Functions
This section lists the functions implemented in SeqAn. Note that SeqAn uses global functions to access data types, e.g. the length of a string str is determined by calling length(str) and not by calling a member function str.length().
Functions

addDefaultValue (ArgumentParser) | Add to the default values of an option of an ArgumentParser.
assignProfile (ProfileSeq Score) | Assign profile to ProfileSeg Score.
assignProfile (ProfileSeqFrac Score) | Assign profile to ProfileSegFrac Score.
atEnd (BamStream) | Check whether a BamStream object is at end when reading.
atEnd (SequenceStream) | Check whether a SequenceStream is at the end of the file.
back (Chained Seed) | Returns a reference to the last seed diagonal.
begin (Chained Seed) | Returns an iterator to the beginning of the seed digonals.
begin (Index) | Returns an iterator pointing to the root node of the virtual string tree/trie of an index. The only exception are Postorder iterators, where begin returns an iterator pointing to the leftmost node in the tree/trie.
beginPosition (Gaps) | Return the clipping begin position as a source position.
build (FaiIndex) | Create FaiIndex from FASTA file.
chainSeedsGlobally | Global chaining of seeds.
clear (BedRecord) | Reset BED record to state after default initialization.
clear (LfTable) | Clears the LF table.
clear (PrefixSumTable) | Clears the prefix sum table.
clear (RankDictionary) | Clears the rank dictionary.
clear (SentinelRankDictionary) | Clears the dictionary.
clear (VcfHeader) | Clear a VcfHeader.
clear (VcfHeaderRecord) | Clear a VcfHeaderRecord.
clippedBeginPosition (Gaps) | Return the begin position of the clipping in the unclipped gapped sequence.
clippedEndPosition (Gaps) | Return the end position of the clipping in the unclipped gapped sequence.
close (BamStream) | Close BamStream object's underlying file.
close (SequenceStream) | Close the SequenceStream.
countOccurrences (SentinelRankDictionary) | Returns the number of occurrences of a specified character from the start to a specified position.
createCompressedSa | This functions creates a compressed suffix array with a specified compression factor.
createLfTable | Creates the LF table
createPrefixSumTable | Creates the prefix sum table
createRankDictionary | This functions creates the dictionary.
createRightArrayBinaryTree | Computes the wavelet tree structure of a text.
createSentinelRankDictionary (SentinelRankDictionary) | This functions creates the dictionary structure.
empty (LfTable) | Clears the LF table.
empty (RankDictionary) | Returns whether or not the rank dictionary is empty.
empty (SentinelRankDictionary) | Returns whether or not the dictionary is empty.
end (Chained Seed) | Returns an iterator to the end of the seed diagonals.
endPosition (Gaps) | Return the clipping end position as a source position.
findTagKey (BamTagsDict) | Find a tag by its key for a BamTagsDict object.
flush (BamStream) | Flush output when writing.
flush (SequenceStream) | Write all data from SequenceStream to disk.
front (Chained Seed) | Returns a reference to the first seed diagonal.
getAlphabetSize (PrefixSumTable) | Returns the number of different characters in the prefix sum table.
getAutoSeqStreamFormatName | Returns
getCharacter (PrefixSumTable) | Returns the character of a given position within the prefix sum table.
getCharacter | This function returns the pivot character of the node the iterator currently points to.
getCharacterPosition (PrefixSumTable) | Returns the position of a given character within the prefix sum table.
getFileFormatExtensions (ArgumentParser) | Returns file format extensions given a format tag.
getLeftChildPos | Returns the position in RightArrayBinaryTree of the left child vertex.
getPosition (RightArrayBinaryTree Iterator) | Returns the position of the iterator in the host.
getRank | Returns the rank (the number of bits set from the start of the bit string) of a specified position.
getRightChildPos | Returns the position in RightArrayBinaryTree of the right child vertex.
getSentinelSubstitute (SentinelRankDictionary) | Returns the character used to substitute the sentinel sign.
getSubTreeSize | Returns the number of vertices in the subtree starting at the position an iterator points to.
getValue (PrefixSumTable) | Returns the prefix sum of a given position.
getValue (RankDictionary) | Returns the character of a specified position.
getValue (SentinelRankDictionary) | Returns the character of a specified position.
goLeftChild | Sets the iterator to the left child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
goRight (RightArrayBinaryTree Iterator) | Iterates to the next sibling in a tree.
goRightChild | Sets the iterator to the right child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
hostToVirtualPosition (Journaled String) | Translates position in host to virtual (view) position.
indexCreate (FMIndex) | Creates a specific Fibre.
indexSupplied (FMIndex) | Returns whether a specific Fibre is present.
infix (Finder) | Returns the segment of the last found match in haystack.
isGood (BamStream) | Check whether the BamStream object has is in the failure state.
isGood (SequenceStream) | Check whether a SequenceStream object is ready for reading.
isSetBit | Returns whether the bit with the given index is set to 1.
length (Chained Seed) | Returns the number of diagonals in the chained seed.
length (PrefixSumTable) | Returns the number of different characters in the prefix-sum table.
open (BamStream) | Open a BamStream object for reading/writing.
open (CompressedSA) | This functions opens a compressed suffix array from disk.
open (Index) | This functions opens an index from disk.
open (LfTable) | This functions loads a LF table from disk.
open (PrefixSumTable) | This functions loads a prefix-sum table from disk.
open (RankDictionary) | This functions loads a dictionary from disk.
open (RankSupportBitString) | This functions saves a RankSupportBitString to disk.
open (RightArrayBinaryTree) | This functions loads a RightArrayBinaryTree from disk.
open (SentinelRankDictionary) | This functions loads a dictionary from disk.
open (SequenceStream) | Open or re-open a file using a SequenceStream.
open (SparseString) | This functions saves a sparse string to disk.
prefixSum (PrefixSumTable) | Returns a reference to the entry of the prefix sum table of a given position.
readAll (SequenceStream) | Read all sequence records from a SequenceStream object.
readBatch (SequenceStream) | Read a given number of sequence records from SequenceStream.
readRecord (BamStream) | Read one BamAlignmentRecord from a BamStream.
readRecord (SequenceStream) | Read the next sequence record from SequenceStream.
reset (BamStream) | Reset BamStream object to status after construction.
resize (PrefixSumTable) | Resize the prefix sum table to be able to store more or less characters.
save (CompressedSA) | This functions saves a compressed suffix array to disk.
save (Index) | This functions saves an index to disk.
save (LfTable) | This functions saves a LF table to disk.
save (PrefixSumTable) | This functions saves a prefix-sum table to disk.
save (RankDictionary) | This functions saves a dictionary to disk.
save (RankSupportBitString) | This functions saves a RankSupportBitString to disk.
save (RightArrayBinaryTree) | This functions saves a RightArrayBinaryTree to disk.
save (SentinelRankDictionary) | This functions saves a dictionary to disk.
save (SparseString) | This functions saves a sparse string to disk.
seedSize (Seed) | Returns the number of matches and mismatches of the seed. This is the longest true diagonal fitting into its dimensions.
sentinelPosition | Returns whether a specified position is a sentinel position.
setBeginPosition (Gaps) | Set the begin position of the clipped gapped sequence, given a source position.
setCharacter (RightArrayBinaryTree Iterator) | setCharacter(iterator, character) sets the character of the node the iterator points to to character.
setClippedBeginPosition (Gaps) | Sets the begin position of the clipping.
setClippedEndPosition (Gaps) | Sets the end position of the clipping.
setDefaultValue (ArgumentParser) | Set default value of an option of an ArgumentParser.
setEndPosition (Gaps) | Set the end position of the clipped gapped sequence, given a source position.
setHelpText (ArgumentParser) | Set help text of argument parser.
setLfTable | Set the LfTable of the compressed suffix array.
setMaxValue (ArgumentParser) | Set largest allowed value for an option or argument of an ArgumentParser.
setMinValue (ArgumentParser) | Set smallest allowed value for an option or argument of an ArgumentParser.
setPrefixSum | Returns a reference to the entry of the prefix-sum table of a given position.
setSentinelPosition (SentinelRankDictionary) | Sets the sentinel position..
setSentinelSubstitute (SentinelRankDictionary) | Sets the character used to substitute the sentinel sign.
setValidValues (ArgumentParser) | Set valid values for an argument or option of an ArgumentParser.
splitAlignment | Compute split alignments.
toSuffixPosition (FMIndex) | This function computes the position of a specified position in the suffix array (additionally containing entries for the sentinels. The returned position correspond to the suffix array of the original text without sentinels.
transpose (Matrix) | Transposes matrix
value (CompressedSA) | Returns the value stored at a specified position in the compressed suffix-array.
virtualToHostPosition (Journaled String) | Translates virtual (view) position to position in host.
write2 (FASTA/FASTQ I/O) | Write FASTA or FASTQ records.
writeAll (SequenceStream) | Write sequence records from to a SequenceStream object.
writeRecord (BamStream) | Write one BamAlignmentRecord to a BamStream.
writeRecord (FASTA/FASTQ I/O) | Write one FASTA or FASTQ record.
writeRecord (SequenceStream) | Write one sequence record from to a SequenceStream object.

