%in%,ANY,GappedAlignments-method	GappedAlignments-class
%in%,GappedAlignments,ANY-method	GappedAlignments-class
%in%,GappedAlignments,GappedAlignments-method	GappedAlignments-class
%in%,GRanges,GRanges-method	GRanges-findOverlaps
%in%,GRanges,GRangesList-method	GRanges-findOverlaps
%in%,GRanges,RangedData-method	GRanges-findOverlaps
%in%,GRanges,RangesList-method	GRanges-findOverlaps
%in%,GRangesList,GRanges-method	GRanges-findOverlaps
%in%,GRangesList,GRangesList-method	GRanges-findOverlaps
%in%,GRangesList,RangedData-method	GRanges-findOverlaps
%in%,GRangesList,RangesList-method	GRanges-findOverlaps
%in%,RangedData,GRanges-method	GRanges-findOverlaps
%in%,RangedData,GRangesList-method	GRanges-findOverlaps
%in%,RangesList,GRanges-method	GRanges-findOverlaps
%in%,RangesList,GRangesList-method	GRanges-findOverlaps
as.data.frame,GappedAlignments-method	GappedAlignments-class
as.data.frame,GRanges-method	GRanges-class
as.data.frame,GRangesList-method	GRangesList-class
c,GRanges-method	GRanges-class
cigar	GappedAlignments-class
cigar,GappedAlignments-method	GappedAlignments-class
cigar-utils	cigar-utils
cigarNarrow	cigar-utils
cigarOpTable	cigar-utils
cigarQNarrow	cigar-utils
cigarToCigarTable	cigar-utils
cigarToIRanges	cigar-utils
cigarToIRangesListByAlignment	cigar-utils
cigarToIRangesListByRName	cigar-utils
cigarToQWidth	cigar-utils
cigarToRleList	cigar-utils
cigarToWidth	cigar-utils
class:GappedAlignments	GappedAlignments-class
class:GRanges	GRanges-class
class:GRangesList	GRangesList-class
coerce,GRanges,RangedData-method	GRanges-class
coerce,GRanges,RangesList-method	GRanges-class
coerce,RangedData,GRanges-method	GRanges-class
coerce,RangedDataList,GRangesList-method	GRangesList-class
coerce,RangesList,GRanges-method	GRanges-class
countOverlaps,ANY,GappedAlignments-method	GappedAlignments-class
countOverlaps,GappedAlignments,ANY-method	GappedAlignments-class
countOverlaps,GappedAlignments,GappedAlignments-method	GappedAlignments-class
countOverlaps,GRanges,GRanges-method	GRanges-findOverlaps
countOverlaps,GRanges,GRangesList-method	GRanges-findOverlaps
countOverlaps,GRanges,RangedData-method	GRanges-findOverlaps
countOverlaps,GRanges,RangesList-method	GRanges-findOverlaps
countOverlaps,GRangesList,GRanges-method	GRanges-findOverlaps
countOverlaps,GRangesList,GRangesList-method	GRanges-findOverlaps
countOverlaps,GRangesList,RangedData-method	GRanges-findOverlaps
countOverlaps,GRangesList,RangesList-method	GRanges-findOverlaps
countOverlaps,RangedData,GRanges-method	GRanges-findOverlaps
countOverlaps,RangedData,GRangesList-method	GRanges-findOverlaps
countOverlaps,RangesList,GRanges-method	GRanges-findOverlaps
countOverlaps,RangesList,GRangesList-method	GRanges-findOverlaps
coverage,GappedAlignments-method	GappedAlignments-class
coverage,GRanges-method	GRanges-class
coverage,GRangesList-method	GRangesList-class
disjoin,GRanges-method	GRanges-class
elementMetadata,GRanges-method	GRanges-class
elementMetadata,GRangesList-method	GRangesList-class
elementMetadata<-,GRanges-method	GRanges-class
elementMetadata<-,GRangesList-method	GRangesList-class
end,GappedAlignments-method	GappedAlignments-class
end,GRanges-method	GRanges-class
end,GRangesList-method	GRangesList-class
end<-,GRanges-method	GRanges-class
end<-,GRangesList-method	GRangesList-class
findOverlaps,ANY,GappedAlignments-method	GappedAlignments-class
findOverlaps,GappedAlignments,ANY-method	GappedAlignments-class
findOverlaps,GappedAlignments,GappedAlignments-method	GappedAlignments-class
