annotation,MVRanges-method	MVRanges-methods
anno_rCRS	anno_rCRS
byStrand	byStrand
callMT	callMT
callMTVars	callMT
chrominfo.rCRS	chrominfo.rCRS
consensusString,MVRanges-method	MVRanges-methods
consensusString,MVRangesList-method	MVRangesList-methods
coverage,MVRanges-method	MVRanges-methods
coverage,MVRangesList-method	MVRangesList-methods
encoding,MVRanges-method	MVRanges-methods
encoding,MVRangesList-method	MVRangesList-methods
fileName,MAlignments-method	MAlignments-methods
fileName,MAlignmentsList-method	MAlignmentsList-methods
filt,MVRanges-method	MVRanges-methods
filt,MVRangesList-method	MVRangesList-methods
filterMT	filterMT
filterMTvars	filterMTvars
fixMetadata	fixMetadata
fpFilter_RSRS	fpFilter_RSRS
fpFilter_Triska	fpFilter_Triska
genes	MVRanges-methods
genes,MVRanges-method	MVRanges-methods
genes,MVRangesList-method	MVRangesList-methods
genome,MVRanges-method	MVRanges-methods
genome,MVRangesList-method	MVRangesList-methods
genomeCoverage	MAlignments-methods
genomeCoverage,MAlignmentsList-method	MAlignmentsList-methods
genomeCoverage,MVRanges-method	MVRanges-methods
genomeCoverage,MVRangesList-method	MVRangesList-methods
genomeLength	MAlignments-methods
genomeLength,MAlignments-method	MAlignments-methods
getAnnotations	MVRanges-methods
getAnnotations,MVRanges-method	MVRanges-methods
getAnnotations,MVRangesList-method	MVRangesList-methods
getMT	getMT
granges,MVRangesList-method	MVRangesList-methods
hg19TorCRS	hg19TorCRS
indexMTGenome	indexMTGenome
injectMTVariants	injectMTVariants
locateVariants	MVRanges-methods
locateVariants,MVRanges,missing,missing-method	MVRanges-methods
locateVariants,MVRangesList,missing,missing-method	MVRangesList-methods
MAlignments	MAlignments-methods
MAlignments-class	MAlignments-class
MAlignments-methods	MAlignments-methods
MAlignmentsList	MAlignmentsList-methods
MAlignmentsList-class	MAlignmentsList-class
MAlignmentsList-methods	MAlignmentsList-methods
mtAnno	mtAnno
mtAnno.rCRS	mtAnno
MTcircos	MTcircos
MTcomplex	MTcomplex
MTcoverage	MTcoverage
mtGenes	mtGenes
mtGenes.rCRS	mtGenes.rCRS
MTHGVS	MTHGVS
MVRanges	MVRanges-methods
MVRanges-class	MVRanges-class
MVRanges-methods	MVRanges-methods
MVRangesList	MVRangesList-methods
MVRangesList-class	MVRangesList-class
MVRangesList-methods	MVRangesList-methods
plot,MVRanges,ANY-method	MVRanges-methods
plot,MVRangesList,ANY-method	MVRangesList-methods
plotMTCoverage	MTcoverage
plotStrandedMTCoverage	MTcoverage
pos,MVRanges-method	MVRanges-methods
predictCoding	MVRanges-methods
predictCoding,MVRanges,missing,missing,missing-method	MVRanges-methods
predictCoding,MVRangesList,missing,missing,missing-method	MVRangesList-methods
rCRSeq	rCRSeq
readLength	MAlignments-methods
readLength,MAlignments-method	MAlignments-methods
readLength,MAlignmentsList-method	MAlignmentsList-methods
s4Methods	s4Methods
scanBamHeader,MAlignments-method	MAlignments-methods
show,MAlignments-method	MAlignments-methods
show,MAlignmentsList-method	MAlignmentsList-methods
show,MVRanges-method	MVRanges-methods
show,MVRangesList-method	MVRangesList-methods
snpCall,MVRanges-method	MVRanges-methods
snpCall,MVRangesList-method	MVRangesList-methods
summarizeVariants,MVRanges,missing,missing-method	MVRanges-methods
summarizeVariants,MVRangesList,missing,missing-method	MVRangesList-methods
Summary,MAlignments-method	MAlignments-methods
Summary,MAlignmentsList-method	MAlignmentsList-methods
tallyVariants,MVRanges-method	MVRanges-methods
type,MVRanges-method	MVRanges-methods
validMetadata	validMetadata