Alignment Free

alignmentFreeComparison | Computes the pairwise similarity scores for a set of sequences
calculateCovariance | Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model.
calculateOverlapIndicator | Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p)
calculatePeriodicity | Calculate word periodicity (indicator for overlaps)
calculateProbability | Calculates the probability of a sequence given a Bernoulli model (String of background frequencies)
calculateVariance | Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model.
countKmers | Counts kmers in a sequence. Optionally, a background model is returned.
cutNs | Cut out all masked sequences from a Dna5String.
stringToStringSet | Transform a String into a StringSet containing this String.

Alignments

addToProfile | Profile-to-sequence alignment with sequence integration.
assignSource (Gaps) | Assign the source of a Gaps object, copying data.
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain.
clearClipping (Gaps) | Clear clipping from Gaps object.
clearGaps (Gaps) | Clear gaps and clipping from Gaps object.
col | A column in an alignment.
cols | The container of columns in an alignment.
countGaps (Gaps) | Reports number of continues gaps right of current iterator position.
gapValue | Return the "gap" value from an alphabet.
getProjectedPosition | Projects a position of one sequence taking part in a pairwise match onto the other sequence.
getScore (LocalAlignmentEnumerator) | Compute next suboptimal local alignment.
globalAlignment | Computes the best global pairwise alignment.
globalAlignmentScore | Computes the best global pairwise alignment score.
globalMsaAlignment | Computes a global multiple alignment.
heaviestCommonSubsequence | Computes the heaviest common subsequence between two strings using the match information given in an alignment graph.
heaviestIncreasingSubsequence | Computes the heaviest increasing subsequence.
host (ConsensusScoreSequenceEntry) | Returns reference to sequence from entry.
insertGap | Insert one gap into a gapped sequence.
insertGaps | Insert multiple gaps into a gapped sequence.
integrateAlign | Integrates an alignment into another by copying the gaps.
isGap (Gaps) | Query whether a given clipped view position is a gap.
isReversed | Returns true if the segment match is in reverse orientation.
length (Gaps) | Return length of the gapped sequence.
localAlignment | Computes the best pairwise local alignment using the Smith-Waterman algorithm.
longestCommonSubsequence | Computes the longest common subsequence.
longestIncreasingSubsequence | Computes the longest increasing subsequence.
matchRefinement | Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
nextLocalAlignment | Compute next suboptimal local alignment.
position (ConsensusScoreSequenceEntry) | Returns position stored in entry.
removeGap | Remove one gap from a gapped sequence.
removeGaps | Remove multiple gaps from a gapped sequence.
row | A row in an alignment.
rows | The container of rows in an alignment.
scoreGap | Score for gaps.
scoreGapExtend | Score for extending gaps.
scoreGapOpen | Score for opening a gap.
scoreMatch | Match score.
scoreMismatch | Mismatch score.
sequenceEntryForScore (Score) | Helper function for element access, depending on score type.
setScoreGap | Set gap opening and extension score.
setScoreGapExtend | Set gap extension score.
setScoreGapOpen | Set gap opening score.
setScoreMatch | Set match score.
setScoreMismatch | Set mismatch score.
setSource (Gaps) | Set the source of a Gaps object, do not copy if possible.
setStrings | Loads the sequences of a stringset into an alignment.
toSourcePosition | Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned.
toViewPosition | Transforms source to view position.
unclippedLength (Gaps) | Return length of the gapped sequence without clipping.
value (ConsensusScoreSequenceEntry) | Returns value of character referenced by entry.

Alphabets

assignQualities | Assign quality values between strings.
assignQualityValue | Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence.
convert | Converts a value into another value.
convertQuality | Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
gapValue | Return the "gap" value from an alphabet.
getQualityValue | Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence.
maxValue | Supremum for a given type.
minValue | Infimum for a given type.
ordValue | Maps an alphabet 1-to-1 to the interval [0..ValueSize).
unknownValue | Return the "unknown" value from an alphabet.
valueSize | Returns size of an alphabet.

Array Handling

arrayClearSpace | Destroys the begin of an array and keeps the rest.
arrayConstruct | Construct objects in a given memory buffer.
arrayConstructCopy | Copy constructs an array of objects into in a given memory buffer.
arrayConstructMove | Move constructs an array of objects into in a given memory buffer.
arrayCopy | Copies a range of objects into another range of objects.
arrayCopyBackward | Copies a range of objects into another range of objects starting from the last element.
arrayCopyForward | Copies a range of objects into another range of objects starting from the first element.
arrayDestruct | Destroys an array of objects.
arrayFill | Assigns one object to each element of a range.
arrayMove | Moves a range of objects into another range of objects.
arrayMoveBackward | Moves a range of objects into another range of objects starting from the last element.
arrayMoveForward | Moves a range of objects into another range of objects starting from the first element.

Atomic Operations

atomicAdd | Atomically add an integer to another integer.
atomicCas | Compare-and-Swap operation.
atomicDec | Atomically decrement an integer.
atomicInc | Atomically increment an integer.
atomicMax | Lock-free implementation of x = max(x, y).
atomicMin | Lock-free implementation of x = min(x, y).
atomicOr | Atomically combine two integers with OR operation.
atomicXor | Atomically combine wto integers with XOR operation.