findOverlaps,GRanges,GRanges-method	GRanges-findOverlaps
findOverlaps,GRanges,GRangesList-method	GRanges-findOverlaps
findOverlaps,GRanges,RangedData-method	GRanges-findOverlaps
findOverlaps,GRanges,RangesList-method	GRanges-findOverlaps
findOverlaps,GRangesList,GRanges-method	GRanges-findOverlaps
findOverlaps,GRangesList,GRangesList-method	GRanges-findOverlaps
findOverlaps,GRangesList,RangedData-method	GRanges-findOverlaps
findOverlaps,GRangesList,RangesList-method	GRanges-findOverlaps
findOverlaps,RangedData,GRanges-method	GRanges-findOverlaps
findOverlaps,RangedData,GRangesList-method	GRanges-findOverlaps
findOverlaps,RangesList,GRanges-method	GRanges-findOverlaps
findOverlaps,RangesList,GRangesList-method	GRanges-findOverlaps
flank,GRanges-method	GRanges-class
GappedAlignments	GappedAlignments-class
GappedAlignments-class	GappedAlignments-class
gaps,GRanges-method	GRanges-class
GRanges	GRanges-class
GRanges-class	GRanges-class
GRangesList	GRangesList-class
GRangesList-class	GRangesList-class
grg	GappedAlignments-class
grg,GappedAlignments-method	GappedAlignments-class
grglist	GappedAlignments-class
grglist,GappedAlignments-method	GappedAlignments-class
intersect,GRanges,GRanges-method	GRanges-setops
length,GappedAlignments-method	GappedAlignments-class
length,GRanges-method	GRanges-class
match,ANY,GappedAlignments-method	GappedAlignments-class
match,GappedAlignments,ANY-method	GappedAlignments-class
match,GappedAlignments,GappedAlignments-method	GappedAlignments-class
match,GRanges,GRanges-method	GRanges-findOverlaps
match,GRanges,GRangesList-method	GRanges-findOverlaps
match,GRanges,RangedData-method	GRanges-findOverlaps
match,GRanges,RangesList-method	GRanges-findOverlaps
match,GRangesList,GRanges-method	GRanges-findOverlaps
match,GRangesList,GRangesList-method	GRanges-findOverlaps
match,GRangesList,RangedData-method	GRanges-findOverlaps
match,GRangesList,RangesList-method	GRanges-findOverlaps
match,RangedData,GRanges-method	GRanges-findOverlaps
match,RangedData,GRangesList-method	GRanges-findOverlaps
match,RangesList,GRanges-method	GRanges-findOverlaps
match,RangesList,GRangesList-method	GRanges-findOverlaps
names,GRanges-method	GRanges-class
names<-,GRanges-method	GRanges-class
narrow,GappedAlignments-method	GappedAlignments-class
pintersect,GappedAlignments,GRanges-method	GappedAlignments-class
pintersect,GRanges,GappedAlignments-method	GappedAlignments-class
pintersect,GRanges,GRanges-method	GRanges-setops
pintersect,GRanges,GRangesList-method	GRanges-setops
pintersect,GRangesList,GRanges-method	GRanges-setops
psetdiff,GRanges,GRanges-method	GRanges-setops
psetdiff,GRanges,GRangesList-method	GRanges-setops
punion,GRanges,GRanges-method	GRanges-setops
punion,GRanges,GRangesList-method	GRanges-setops
punion,GRangesList,GRanges-method	GRanges-setops
qnarrow	GappedAlignments-class
qnarrow,GappedAlignments-method	GappedAlignments-class
queryLoc2refLoc	cigar-utils
queryLocs2refLocs	cigar-utils
qwidth	GappedAlignments-class
qwidth,GappedAlignments-method	GappedAlignments-class
range,GRanges-method	GRanges-class
ranges,GRanges-method	GRanges-class
ranges,GRangesList-method	GRangesList-class
ranges<-,GRanges-method	GRanges-class
ranges<-,GRangesList-method	GRangesList-class
readGappedAlignments	GappedAlignments-class
reduce,GRanges-method	GRanges-class
resize,GRanges-method	GRanges-class
rev,GRanges-method	GRanges-class
rglist	GappedAlignments-class
rglist,GappedAlignments-method	GappedAlignments-class
