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appendAlignedRead
appendMatePair
appendName
appendRead
assignValueByKey
buildIndex (BamTagsDict)
calculateInsertSizes
calculateMateIndices
clearContigs
clearReads
clearValues
compactAlignedReads
compactPairMatchIds
convertMatchesToGlobalAlignment
convertPairWiseToGlobalAlignment
createLeftChild
createRightChild
createSibling
getAnnotation
getClrRange
getIdByName
getMateNo
getName (AnnotationTree Iterator)
getParentName
getRead
getType
getUniqueName
getValueByKey
goDown (AnnotationTree Iterator)
goNextRight (AnnotationTree Iterator)
goNextUp (AnnotationTree Iterator)
goRight (AnnotationTree Iterator)
goRoot (AnnotationTree Iterator)
goTo
goUp (AnnotationTree Iterator)
hasIndex (BamTagsDict)
isLastChild
layoutAlignment
loadContig
loadContigs
loadReads
lockContig
lockContigs
lowerBoundAlignedReads
nodeDown (AnnotationTree Iterator)
nodeRight (AnnotationTree Iterator)
nodeUp (AnnotationTree Iterator)
positionGapToSeq
positionSeqToGap
printAlignment
read
refresh
setName (AnnotationTree Iterator)
setType
sortAlignedReads
unlockAndFreeContig
unlockAndFreeContigs
unlockContig
unlockContigs
upperBoundAlignedReads
write
writeContigs
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