BAM I/O

assignTagsBamToSam | Assign tags in BAM format to tags in SAM format.
assignTagsSamToBam | Assign tags in SAM format to tags in BAM format.
bamRecordToAlignment | Convert BamAlignmentRecord to an Align object.
eraseTag (BamTagsDict) | Erase tag from BamTagsDict.
extractTagValue (BamTagsDict) | Extract and cast "atomic" value from tags string with index idx.
findTagKey (BamHeaderRecord) | Find a tag's key of a BamHeaderRecord.
getAlignmentLengthInRef | Returns length of BamAlignmentRecord's projection in reference.
getBamTypeChar | Return char identifying the type of the atomic argument.
getBamTypeSize | Return size of the type identified by c.
getTagKey (BamTagsDict) | Return key of a tag by index.
getTagType (BamTagsDict) | Get key of a tag by index.
getTagValue (BamHeaderRecord) | Return tag value from a BamHeaderRecord or BamTagsDict.
getTagValue (BamTagsDict) | Return the value of a tag by its index in the BamTagsDict.
getUnalignedCount (BamIndex) | Query index for number of unaligned reads.
hasFlagAllProper | Return true if a BamAlignmentRecord has the "all properly aligned" flag set.
hasFlagDuplicate | Return true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set.
hasFlagFirst | Return true if a BamAlignmentRecord has the "first fragment of template" flag set.
hasFlagLast | Return true if a BamAlignmentRecord has the "last fragment of template" flag set.
hasFlagMultiple | Return true if a BamAlignmentRecord has the "multiple" flag set.
hasFlagNextRC | Return true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set.
hasFlagNextUnmapped | Return true if a BamAlignmentRecord has the "next fragment unmapped" flag set.
hasFlagQCNoPass | Return true if a BamAlignmentRecord has the "does not pass quality controls" flag set.
hasFlagRC | Return true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagRC | Return true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagSecondary | Return true if a BamAlignmentRecord has the "secondary alignment" flag set.
hasFlagUnmapped | Return true if a BamAlignmentRecord has the "fragment unmapped" flag set.
jumpToOrphans (BamIndex) | Seek to orphans block in BAM BGZF stream using an index.
jumpToRegion (BamIndex) | Seek in BAM BGZF stream using an index.
nameStore (BamIOContext) | Return reference to name store from BamIOContext.
nameStoreCache (BamIOContext) | Return reference to name store cache from BamIOContext.
read (BamIndex) | Load a BAM index from a given file name.
setTagValue (BamHeaderRecord) | Set tag value of a BamHeaderRecord.
setTagValue (BamTagsDict) | Set the value of a tag through a BamTagsDict.

BED I/O

addSequenceName (BedStream) | Add the name of a sequence to a BedStream.
atEnd (BedStream) | Query a BedStream for being at the end of the file.
close (BedStream) | Closes a BedStream
flush (BedStream) | Flush to a BedStream
isGood (BedStream) | Query a BedStream for errors.
nameStore (BedIOContext) | Return reference to name store from BedIOContext.
nameStoreCache (BedIOContext) | Return reference to name store cache from BedIOContext.
open (BedStream) | Open a BedStream.
readRecord (BedRecord) | Read a BED record from a file.
readRecord (BedStream) | Read a record from a BedStream
writeRecord (BedRecord) | Write a BED record to a file.
writeRecord (BedStream) | Write a record to a BedStream

Basic

nukeCopies | Reset all pointers connected to a given one.
source | Return underlying object.

Bit Twiddling

clearAllBits | Set all bits to 0.
clearBit | Set the bit with the given index to 0.
isBitSet | Returns whether the bit with the given index is set to 1.
popCount | Returns number of set bits in an integer.
setBit | Set the bit with the given index to 1.
setBitTo | Set the bit with the given index to the given value.

C++ built-in

cast operator | C++ built-in cast operator.
operator delete | C++ built-in deallocation operator.
operator delete[] | C++ built-in array deallocation operator.
operator new | C++ built-in allocation operator.
operator new[] | C++ built-in array allocation operator operator.
operator! | C++ built-in logical negation operator.
operator!= | C++ built-in inequal comparison operator.
operator% | C++ built-in modulo operator.
operator%= | C++ built-in modulo assignment operator.
operator& | C++ built-in bitwise AND operator.
operator& (reference) | C++ built-in reference/address-of operator.
operator&& | C++ built-in logical AND operator.
operator&= | C++ built-in bitwise AND assignment operator.
operator> | C++ built-in greater-than comparison operator.
operator>> | C++ built-in bitwise right shift operator.
operator>> (Stream) | C++ built-in bitwise get-from/stream extraction operator.
operator>>= | C++ built-in bitwise right shift assignment operator.
operator>= | C++ built-in greather-than-or-equal comparison operator.
operator< | C++ built-in less-than comparison operator.
operator<< | C++ built-in bitwise left shift operator.
operator<< (Stream) | C++ built-in bitwise put-to/stream insertion operator.
operator<<= | C++ built-in bitwise left shift assignment operator.
operator<= | C++ built-in less-than-or-equal comparison operator.
operator() | C++ built-in function call operator.
operator* | C++ built-in multiplication operator.
operator* (indirection) | C++ built-in indirection/object-pointed-to-by operator.
operator*= | C++ built-in multiplication assignment operator.
operator+ | C++ built-in addition operator.
operator+ (unary) | C++ built-in unary plus (integer promotion) operator.
operator++ (prefix) | C++ built-in prefix increment operator.
operator++ (suffix) | C++ built-in suffix increment operator.
operator+= | C++ built-in addition assignment operator.
operator, | C++ built-in comma operator.
operator- | C++ built-in subtraction operator.
operator- (unary) | C++ built-in unary minus (additive inverse) operator.
operator-> | C++ built-in structure dereference operator.
operator->* | C++ built-in member-pointed-to-by-b-of-object-pointed-to-by-a operator.
operator-- (prefix) | C++ built-in prefix decrement operator.
operator-- (suffix) | C++ built-in suffix decrement operator.
operator-= | C++ built-in subtraction assignment operator.
operator/ | C++ built-in division operator.
operator/= | C++ built-in division assignment operator.
operator= | C++ built-in Assignment operator.
operator== | C++ built-in equal comparison operator.
operator[] | C++ built-in array subscript operator.
operator^ | C++ built-in bitwise XOR operator.
operator^= | C++ built-in bitwise XOR assignment operator.
operator~ | C++ built-in bitwise NOT operator.

Class: Align

integrateAlign | Integrates an alignment into another by copying the gaps.

Comparisons

compare | Compares two objects.
hasPrefix | Test whether a sequence is prefix of another sequence.
isEqual | Operator "==".
isGreater | Operator ">".
isGreaterOrEqual | Operator ">=".
isLess | Operator "<".
isLessOrEqual | Operator "<=".
isNotEqual | Operator "!=".
isPrefix | Test whether a sequence is prefix of another sequence.
lcpLength | Length of longest common prefix.

Concepts

ignoreUnusedVariableWarning | Removes unused variable warning.
requireBooleanExpr | Tests for a boolean expression.
sameType | Tests for equality of types.

Consensus

consensusAligment | Compute consensus alignment.
reAlign | Perform realignment similar to Anson-Myers algorithm.

Containers

back | The last item in container.
begin | The begin of a container.
beginPosition | Begin position of object in host.
capacity | The maximal length.
clear | Resets an object.
create | Makes an object to owner of its content.
empty | Test a container for being empty.
end | The end of a container.
endPosition | End position of object in host.
erase | Erases a part of a container
eraseBack | Deletes the last item of a container and reduces its size by 1. The container must have a size greater than or equal to 1.
front | The first item in container.
getValue | Access to the value.
infix | Creates infix object.
infixWithLength | Creates infix object.
iter | Iterator to item at given position.
length | The number of items/characters.
prefix | Creates prefix object.
reserve | Increases the capacity.
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resizeSpace | Makes free space in container
shrinkToFit | Resizes container to minimum capacity
suffix | Creates suffix object.
toCString | Access sequence as c-style string.
value | Reference to the value.

