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