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appendAlignedRead
appendMatePair
appendName
appendRead
calculateInsertSizes
calculateMateIndices
clearReads
compactAlignedReads
compactPairMatchIds
convertMatchesToGlobalAlignment
convertPairWiseToGlobalAlignment
getIdByName
getMateNo
getRead
layoutAlignment
loadContig
loadContigs
loadReads
lockContig
lockContigs
lowerBoundAlignedReads
printAlignment
read
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unlockAndFreeContig
unlockAndFreeContigs
unlockContig
unlockContigs
upperBoundAlignedReads
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writeContigs
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