Content Manipulation

append | Concatenate two containers.
appendValue | Appends a value to a container.
assign | Assigns one object to another object.
assignValue | Assigns value to item.
getValue | Access to the value.
insert | Inserts a sequence into a container.
insertValue | Inserts a single value into a container.
move | Hands over content from one container to another container.
moveValue | Assigns value to item.
pop (PriorityType) | Deletes item with the highest priority and adjusts the priority queue.
push (PriorityType) | Inserts a new item and adjusts the priority queue if necessary.
replace | Replaces a part of a container with another container.
set | Assigns one object to another object avoiding to copy contents.
setValue | Makes holder dependent.
swap | Swaps the contents of two values.
top (PriorityType) | Reference to the item with the highest priority.
valueConstruct | Constructs an object at specified position.
valueDestruct | Destoys an object at specified position.

Dependent Object

assignHost | Assign to the host of a given value.
clearHost | Clear the host of the given object.
createHost | Construct the host of the given object.
dependentHost | Query dependent state of a hosted object.
emptyHost | Query emptiness state of a hosted object.
moveHost | Assign to the host of a given value.

Dependent Objects

create | Makes an object to owner of its content.
dependent | Test whether object depends on other objects.
detach | Makes an object independent from other objects.
host | The object a given object depends on.
hostIterator | Return host iterator.
setBegin | Sets begin of object in host.
setBeginPosition | Sets begin position of object in host.
setContainer | Set container of an adaptor iterator.
setEnd | Sets end of object in host.
setEndPosition | Sets begin position of object in host.
setHost | Sets the host of an object.
setPosition | Sets the position of a finder.

Fragment Store

appendAlignedRead | Appends an aligned read entry to a fragment store.
appendMatePair | Appends two paired-end reads to a fragment store.
appendName | Appends a name to a name store.
appendRead | Appends a read to a fragment store.
assignValueByKey | Add or update a key-value pair of the current annotation.
buildIndex (BamTagsDict) | Build index for a BamTagsDict object.
calculateInsertSizes | Calculates a string with insert sizes for each pair match.
calculateMateIndices | Calculates a string that maps the readId of a read to the readId of its mate.
clearContigs | Removes all contigs from a fragment store.
clearReads | Removes all reads from a fragment store.
clearValues | Clear all key-value pairs of the current annotation.
compactAlignedReads | Removes invalid aligned reads and rename alignId sequentially beginning with 0.
compactPairMatchIds | Renames pairMatchId sequentially beginning with 0.
convertMatchesToGlobalAlignment | Converts all matches to a multiple global alignment in gap-space.
convertPairWiseToGlobalAlignment | Converts pair-wise alignments to a multiple global alignment.
createLeftChild | Creates a new left-most child of the current node and returns an iterator to it.
createRightChild | Creates a new right-most child of the current node and returns an iterator to it.
createSibling | Creates a new right sibling of the current node and returns an iterator to it.
getAnnotation | Returns the current annotation.
getClrRange | Get the "clear" range of a read alignment.
getIdByName | Get the id/index of a string in a name store with a cache.
getMateNo | Returns the mate number of read for a given readId.
getName (AnnotationTree Iterator) | Returns the identifier of the current annotation.
getParentName | Returns the identifier of the parent node in the annotation tree of the current annotation.
getRead | Returns the read with the given readId.
getType | Returns the type name of the current annotation.
getUniqueName | Returns a unique name of the current annotation.
getValueByKey | Given a key, retrieve its value of the current annotation.
goDown (AnnotationTree Iterator) | Move the iterator down to the left-most child in the annotation tree.
goNextRight (AnnotationTree Iterator) | Go to the next node in preorder DFS skipping the current node's subtree.
goNextUp (AnnotationTree Iterator) | Go to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings.
goRight (AnnotationTree Iterator) | Move the iterator right to the next sibling in the annotation tree.
goRoot (AnnotationTree Iterator) | Go to the root node in the annotation tree.
goTo | Moves the iterator to an arbitrary node given its annotationId.
goUp (AnnotationTree Iterator) | Move the iterator up in the annotation tree.
hasIndex (BamTagsDict) | Return true if BamTagsDict has an index.
isLastChild | Returns a boolean value that indicates whether the current node is the last child.
layoutAlignment | Calculates a visible layout of aligned reads.
loadContig | Manually loads a contig sequence.
loadContigs | Loads contigs into fragment store.
loadReads | Loads reads into fragment store.
lockContig | Locks a contig sequence from being removed.
lockContigs | Locks all contig sequences from being removed.
lowerBoundAlignedReads | Performs a binary lower bound search on the aligned reads.
nodeDown (AnnotationTree Iterator) | Returns a new iterator to the first child node of the current annotation in the annotation tree.
nodeRight (AnnotationTree Iterator) | Returns a new iterator to the right sibling of the current annotation in the annotation tree.
nodeUp (AnnotationTree Iterator) | Returns a new iterator to the parent node of the current annotation in the annotation tree.
positionGapToSeq | Convert from gap-space in the global alignment to the sequence-space on the reference.
positionSeqToGap | Convert from sequence space on the reference to gap space in the global alignment.
printAlignment | Prints a window of the visible layout of reads into a outstream.
read | Loads records from a file.
refresh | Recreate a name store cache.
setName (AnnotationTree Iterator) | Sets the identifier of the current annotation.
setType | Sets the type name of the current annotation.
sortAlignedReads | Stably sort aligned reads.
unlockAndFreeContig | Removes a previous contig lock and clears sequence no further lock exist.
unlockAndFreeContigs | Removes a previous lock for all contigs and clears sequences without lock.
unlockContig | Removes a previous contig lock.
unlockContigs | Removes a previous lock for all contigs.
upperBoundAlignedReads | Performs a binary upper bound search on the aligned reads.
write | Saves records to a file.
writeContigs | Write contigs from fragment store into file.

