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Seed Handling

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Testing & Debugging

VCF I/O

internal

addDefaultValue (ArgumentParser)

atEnd (BamStream)

atEnd (SequenceStream)

back (Chained Seed)

begin (Chained Seed)

begin (Index)

beginPosition (Gaps)

build (FaiIndex)

chainSeedsGlobally

clear (BedRecord)

clear (LfTable)

clear (PrefixSumTable)

clear (RankDictionary)

clear (SentinelRankDictionary)

clear (VcfHeader)

clear (VcfHeaderRecord)

clippedBeginPosition (Gaps)

clippedEndPosition (Gaps)

close (BamStream)

close (SequenceStream)

countOccurrences (SentinelRankDictionary)

createCompressedSa

createLfTable

createPrefixSumTable

createRankDictionary

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 (RightArrayBinaryTree Iterator)

getRank

getRightChildPos

getSentinelSubstitute (SentinelRankDictionary)

getSubTreeSize

getValue (PrefixSumTable)

getValue (RankDictionary)

getValue (SentinelRankDictionary)

goLeftChild

goRight (RightArrayBinaryTree Iterator)

goRightChild

hostToVirtualPosition (Journaled String)

indexCreate (FMIndex)

indexSupplied (FMIndex)

infix (Finder)

isGood (BamStream)

isGood (SequenceStream)

isSetBit

length (Chained Seed)

length (PrefixSumTable)

open (BamStream)

open (CompressedSA)

open (Index)

open (LfTable)

open (PrefixSumTable)

open (RankDictionary)

open (RankSupportBitString)

open (RightArrayBinaryTree)

open (SentinelRankDictionary)

open (SequenceStream)

open (SparseString)

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

setBeginPosition (Gaps)

setCharacter (RightArrayBinaryTree Iterator)

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)

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