rname	GappedAlignments-class
rname,GappedAlignments-method	GappedAlignments-class
rname<-	GappedAlignments-class
rname<-,GappedAlignments-method	GappedAlignments-class
seqlengths	seqnames
seqlengths,GappedAlignments-method	GappedAlignments-class
seqlengths,GRanges-method	GRanges-class
seqlengths,GRangesList-method	GRangesList-class
seqlengths<-	seqnames
seqlengths<-,GappedAlignments-method	GappedAlignments-class
seqlengths<-,GRanges-method	GRanges-class
seqlengths<-,GRangesList-method	GRangesList-class
seqnames	seqnames
seqnames,GappedAlignments-method	GappedAlignments-class
seqnames,GRanges-method	GRanges-class
seqnames,GRangesList-method	GRangesList-class
seqnames<-	seqnames
seqnames<-,GappedAlignments-method	GappedAlignments-class
seqnames<-,GRanges-method	GRanges-class
seqnames<-,GRangesList-method	GRangesList-class
seqselect,GRanges-method	GRanges-class
seqselect<-,GRanges-method	GRanges-class
setdiff,GRanges,GRanges-method	GRanges-setops
shift,GRanges-method	GRanges-class
shift,GRangesList-method	GRangesList-class
show,GappedAlignments-method	GappedAlignments-class
show,GRanges-method	GRanges-class
show,GRangesList-method	GRangesList-class
split,GRanges-method	GRanges-class
splitCigar	cigar-utils
start,GappedAlignments-method	GappedAlignments-class
start,GRanges-method	GRanges-class
start,GRangesList-method	GRangesList-class
start<-,GRanges-method	GRanges-class
start<-,GRangesList-method	GRangesList-class
strand	strand
strand,character-method	strand
strand,DataTable-method	strand
strand,factor-method	strand
strand,GappedAlignments-method	GappedAlignments-class
strand,GRanges-method	GRanges-class
strand,GRangesList-method	GRangesList-class
strand,integer-method	strand
strand,logical-method	strand
strand,missing-method	strand
strand-methods	strand
strand<-	strand
strand<-,GRanges-method	GRanges-class
strand<-,GRangesList-method	GRangesList-class
subsetByOverlaps,ANY,GappedAlignments-method	GappedAlignments-class
subsetByOverlaps,GappedAlignments,ANY-method	GappedAlignments-class
subsetByOverlaps,GappedAlignments,GappedAlignments-method	GappedAlignments-class
subsetByOverlaps,GRanges,GRanges-method	GRanges-findOverlaps
subsetByOverlaps,GRanges,GRangesList-method	GRanges-findOverlaps
subsetByOverlaps,GRanges,RangedData-method	GRanges-findOverlaps
subsetByOverlaps,GRanges,RangesList-method	GRanges-findOverlaps
subsetByOverlaps,GRangesList,GRanges-method	GRanges-findOverlaps
subsetByOverlaps,GRangesList,GRangesList-method	GRanges-findOverlaps
subsetByOverlaps,GRangesList,RangedData-method	GRanges-findOverlaps
subsetByOverlaps,GRangesList,RangesList-method	GRanges-findOverlaps
subsetByOverlaps,RangedData,GRanges-method	GRanges-findOverlaps
subsetByOverlaps,RangedData,GRangesList-method	GRanges-findOverlaps
subsetByOverlaps,RangesList,GRanges-method	GRanges-findOverlaps
subsetByOverlaps,RangesList,GRangesList-method	GRanges-findOverlaps
summarizeCigarTable	cigar-utils
union,GRanges,GRanges-method	GRanges-setops
unlist,GRangesList-method	GRangesList-class
validCigar	cigar-utils
width,GappedAlignments-method	GappedAlignments-class
width,GRanges-method	GRanges-class
width,GRangesList-method	GRangesList-class
width<-,GRanges-method	GRanges-class
width<-,GRangesList-method	GRangesList-class
window,GRanges-method	GRanges-class
[,GappedAlignments-method	GappedAlignments-class
[,GRanges-method	GRanges-class
[,GRangesList-method	GRangesList-class
[<-,GRanges-method	GRanges-class
[<-,GRangesList-method	GRangesList-class