GFF I/O

addSequenceName (GffStream) | Add the name of a sequence to a GffStream.
atEnd (GffStream) | Query a GffStream for being at the end of the file.
close (GffStream) | Closes a GffStream
flush (GffStream) | Flush to a GffStream
isGood (GffStream) | Query a GffStream for errors.
nameStore (GffIOContext) | Return reference to name store from GffIOContext.
nameStoreCache (GffIOContext) | Return reference to name store cache from GffIOContext.
open (GffStream) | Open a GffStream.
readRecord (GffStream) | Read a record from a GffStream
writeRecord (GffStream) | Write a record to a GffStream

Graph

addChild | Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
addEdge | Adds a new edge to the graph, either with or without cargo.
addEdges | Shortcut to add multiple edges at once. Creates vertices implicitly.
addVertex | Adds a new vertex to the graph.
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
allPairsShortestPath | Finds shortest paths between all pairs of vertices in a graph.
assignBeginState | Assigns a begin state.
assignCargo | Assigns a new cargo to the edge.
assignEdgeMap | Initializes a vertex map with values of an array.
assignEmissionProbability | Assigns a new emission probability.
assignEndState | Assigns an end state.
assignNextS | Assigns another EdgeStump to the next source pointer.
assignNextT | Assigns another EdgeStump to the next target pointer.
assignProperty | Assigns a property to an item in the property map.
assignRoot | Assigns a new root vertex to the graph.
assignSilentStatus | Assigns a silent status to a state.
assignSource (Graph) | Assigns a source vertex to an edge.
assignStringSet | Assigns a new string set to an alignment graph.
assignTarget | Assigns a target vertex to an edge.
assignTransitionProbability | Assigns a new transition probability to an existing edge.
assignVertexMap | Initializes a vertex map with values of an array.
atBegin | Determines whether an iterator is at the beginning position.
atEnd | Determines whether an iterator is at the end position.
backwardAlgorithm | Implements the backward algorithm.
beginState | Returns a reference to the begin state.
bellmanFordAlgorithm | Computes shortest paths from a single source in a directed graph.
breadthFirstSearch | Implements a breadth-first search on a graph.
buildAlignmentGraph | Builds an Alignment Graph from a set of input alignments.
canParseString | Test whether an automaton can parse a string completely.
cargo | Access to the cargo.
childVertex | Returns the child vertex of an edge.
clear | Resets an object.
clearEdges | Removes all edges in a graph.
clearVertices | Removes all vertices in a graph.
collectLeaves | Returns all leaves underneath a given vertex.
connectedComponents | Decomposes an undirected graph into its connected components.
convertAlignment | Converts an alignment graph into an alignment matrix.
createOracle | Creates a factor oracle.
createOracleOnReverse | Creates a factor oracle for the reversed string.
createRoot | Creates the root in a tree or an automaton.
createSuffixTrie | Creates a trie of all suffixes of a text.
createTrie | Creates a trie.
createTrieOnReverse | Creates a trie for all reversed keywords.
dagShortestPath | Computes shortest paths from a single source in a directed acyclic graph (DAG).
degree | Number of incident edges for a given vertex.
depthFirstSearch | Implements a depth-first search on a graph.
dijkstra | Computes shortest paths from a single source in a graph.
emissionProbability | Returns a reference to the emission probability.
empty | Test a container for being empty.
endState | Returns a reference to the end state.
findEdge | Finds an edge.
findVertex | Finds a vertex given a sequence id and a position.
floydWarshallAlgorithm | Finds shortest paths between all pairs of vertices in a graph.
fordFulkersonAlgorithm | Computes a maximum flow in a directed graph.
forwardAlgorithm | Implements the forward algorithm.
fragmentBegin | Gets the begin position for this fragment or this vertex descriptor in the sequence.
fragmentLength | Gets the length of the label of a given vertex descriptor in the sequence.
generateSequence | Generates random state and alphabet sequences of a given HMM.
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph.
getBeginState | Returns the begin state.
getCargo | Get method for the edge cargo.
getDistanceMatrix | Computes a pairwise distance matrix from an alignment graph.
getEmissionProbability | Returns the emission probability.
getEndState | Returns the end state.
getFirstCoveredPosition | Finds the first position in a sequence that is not assigned to a nil vertex.
getIdLowerBound | Returns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far.
getIdUpperBound | Returns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids.
getLastCoveredPosition | Finds the last position in a sequence that is not assigned to a nil vertex.
getNextS | Get method for the next source pointer.
getNextT | Get method for the next target pointer.
getNil | Utility function returning a value that represents nil. Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc.
getProperty | Get method for an item's property.
getRoot | Get method for the root of a tree or an automaton.
getSource | Get method for the source.
getStringSet | Gets the string set of an alignment graph.
getSuccessor | Gets the successor for a given vertex and an edge label. For an automaton a single character is required whereas for a word graph getSuccessor takes a string.
getTarget | Get method for the target.
getTransitionProbability | Returns the transition probability.
getValue | Access to the value.
goBegin | Iterates to the first position of a container.
goEnd | Iterates to the last position of a container.
goNext | Iterates to next position.
goPrevious | Iterates to pevious position.
hostGraph | The graph this iterator is working on.
idCount | Determines the number of ids that were obtained.
idInUse | Checks whether the given id is in use or not.
inDegree | Number of incoming edges for a given vertex.
isLeaf (Graph) | Tests whether a given vertex is a leaf or not.
isRoot (Graph) | Tests whether a given vertex is the root or not.
isSilent | Indicates whether a state is silent or not.
kruskalsAlgorithm | Computes a minimum spanning tree on a graph.
label (Automaton) | Returns the label of the out-edge this iterator points to (for automatons).
label | Gets the label that is associated with this vertex descriptor.
nextS | Accesses the next source pointer.
nextT | Accesses the next target pointer.
njTree | Computes a guide tree from a distance matrix.
numChildren | Number of children of a given tree vertex.
numEdges | Number of edges in a graph.
numTreeEdges | Number of tree edges.
numVertices | Number of vertices in a graph.
obtainId | Obtains a new id from the id manager.
outDegree | Number of outgoing edges for a given vertex.
parentVertex | Returns the parent vertex of an edge or vertex.
parseString | Parses a string one character at a time and moves accordingly in the automaton.
primsAlgorithm | Computes a minimum spanning tree on a graph.
progressiveAlignment | Performs a progressive alignment.
property | Accesses the property of an item in the property map.
releaseAll | Releases all ids handled by this id manager at once.
releaseId | Releases a given id so it can be redistributed later on.
removeAllChildren | Removes all children from the tree given a parent.
removeChild | Removes a child from the tree given a parent.
removeEdge | Removes an edge from the graph. For automatons a label is required.
removeInEdges | Removes the incoming edges of a given vertex.
removeOutEdges | Removes the outgoing edges of a given vertex.
removeVertex | Removes a vertex.
resizeEdgeMap | Initializes an edge map
resizeVertexMap | Initializes a vertex map.
root | Gets a reference to the root of the tree.
sequenceId | Gets the sequence id that is associated with this vertex descriptor or with a sequence of a fragment.
silentStatus | Reference to the silent status of a state.
sourceVertex | Returns the source vertex of an edge.
stringSet | Gets the string set of an alignment graph.
stronglyConnectedComponents | Decomposes a directed graph into its strongly connected components.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.
target | Accesses the target of an EdgeStump.
targetVertex | Returns the target vertex of an edge.
topologicalSort | Performs a topological sort on a directed acyclic graph (DAG).
transitionProbability | Returns a reference to the transition probability.
transitiveClosure | Determines whether there is a path between any two given vertices or not.
transpose | Transposes a graph, either in-place or from source to dest.
tripletLibraryExtension | Performs a full or group-based consistency extension.
upgmaTree | Computes a guide tree from a distance matrix.
value | Reference to the value.
viterbiAlgorithm | Implements the Viterbi algorithm
weaklyConnectedComponents | Compute weakly connected components of a directed graph.

