MAGIC_NUMBER
TwoBitFile
MASK
TwoBitFile
MDTagging
read
MapTargets
Timers
MapTools
util
MarkDuplicatesInDriver
Timers
MarkReads
Timers
Match
MdTagEvent
MdTag
util
MdTagEvent
util
Mismatch
MdTagEvent
MultiContigNonoverlappingRegions
models
main
PhredUtils
makeHeader
VcfHeaderUtils
mapToJavaMap
ADAMContext
mapped
FlagStatMetrics
mapq
AlignmentRecordField
mapq0Reads
VariantCallingAnnotationsField
matches
MdTag
RegExp
mateAlignmentStart
AlignmentRecordField
mateContig
AlignmentRecordField
mateMapped
AlignmentRecordField
mateNegativeStrand
AlignmentRecordField
maxLogP
RecalibrationTable
maxQualScore
RecalibrationTable
maybeMDTagRead
MDTagging
maybeSaveBam
AlignmentRecordRDDFunctions
maybeSaveFastq
AlignmentRecordRDDFunctions
md5
SequenceRecord
mdTag
IncorrectMDTagException
RichAlignmentRecord
mdTagsAdded
MDTagging
mdTagsExtant
MDTagging
merge
ReferenceRegion
IndelRealignmentTarget
mergeAnnotations
VariantAnnotationConverter
mergeFragments
NucleotideContigFragmentRDDFunctions
mergeRegions
NonoverlappingRegions
minAcceptableQuality
BaseQualityRecalibration
Recalibrator
mismatchedBase
MdTag
mismatches
Observation
MdTag
mismatchingPositions
AlignmentRecordField
models
adam
moveAlignment
MdTag
moveLeft
RichCigar
moveMatrix
SmithWaterman
mqRankSum
VariantCallingAnnotationsField
mutationTasterPred
DatabaseVariantAnnotationField
mutationTasterScore
DatabaseVariantAnnotationField
mutationTasterScoreConverted
DatabaseVariantAnnotationField