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
MultisampleAvroGenomicRDD
rdd
MultisampleGenomicRDD
rdd
main
PhredUtils
makeFormatter
AnySAMInFormatterCompanion BAMInFormatter SAMInFormatter
makeIterator
FullOuterShuffleRegionJoin InnerShuffleRegionJoin InnerShuffleRegionJoinAndGroupByLeft LeftOuterShuffleRegionJoin RightOuterShuffleRegionJoin RightOuterShuffleRegionJoinAndGroupByLeft ShuffleRegionJoin
makeWriter
AnySAMInFormatter BAMInFormatter SAMInFormatter
mapped
FlagStatMetrics
mapq
AlignmentRecordField
mapq0Reads
VariantCallingAnnotationsField
markDuplicates
AlignmentRecordRDD
matches
MdTag RegExp
mateAlignmentStart
AlignmentRecordField
mateContigName
AlignmentRecordField
mateMapped
AlignmentRecordField
mateNegativeStrand
AlignmentRecordField
maxLogP
RecalibrationTable
maxQualScore
RecalibrationTable
maybeMDTagRead
MDTagging
md5
SequenceRecord
mdTag
IncorrectMDTagException RichAlignmentRecord
mdTagsAdded
MDTagging
mdTagsExtant
MDTagging
merge
ReferenceRegion IndelRealignmentTarget
mergeAnnotations
VariantContext
mergeFragments
NucleotideContigFragmentRDD
mergeRegions
NonoverlappingRegions
minAcceptableQuality
BaseQualityRecalibration Recalibrator
mismatchedBase
MdTag
mismatches
Observation MdTag
mismatchingPositions
AlignmentRecordField
models
adam
moveAlignment
MdTag
moveLeft
RichCigar
mqRankSum
VariantCallingAnnotationsField
mutationTasterPred
DatabaseVariantAnnotationField
mutationTasterScore
DatabaseVariantAnnotationField
mutationTasterScoreConverted
DatabaseVariantAnnotationField