Index

appendValue (RankSupportBitString) | Appends a value to a container.
bwtAt (IndexEsa) | Shortcut for value(indexBwt(..), ..).
childAt (IndexEsa) | Shortcut for value(indexChildtab(..), ..).
childrenAreLeaves | Test whether iterator points to a node with only leaf-children.
countChildren | Count the number of children of a tree node.
countOccurrences (RankDictionary) | Returns the rank (number of occurrences) of a specified character up to a specified position.
countOccurrences | Returns the number of occurrences of representative substring or a q-gram in the index text.
countOccurrencesMultiple | Returns the number of occurrences of a q-gram for every sequence of a StringSet .
countSequences | Return the number of sequences in an index' underlying text.
createBWTable | Creates a Burrows-Wheeler table from a given text and suffix array.
createChildtab | Creates a child table from a given lcp table.
createCountArray | Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
createLcpTable | Creates a lcp table from a given text and suffix array.
createQGramIndex | Builds a q-gram index on a sequence.
createQGramIndexDirOnly | Builds the directory of a q-gram index on a sequence.
createQGramIndexSAOnly | Builds the suffix array of a q-gram index on a sequence.
createSuffixArray | Creates a suffix array from a given text.
createWotdIndex | Builds a q-gram index on a sequence.
dirAt | Shortcut for value(indexDir(..), ..).
emptyParentEdge | Returns true iff the edge label from the iterator node to its parent is empty.
findRepeats | Search for repeats in a text.
getFibre (CompressedSA) | Returns a specific fibre of a container.
getFibre (FMIndex) | Returns a specific fibre of a fm index.
getFibre (LfTable) | Returns a specific fibre of a container.
getFibre (PrefixSumTable) | Returns a specific fibre of a prefix-sum table.
getFibre (RankDictionary) | Returns a specific fibre of a dictionary.
getFibre (RankSupportBitString) | Returns a specific fibre of a container.
getFibre (RightArrayBinaryTree) | Returns a specific fibre of a container.
getFibre (SentinelRankDictionary) | Returns a specific fibre of a dictionary.
getFibre (SparseString) | Returns a specific fibre of a container.
getFibre | Returns a specific fibre of a container.
getFrequency | Returns the number of sequences, which contain the representative as a substring.
getKmerSimilarityMatrix | Creates a matrix storing the number of common q-grams between all pairs of sequences.
getOccurrence | Returns an occurrence of the representative substring or a q-gram in the index text.
getOccurrences | Returns all occurrences of the representative substring or a q-gram in the index text.
getOccurrencesBwt | Returns the characters left beside all occurrence of the representative substring in the index text.
getStepSize | Return the q-gram step size used for index creation.
goDown | Iterates down one edge or a path in a tree.
goRight | Iterates to the next sibling in a tree.
goRoot | Move iterator to the root node.
goUp | Iterates up one edge to the parent in a tree.
hash | Computes a (lower) hash value for a shape applied to a sequence.
hash2 | Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
hash2Next | Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hash2Upper | Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
hashInit | Preprocessing step of a pure hashNext loop.
hashNext | Computes the hash value for the adjacent shape.
hashUpper | Computes an upper hash value for a shape applied to a sequence.
indexBucketMap | Shortcut for getFibre(.., QGramBucketMap).
indexBwt (IndexEsa) | Shortcut for getFibre(.., EsaBwt).
indexChildtab (IndexEsa) | Shortcut for getFibre(.., EsaChildtab).
indexCounts | Shortcut for getFibre(.., QGramCounts).
indexCountsDir | Shortcut for getFibre(.., QGramCountsDir).
indexCreate | Creates a specific Fibre.
indexDir | Shortcut for getFibre(.., QGramDir).
indexLcp (IndexEsa) | Shortcut for getFibre(.., EsaLcp).
indexLcpe (IndexEsa) | Shortcut for getFibre(.., EsaLcpe).
indexRawSA | Shortcut for getFibre(.., EsaRawSA).
indexRawText | Shortcut for getFibre(.., EsaRawText).
indexRequire | On-demand creation of a specific Fibre.
indexSA | Shortcut for getFibre(.., FibreSA).
indexShape | Shortcut for getFibre(.., QGramShape).
indexSupplied | Returns whether a specific Fibre is present.
indexText | Shortcut for getFibre(index, FibreText()).
isLeaf | Test whether a tree iterator points to a leaf.
isLeftMaximal | Test whether the occurrences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensible | Test whether the characters left of the two occurrences of representative are equal.
isRightTerminal | Test whether iterator points to a suffix.
isRoot | Test whether a tree iterator points to the root node.
isUnique | Test whether the representative occurs only once in every sequence.
lca | Returns the last common ancestor of two tree nodes.
lcp | Returns the length of the longest-common-prefix of two suffix tree nodes.
lcpAt (IndexEsa) | Shortcut for value(indexLcp(..), ..).
lcpeAt (IndexEsa) | Shortcut for value(indexLcpe(..), ..).
length (Index) | The number of characters in the underlying text of the index is returned.
lfMapping | Returns the position of an character at a specified position of L in F. L corresponds to the last column of the sorted cyclic rotations of the original text, while F correspond to the first column.
nodeDepth | Returns the zero-based node depth of the iterator node.
nodeHullPredicate | If false this node and its subtree is concealed.
nodePredicate | If false this node will be skipped during the bottom-up traversal.
nodeUp | Returns the vertex descriptor of the parent node.
orderOccurrences | Sorts a string of occurrences.
parentEdgeFirstChar | Returns the first character of the edge from an iterator node to its parent.
parentEdgeLabel | Returns a substring representing the edge from an iterator node to its parent.
parentEdgeLength | Returns the length of the edge from the iterator node to its parent.
parentRepLength | Returns the length of the substring representing the path from root to iterator's parent node.
range | Returns the suffix array interval borders of occurrences of representative substring or a q-gram in the index text.
rawsaAt | Shortcut for value(indexRawSA(..), ..).
rawtextAt | Shortcut for value(indexRawText(..), ..).
repLength | Returns the length of the substring representing the path from root to iterator node.
representative | Returns a substring representing the path from root to iterator node.
resizeVertexMap | Initializes a vertex map.
saAt | Shortcut for value(indexSA(..), ..).
setStepSize | Change the q-gram step size used for index creation.
shapeToString | Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
stringToShape | Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
textAt | Shortcut for value(indexText(..), ..).
unhash | Inverse of the hash function; for ungapped shapes.
weight | Number of relevant positions in a shape.

