MapQualityScores
metrics
MapTools
util
MappedPosition
metrics
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
mapq
ADAMRecordField
mapq0Reads
VariantCallingAnnotationsField
matchedByName
BaseQualityScores
BucketComparisons
CombinedComparisons
DupeMismatch
MapQualityScores
MappedPosition
OverMatched
matches
OverMatched
Pileup
RegExp
mateAlignmentStart
ADAMRecordField
mateContig
ADAMRecordField
mateMapped
ADAMRecordField
mateNegativeStrand
ADAMRecordField
max
SmithWaterman
maxLogP
RecalibrationTable
maxQualScore
RecalibrationTable
maxX
SmithWaterman
maxY
SmithWaterman
md5
SequenceRecord
mdTag
RichADAMRecord
merge
GenericRange
IndelRange
IndelRealignmentTarget
SNPRange
ReferenceRegion
mergeAnnotations
VariantAnnotationConverter
mergeRegions
NonoverlappingRegions
metrics
adam
minAcceptableQuality
BaseQualityRecalibration
Recalibrator
mismatchThreshold
IndelRealignmentTarget
mismatchedBase
MdTag
MismatchEvent
mismatches
Observation
DecadentRead
Pileup
mismatchesOption
DecadentRead
mismatchingPositions
ADAMRecordField
models
adam
moveAlignment
MdTag
moveLeft
RichCigar
mqRankSum
VariantCallingAnnotationsField
multipleNucleotideVariantCount
GenotypesSummaryCounts
mutationTasterPred
ADAMDatabaseVariantAnnotationField
mutationTasterScore
ADAMDatabaseVariantAnnotationField
mutationTasterScoreConverted
ADAMDatabaseVariantAnnotationField