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Seed Handling
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Testing & Debugging
internal
addDefaultValue (ArgumentParser)
atEnd (BamStream)
atEnd (SequenceStream)
back (Chained Seed)
begin (Chained Seed)
beginPosition (Gaps)
build (FaiIndex)
chainSeedsGlobally
clear (LfTable)
clear (PrefixSumTable)
clear (RankDictionary)
clear (SentinelRankDictionary)
clippedBeginPosition (Gaps)
clippedEndPosition (Gaps)
close (BamStream)
close (SequenceStream)
countOccurrences (SentinelRankDictionary)
createCompressedSa (CompressedSA)
createLfTable
createPrefixSumTable (PrefixSumTable)
createRankDictionary (RankDictionary)
createRightArrayBinaryTree
createSentinelRankDictionary (SentinelRankDictionary)
empty (LfTable)
empty (RankDictionary)
empty (SentinelRankDictionary)
end (Chained Seed)
endPosition (Gaps)
findTagKey (BamTagsDict)
flush (BamStream)
flush (SequenceStream)
front (Chained Seed)
getAlphabetSize (PrefixSumTable)
getAutoSeqStreamFormatName
getCharacter (PrefixSumTable)
getCharacter
getCharacterPosition (PrefixSumTable)
getFileFormatExtensions (ArgumentParser)
getLeftChildPos
getPosition
getPrefixSum (PrefixSumTable)
getRank
getRightChildPos
getSentinelSubstitute (SentinelRankDictionary)
getSubTreeSize
getValue (RankDictionary)
getValue (SentinelRankDictionary)
getvalue (PrefixSumTable)
goLeftChild
goRightChild
hostToVirtualPosition (Journaled String)
indexCreate (FMIndex)
indexSupplied (FMIndex)
infix (Finder)
isGood (BamStream)
isGood (SequenceStream)
isSetBit
length (Chained Seed)
length (PrefixSumTable)
open (BamStream)
open (Index)
open (LfTable)
open (PrefixSumTable)
open (RankDictionary)
open (RightArrayBinaryTree)
open (SentinelRankDictionary)
open (SequenceStream)
prefixSum (PrefixSumTable)
readAll (SequenceStream)
readBatch (SequenceStream)
readRecord (BamStream)
readRecord (SequenceStream)
reset (BamStream)
resize (PrefixSumTable)
save (CompressedSA)
save (Index)
save (LfTable)
save (PrefixSumTable)
save (RankDictionary)
save (RankSupportBitString)
save (RightArrayBinaryTree)
save (SentinelRankDictionary)
save (SparseString)
seedSize (Seed)
sentinelPosition (SentinelRankDictionary)
setBeginPosition (Gaps)
setCharacter
setClippedBeginPosition (Gaps)
setClippedEndPosition (Gaps)
setDefaultValue (ArgumentParser)
setEndPosition (Gaps)
setHelpText (ArgumentParser)
setLfTable
setMaxValue (ArgumentParser)
setMinValue (ArgumentParser)
setPrefixSum
setSentinelPosition (SentinelRankDictionary)
setSentinelSubstitute (SentinelRankDictionary)
setValidValues (ArgumentParser)
splitAlignment
toSuffixPosition (FMIndex)
transpose (Matrix)
value (CompressedSA)
virtualToHostPosition (Journaled String)
write2 (FASTA/FASTQ I/O)
writeAll (SequenceStream)
writeRecord (BamStream)
writeRecord (FASTA/FASTQ I/O)
writeRecord (SequenceStream)
Metafunctions
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