Input/Output

adviseFileSegment | Give advice about use of a memory-mapped file segment.
appendSeqs | Appends all sequences stored in files of directory to a StringSet.
assignCroppedSeqId | Extracts the sequence id up to the first whitespace of a sequence file fragment.
assignQual | Extracts the quality values of a sequence file fragment.
assignQualId | Extracts the quality value id of a sequence file fragment.
assignSeq | Extracts the sequence part of a sequence file fragment.
assignSeqId | Extracts the sequence id of a sequence file fragment.
asyncReadAt | Asynchronously loads records from a specific position in a file.
asyncWriteAt | Asynchronously saves records to a specific position in a file.
atEnd (RecordReader) | Returns true if there is no more data to be read.
attachToFile | Attach to already open input / output file.
cancel | Cancels an asynchronous request.
cancelFileSegment | Cancel all outstanding transactions of a memory-mapped file segment.
checkEof | Check that the EOF marker is present in a BGZF(/BAM) file.
clear (FaiIndex) | Reset a FaiIndex object to the state after default construction.
clear (GenomicRegion) | Reset a GenomicRegion object to the same state after default construction.
clear (GffRecord) | Reset a GffRecord object.
close (FileMapping) | Close a file and its memory mapping.
close | Closes a file.
closeAndResize (FileMapping) | Close a memory mapping and resize and close the underlying file.
countLine | count characters in a line not including \r and \n
endsWith | Check whether a sequence ends with a given suffix.
flush | Waits for all open requests to complete.
flushFileSegment | Wait for all outstanding transactions of a memory-mapped file segment.
getIdByName (FaiIndex) | Return id (numeric index in the file) of a sequence in a FAI file.
goNext (RecordReader) | Advance record reader to next position.
goNext | Iterates to next position.
guessFileFormat | Tries to determine the format of a file.
guessFormat | Guesses a file format from the contents of a sequence file.
guessFormatFromFilename | Guesses a file format from a sequence file name.
guessStreamFormat | check whether the data provided by reader is (one of) the specified format(s).
isDirect | Query a GZ File Stream for being "direct."
isalnum | Check if character is alpha-numeric
isalpha | Check if character is a upper or lowercase letter
isblank | Check if character is either ' ' or '\t'
iscntrl | Check if character is a control character
isdigit | Check if character is a digit
isgraph | Check if character is printable and not white space
isprint | Check if character is printable, i.e. not a control character
isspace | Check if character is a white-space character
length (FileMapping) | Return the file size of a memory mapping.
length | The number of items/characters.
lexicalCast | Cast from a String-type to a numerical type
lexicalCast2 | Cast from a String-type to a numerical type
loadScoreMatrix | Load a score matrix from a file.
mapFileSegment | Map a segment of a file into memory.
nextIs (RecordReader) | Query whether the next record is of a given type.
numSeqs (FaiIndex) | Return number of sequences known to an FaiIndex.
open (FileMapping) | Open a file to be mapped into memory.
open | Opens a file, stream, or persistent string.
openTemp (FileMapping) | Open a temporary file to be mapped into memory.
openTemp | Opens a temporary file.
parse (GenomicRegion) | Parse genomic region string store results in GenomicRegion.
position (RecordReader) | Returns the current position of the reader.
read (FaiIndex) | Read a FAI index.
read (FileFormat) | Loads a record from file.
read | Loads records from a file.
read2 | reads an entire document from a StreamConcept, by the means of RecordReader
readAlphaNums | Read characters from stream as long as characters are letters
readAt | Loads records from a specific position in a file.
readDigits | Read characters from stream as long as characters are digits
readDna5IgnoringWhitespaces | Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
readFasta | Read first sequence from a FASTA file.
readFeature | Finds the first feature specified by 'key' starting from position 'start' in the feature table (the feature table can be obtained by calling readLineType with the two-character code "FT").
readFloat | Read characters from stream as long as the number is a valid floating point numbers.
readGraphs | Read characters from stream as long as characters are graph characters.
readIdentifier | Read characters from stream as long as characters are identifiers (alphanumeric, '-', and '_').
readLetters | Read characters from stream as long as characters are letters
readLine | Read a line from stream and save it to buffer
readLineStripTrailingBlanks | Read a line from stream and save it to buffer, remove trailing blanks
readLineType | Reads the information belonging to the two-character line code specified.
readMeta | Read meta information from file.
readNChars | Read exactly n characters from stream into buffer
readNCharsIgnoringWhitespace | Read n characters from stream into buffer, but skip certain Chars
readRecord (GffRecord) | Read one gff record.
readRecord | reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
readRegion (FaiIndex) | Load the infix of a sequence from a FaiIndex.
readSequence (FaiIndex) | Load a whole sequence from an FaiIndex.
readUntilBlank | Read characters from stream into buffer until Blank is encountered
readUntilChar | Read characters from stream into buffer until Char is encountered
readUntilOneOf | Read characters from stream into buffer until one of the given characters is encountered
readUntilTabOrLineBreak | Read characters from stream until a tab or line-break occurs.
readUntilWhitespace | Read characters from stream into buffer until Whitespace is encountered
remapFileSegment | Change the size of a memory-mapped file segment.
resize (FileMapping) | Resize the underlying file.
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resultCode (RecordReader) | Returns int current status code for reader (0 on success).
rewind | Sets the current file pointer to the beginning.
seek | Changes the current file pointer.
sequenceLength (FaiIndex) | Return length of the sequence with the given id in the FaiIndex.
sequenceName (FaiIndex) | Return the name of the sequence with the given id in the FaiIndex.
setEof | Sets the file end to the current pointer.
setPosition (RecordReader) | Returns the current position of the reader.
size | Gets the file size.
skipBlanks | Skip (i.e. read without saving) characters from stream until non-Blank is encountered
skipChar | Skip one character that must be equal to a given one for this function to succeed.
skipLine | Skip a line in stream and go to beginning of next
skipNChars | Skip exactly n characters from stream
skipNCharsIgnoringWhitespace | Skip n characters from stream, not counting whitespaces
skipUntilBlank | Skip (i.e. read without saving) characters from stream until Blank is encountered
skipUntilChar | Skip (i.e. read without saving) characters from stream until Char is encountered
skipUntilGraph | Skip (i.e. read without saving) characters from stream until printable, non-' ' character is encountered
skipUntilLineBeginsWithChar | Skip input until the first graphical(see isgraph) character of a line is equal to c
skipUntilLineBeginsWithOneCharOfStr | Skip input until a line begins with a one of the characters in str
skipUntilLineBeginsWithStr | Skip input until a line begins with str.
skipUntilString | Skip (i.e. read without saving) characters from stream until String is encountered
skipUntilWhitespace | Skip (i.e. read without saving) characters from stream until Whitespace is encountered
skipWhitespaces | Skip (i.e. read without saving) characters from stream until non-Whitespace is encountered
split | Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter.
splitEmblHeader | Split an EMBL header line.
splitGenBankHeader | Split an GenBank header field/value.
startFirstPass | Start the first reading pass.
startSecondPass | Start the second reading pass.
startsWith | Check whether a sequence starts with a given prefix.
streamEof | Check end-of-file state of a StreamConcept.
streamError | Return the stream's error code.
streamFlush | Flush the underlying stream.
streamPeek | Read next character from stream without advancing current position.
streamPut | Write different types to stream
streamReadBlock | Read a block of bytes into a buffer.
streamReadChar | Read next character from stream and advance the current position.
streamSeek | Perform a seek operation on the stream.
streamTell | Get the position in the current stream.
streamWriteBlock | Write a block of bytes from a buffer into a stream.
streamWriteChar | Write one character to the stream.
tell | Gets the current file pointer.
unmapFileSegment | Unmap a memory-mapped file segment.
value (RecordReader) | Returns the current value of the reader.
waitFor | Waits for an asynchronous request to complete.
write (FaiIndex) | Write out an FaiIndex object.
write (FileFormat) | Writes to stream.
write (Score Matrix) | Write a score matrix to a stream.
write | Saves records to a file.
write2 | writes an entire document to a StreamConcept
writeAt | Saves records to a specific position in a file.
writeRecord (GffRecord) | Writes one gff record to a stream.
writeRecord | write one record (e.g. a single DNA-sequence and its meta data) to a StreamConcept

Iteration

assignValue | Assigns value to item.
atBegin | Determines whether an iterator is at the beginning position.
atEnd (VSTree Iterator) | Determines whether an virtual string tree iterator is at the end position.
atEnd | Determines whether an iterator is at the end position.
atNil | Tests whether iterator is at nil position.
begin | The begin of a container.
container | Container of an iterator.
difference | The difference between two iterators.
end | The end of a container.
getValue | Access to the value.
goBegin | Iterates to the first position of a container.
goEnd | Iterates to the last position of a container.
goFurther | Iterates some steps further.
goNext | Iterates to next position.
goNil | Moves iterator to nil position.
goPrevious | Iterates to pevious position.
moveValue | Assigns value to item.
position | Position of an iterator.
value | Reference to the value.

