MAGIC_NUMBER
TwoBitFile
MASK
TwoBitFile
MapTargets
Timers
MapTools
util
MarkDuplicatesInDriver
Timers
MarkReads
Timers
Match
MdTagEvent
MdTag
util
MdTagEvent
util
Mismatch
MdTagEvent
main
PhredUtils
makeHeader
VcfHeaderUtils
mapToJavaMap
ADAMContext
mapped
FlagStatMetrics
mapq
AlignmentRecordField
mapq0Reads
VariantCallingAnnotationsField
maskBlocks
TwoBitRecord
matches
MdTag 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
minAcceptableQuality
BaseQualityRecalibration Recalibrator
mismatchedBase
MdTag
mismatches
Observation DecadentRead MdTag
mismatchesOption
DecadentRead
mismatchingPositions
AlignmentRecordField
models
adam
moveAlignment
MdTag
moveLeft
RichCigar
moveMatrix
SmithWaterman
mqRankSum
VariantCallingAnnotationsField
mutationTasterPred
DatabaseVariantAnnotationField
mutationTasterScore
DatabaseVariantAnnotationField
mutationTasterScoreConverted
DatabaseVariantAnnotationField