as.list,BamTallyParam-method	BamTallyParam-class
bamPaths,GsnapOutput-method	GsnapOutput-class
BamTallyParam	BamTallyParam-class
BamTallyParam-class	BamTallyParam-class
bam_tally	bam_tally-methods
bam_tally,BamFile-method	bam_tally-methods
bam_tally,character-method	bam_tally-methods
bam_tally,GmapBamReader-method	bam_tally-methods
bam_tally-methods	bam_tally-methods
cmetindex	cmetindex
coerce,BamTallyParam,list-method	BamTallyParam-class
coerce,GmapGenome,DNAStringSet-method	GmapGenome-class
directory	directory
directory,GmapSnps-method	GmapSnps-class
genome,GmapGenome-method	GmapGenome-class
genome,GmapGenomeDirectory-method	GmapGenomeDirectory-class
genome,TallyIIT-method	bam_tally-methods
getSeq,GmapGenome-method	GmapGenome-class
GmapGenome	GmapGenome-class
GmapGenome-class	GmapGenome-class
GmapGenomeDirectory	GmapGenomeDirectory-class
GmapGenomeDirectory-class	GmapGenomeDirectory-class
GmapSnpDirectory	GmapSnpDirectory-class
GmapSnpDirectory-class	GmapSnpDirectory-class
GmapSnps	GmapSnps-class
GmapSnps-class	GmapSnps-class
gmap_build,ANY,GmapGenome-method	gmap_build-methods
gmap_build,character,GmapGenome-method	gmap_build-methods
gmap_build,DNAStringSet,GmapGenome-method	gmap_build-methods
gmap_build-methods	gmap_build-methods
gsnap	gsnap-methods
gsnap,character,character_OR_NULL,GsnapParam-method	gsnap-methods
gsnap-methods	gsnap-methods
GsnapOutput	GsnapOutput-class
GsnapOutput-class	GsnapOutput-class
GsnapParam	GsnapParam-class
GsnapParam-class	GsnapParam-class
length,GmapSnpDirectory-method	GmapSnpDirectory-class
makeGmapGenomePackage	makeGmapGenomePackage
names,GmapSnpDirectory-method	GmapSnpDirectory-class
path,GmapBamReader-method	internals
path,GmapGenome-method	GmapGenome-class
path,GmapGenomeDirectory-method	GmapGenomeDirectory-class
path,GmapSnpDirectory-method	GmapSnpDirectory-class
path,GsnapOutput-method	GsnapOutput-class
path,NULL-method	GmapGenomeDirectory-class
seqinfo,GmapGenome-method	GmapGenome-class
snps<-	GmapGenome-class
snps<-,GmapGenome,ANY,ANY-method	GmapGenome-class
snps<-,GmapSnpDirectory,character,character-method	GmapSnpDirectory-class
snps<-,GmapSnpDirectory,character,VCF-method	GmapSnpDirectory-class
spliceSites<-	GmapGenome-class
spliceSites<-,GmapGenome,GRangesList-method	GmapGenome-class
spliceSites<-,GmapGenome,TxDb-method	GmapGenome-class
TP53Genome	TP53Genome
TP53Which	TP53Genome
variantSummary	bam_tally-methods
[[<-,GmapSnpDirectory,ANY,ANY-method	GmapSnpDirectory-class
