
pileLettersAt	pileLettersAt
pintersect,GAlignments,GRanges-method	setops-methods
pintersect,GRanges,GAlignments-method	setops-methods
qnarrow	intra-range-methods
qnarrow,GAlignments-method	intra-range-methods
qnarrow,GAlignmentsList-method	intra-range-methods
qnarrow,GappedReads-method	intra-range-methods
qseq	GappedReads-class
qseq,GappedReads-method	GappedReads-class
queryLoc2refLoc	cigar-utils
queryLocs2refLocs	cigar-utils
qwidth	GAlignments-class
qwidth,GAlignments-method	GAlignments-class
qwidth,GAlignmentsList-method	GAlignmentsList-class
qwidth,GappedReads-method	GappedReads-class
ranges,GAlignments-method	GAlignments-class
ranges,GAlignmentsList-method	GAlignmentsList-class
readGAlignmentPairs	readGAlignments
readGAlignmentPairsFromBam	readGAlignments
readGAlignmentPairsFromBam,BamFile-method	readGAlignments
readGAlignmentPairsFromBam,character-method	readGAlignments
readGAlignments	readGAlignments
readGAlignmentsFromBam	readGAlignments
readGAlignmentsFromBam,BamFile-method	readGAlignments
readGAlignmentsFromBam,BamViews-method	readGAlignments
readGAlignmentsFromBam,character-method	readGAlignments
readGAlignmentsList	readGAlignments
readGAlignmentsListFromBam	readGAlignments
readGAlignmentsListFromBam,BamFile-method	readGAlignments
readGAlignmentsListFromBam,character-method	readGAlignments
readGappedReads	readGAlignments
readGappedReadsFromBam	readGAlignments
readGappedReadsFromBam,BamFile-method	readGAlignments
readGappedReadsFromBam,character-method	readGAlignments
readSTARJunctions	junctions-methods
readTopHatJunctions	junctions-methods
relistToClass,GAlignments-method	GAlignmentsList-class
Rencoding	OverlapEncodings-class
Rencoding,character-method	OverlapEncodings-class
Rencoding,factor-method	OverlapEncodings-class
Rencoding,OverlapEncodings-method	OverlapEncodings-class
rglist,GAlignments-method	GAlignments-class
rglist,GAlignmentsList-method	GAlignmentsList-class
right	GAlignmentPairs-class
right,GAlignmentPairs-method	GAlignmentPairs-class
rname	GAlignments-class
rname,GAlignments-method	GAlignments-class
rname,GAlignmentsList-method	GAlignmentsList-class
rname<-	GAlignments-class
rname<-,GAlignments-method	GAlignments-class
rname<-,GAlignmentsList-method	GAlignmentsList-class
Rngap	OverlapEncodings-class
Rnjunc	OverlapEncodings-class
Rnjunc,character-method	OverlapEncodings-class
Rnjunc,factor-method	OverlapEncodings-class
Rnjunc,OverlapEncodings-method	OverlapEncodings-class
Roffset	OverlapEncodings-class
Roffset,OverlapEncodings-method	OverlapEncodings-class
selectEncodingWithCompatibleStrand	encodeOverlaps-methods
seqinfo,GAlignmentPairs-method	GAlignmentPairs-class
seqinfo,GAlignments-method	GAlignments-class
seqinfo,GAlignmentsList-method	GAlignmentsList-class
seqinfo<-,GAlignmentPairs-method	GAlignmentPairs-class
seqinfo<-,GAlignments-method	GAlignments-class
seqinfo<-,GAlignmentsList-method	GAlignmentsList-class
seqlevelsInUse,GAlignmentPairs-method	GAlignmentPairs-class
seqnames,GAlignmentPairs-method	GAlignmentPairs-class
seqnames,GAlignments-method	GAlignments-class
seqnames,GAlignmentsList-method	GAlignmentsList-class
seqnames<-,GAlignments-method	GAlignments-class
seqnames<-,GAlignmentsList-method	GAlignmentsList-class
sequenceLayer	sequenceLayer
setops-methods	setops-methods
show,GAlignmentPairs-method	GAlignmentPairs-class
show,GAlignments-method	GAlignments-class
show,GAlignmentsList-method	GAlignmentsList-class
show,OverlapEncodings-method	OverlapEncodings-class
splitAsListReturnedClass,GAlignments-method	GAlignments-class
stackStringsFromBam	stackStringsFromBam
start,GAlignments-method	GAlignments-class
start,GAlignmentsList-method	GAlignmentsList-class
strand,GAlignmentPairs-method	GAlignmentPairs-class
strand,GAlignments-method	GAlignments-class
strand,GAlignmentsList-method	GAlignmentsList-class
strand<-,GAlignmentPairs-method	GAlignmentPairs-class
strand<-,GAlignments-method	GAlignments-class
strand<-,GAlignmentsList-method	GAlignmentsList-class
subsetByOverlaps	findOverlaps-methods
subsetByOverlaps,GAlignmentPairs,GAlignmentPairs-method	findOverlaps-methods
subsetByOverlaps,GAlignmentPairs,Vector-method	findOverlaps-methods
subsetByOverlaps,GAlignments,GAlignments-method	findOverlaps-methods
subsetByOverlaps,GAlignments,Vector-method	findOverlaps-methods
subsetByOverlaps,GAlignmentsList,GAlignmentsList-method	findOverlaps-methods
subsetByOverlaps,GAlignmentsList,Vector-method	findOverlaps-methods
subsetByOverlaps,Vector,GAlignmentPairs-method	findOverlaps-methods
subsetByOverlaps,Vector,GAlignments-method	findOverlaps-methods
subsetByOverlaps,Vector,GAlignmentsList-method	findOverlaps-methods
summarizeJunctions	junctions-methods
summarizeOverlaps	summarizeOverlaps-methods
summarizeOverlaps,BamViews,missing-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,BamFile-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,BamFileList-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,character-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,GAlignmentPairs-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,GAlignments-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,GAlignmentsList-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,GRanges-method	summarizeOverlaps-methods
summarizeOverlaps,GRanges,GRangesList-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,BamFile-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,BamFileList-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,character-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,GAlignmentPairs-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,GAlignments-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,GAlignmentsList-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,GRanges-method	summarizeOverlaps-methods
summarizeOverlaps,GRangesList,GRangesList-method	summarizeOverlaps-methods
summarizeOverlaps-methods	summarizeOverlaps-methods
Union	summarizeOverlaps-methods
unlist,GAlignmentPairs-method	GAlignmentPairs-class
updateObject,GAlignments-method	GAlignments-class
updateObject,GAlignmentsList-method	GAlignmentsList-class
validCigar	cigar-utils
width,GAlignments-method	GAlignments-class
width,GAlignmentsList-method	GAlignmentsList-class
[[,GAlignmentPairs,ANY,ANY-method	GAlignmentPairs-class
