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Alignment Free
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BAM I/O
assignTagsBamToSam
assignTagsSamToBam
bamRecordToAlignment
eraseTag (BamTagsDict)
extractTagValue (BamTagsDict)
findTagKey (BamHeaderRecord)
getAlignmentLengthInRef
getBamTypeChar
getBamTypeSize
getTagKey (BamTagsDict)
getTagType (BamTagsDict)
getTagValue (BamHeaderRecord)
getTagValue (BamTagsDict)
getUnalignedCount (BamIndex)
hasFlagAllProper
hasFlagDuplicate
hasFlagFirst
hasFlagLast
hasFlagMultiple
hasFlagNextRC
hasFlagNextUnmapped
hasFlagQCNoPass
hasFlagRC
hasFlagRC
hasFlagSecondary
hasFlagUnmapped
jumpToOrphans (BamIndex)
jumpToRegion (BamIndex)
nameStore (BamIOContext)
nameStoreCache (BamIOContext)
read (BamIndex)
setTagValue (BamHeaderRecord)
setTagValue (BamTagsDict)
BED I/O
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