MAGIC_NUMBER
TwoBitFile
MASK
TwoBitFile
MapQualityScores
metrics
MapTargets
Timers
MapTools
util
MappedPosition
metrics
MarkDuplicatesInDriver
Timers
MarkReads
Timers
Match
MdTagEvent
MatchEvent
util
MdTag
util
MdTagEvent
util
Mismatch
MdTagEvent
MismatchEvent
util
MultiContigNonoverlappingRegions
rdd
main
PhredUtils
makeHeader
VcfHeaderUtils
mapQ
DeletionEvent InsertionEvent MatchEvent MismatchEvent
mapToJavaMap
ADAMContext
mapped
FlagStatMetrics
mappedPositionCheck
ReferencePosition
mapping
OrderedTrackedLayout
mapq
AlignmentRecordField
mapq0Reads
VariantCallingAnnotationsField
maskBlocks
TwoBitRecord
matchedByName
BaseQualityScores BucketComparisons CombinedComparisons DupeMismatch MapQualityScores MappedPosition OverMatched
matches
OverMatched MdTag Pileup RegExp
mateAlignmentStart
AlignmentRecordField
mateContig
AlignmentRecordField
mateMapped
AlignmentRecordField
mateNegativeStrand
AlignmentRecordField
maxLogP
RecalibrationTable
maxQualScore
RecalibrationTable
maybeSaveBam
AlignmentRecordRDDFunctions
maybeSaveFastq
AlignmentRecordRDDFunctions
md5
SequenceRecord
mdTag
RichAlignmentRecord
merge
ReferenceRegion IndelRealignmentTarget
mergeAnnotations
VariantAnnotationConverter
mergeRegions
NonoverlappingRegions
metrics
adam
minAcceptableQuality
BaseQualityRecalibration Recalibrator
mismatchedBase
MdTag MismatchEvent
mismatches
Observation DecadentRead MdTag Pileup
mismatchesOption
DecadentRead
mismatchingPositions
AlignmentRecordField
models
adam
moveAlignment
MdTag
moveLeft
RichCigar
moveMatrix
SmithWaterman
mqRankSum
VariantCallingAnnotationsField
multipleNucleotideVariantCount
GenotypesSummaryCounts
mutationTasterPred
DatabaseVariantAnnotationField
mutationTasterScore
DatabaseVariantAnnotationField
mutationTasterScoreConverted
DatabaseVariantAnnotationField