Local Match Store

appendLocalMatch | Append a new local match to a LocalMatchStore
readRecord (LocalMatchStore) | Read Lastz "general" format record.
readRecord (LocalMatchStore) | Read Lastz "general" format record.
readRecord (LocalMatchStore) | Read Lastz "general" format record.

Map

add (Map) | Insert another value into a multi map.
cargo (Map) | Returns a cargo given a key.
erase (Map) | Removes a value from a map.
eraseAll (Map) | Removes a value from a map.
find (Map) | Find a value in a map.
hasKey (Map) | Determines whether a map contains a value given key.
insert (Map) | Insert new value into map.
mapValue | Subscript operator [ ] of maps.
value (Map) | Returns a value given a key.

Memory

allocate | Allocates memory from heap.
clear (Allocator) | Deallocates all memory blocks.
deallocate | Deallocates memory.
memset | An implementation of memset with fixed number of bytes using Metaprogramming.

Miscellaenous

getFileExtension (ArgParseArgument) | Returns the file extension for the given file argument.

Miscellaneous

addArgument (ArgumentParser) | Adds a ArgParseArgument object to the ArgumentParser.
addDefaultValue (ArgParseOption) | Adds/appends a new value to the list of default values.
addDescription (ArgumentParser) | Appends a description paragraph to the ArgumentParser documentation.
addInterval | Adds an interval to an interval tree.
addLine (ArgumentParser) | Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItem (ArgumentParser) | Appends a list item to the ArgumentParser.
addListItem (ToolDoc) | Add list item to ToolDoc object.
addOption (ArgumentParser) | Adds a ArgParseOption object to the ArgumentParser.
addSection (ArgumentParser) | Begins a new section of ArgParseOption the help output of the ArgumentParser.
addSection (ToolDoc) | Add section to ToolDoc object.
addSubSection (ToolDoc) | Add subsection to ToolDoc object.
addText (ArgumentParser) | Appends a text paragraph to the ArgumentParser.
addText (ToolDoc) | Add text line/paragraph to ToolDoc.
addTextSection (ArgumentParser) | Adds a text section to the ArgumentParser.
addTextSubSection (ArgumentParser) | Adds a text subsection to the ArgumentParser.
addUsageLine (ArgumentParser) | Adds a line of text to the usage output of the ArgumentParser.
adjustTop | Adjusts the priority of the first item.
append (ToolDoc) | Append two ToolDoc objects.
average (Accumulator) | Return average from an accumulator.
clearEntries (ToolDoc) | Clear entries from ToolDoc object.
count (Accumulator) | Return sum from an accumulator.
cpuTime | Returns the cpu time in seconds.
createIntervalTree | Create an interval tree.
findIntervals | Find all intervals that contain the query point or overlap with the query interval.
findIntervalsExcludeTouching | Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query point equals the start or end point.
findSet | Return set identifier, given an element identifier.
getAppName (ArgumentParser) | Get tool name of ArgumentParser object.
getArgument (ArgumentParser) | Returns a reference to the specified argument.
getArgumentFileExtension (ArgumentParser) | Returns the extension of a file argument.
getArgumentLabel | Returns the label for the given ArgParseArgument. Either the user defined label is returned or a default label (based on the ArgumentType is used).
getArgumentValue (ArgParseArgument) | Returns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned.
getArgumentValue (ArgumentParser) | Retrieves the value of an argument given by its position.
getArgumentValueCount (ArgumentParser) | Returns the number of values stored in the specified option.
getArgumentValues (ArgumentParser) | Returns all values of an option given on the command line.
getArgumentValues | Returns all values of the ArgParseArgument object as const std::vector.
getCategory (ArgumentParser) | Get tool category of ArgumentParser object.
getCategory (ToolDoc) | Get tool category of ToolDoc object.
getDate (ToolDoc) | Get date string from ToolDoc object.
getLeftBoundary | Get method for the left boundary.
getManTitle (ToolDoc) | Get man title from ToolDoc object.
getName (ToolDoc) | Get tool name of ToolDoc object.
getObjectId | A value that identifies the underlying sequence.
getOption (ArgumentParser) | Returns a reference to the specified option.
getOptionFileExtension (ArgumentParser) | Returns the extension of a file option.
getOptionValue (ArgumentParser) | Retrieves the value of an option given either the short or long name.
getOptionValueCount (ArgumentParser) | Returns the number of values stored in the specified option.
getOptionValues (ArgumentParser) | Returns all values of an option given on the command line.
getRightBoundary | Get method for the right boundary.
getShortDescription (ArgumentParser) | Gets short description of ArgumentParser.
getShortDescription (ToolDoc) | Get short description of ToolDoc object.
getTerminalSize | Retrieve size of terminal.
getVersion (ArgumentParser) | Get version string from ArgumentParser object.
getVersion (ToolDoc) | Get version string from ToolDoc object.
hasDefault (ArgParseArgument) | Returns true if a default value was given for that argument.
hasDefault (ArgumentParser) | Returns whether an option has a default value or not.
hasOption (ArgumentParser) | Returns whether a certain option is registered in the parser.
hasValue (ArgParseArgument) | Returns true if a value for the given position is available.
hideOption (ArgParseOption) | Hides the ArgParseOption from the help screen.
hideOption (ArgumentParser) | Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen.
isAnsiColorTerminal | Check whether we are printing to a terminal.
isBooleanOption (ArgParseOption) | Returns whether option is a switch.
isDoubleArgument | Returns whether the argument is a double.
isHidden (ArgParseOption) | Returns whether option is hidden on the help screen. Default is false.
isInputFileArgument | Returns whether the argument is an input file.
isInt64Argument | Returns whether the argument is a 64 bit integer.
isIntegerArgument | Returns whether the argument is an integer.
isListArgument | Returns whether the argument can be given multiple times.
isOutputFileArgument | Returns whether the argument is an output file.
isRequired (ArgParseOption) | Returns whether the option is mandatory.
isSet (ArgParseArgument) | Returns true if a value was assigned to the argument.
isSet (ArgumentParser) | Returns whether an option was set on the parsed command line.
isStringArgument | Returns whether the argument is a string.
isTerminal() | Check whether we are printing to a terminal.
joinSets | UNION() operation for UF data structure.
leftBoundary | Access to the left boundary.
log2 | Computes floored logarithm of base 2 for integer types
numberOfAllowedValues | Returns the number of allowed values for this ArgParseArgument.
parse (ArgumentParser) | Parses the command line.
partialSum | Computes the partial sum of a sequence.
print (ToolDoc) | Print ToolDoc object in a given format.
printHelp (ArgumentParser) | Prints the complete help message for the parser to a stream.
printShortHelp (ArgumentParser) | Prints a short help message for the parser to a stream
printVersion (ArgumentParser) | Prints the version information of the parser to a stream.
push (Accumulator) | Adds a value to an accumulator.
removeInterval | Removes an interval from the interval tree.
rightBoundary | Access to the right boundary.
setAppName (ArgumentParser) | Sets application name of ArgumentParser.
setCategory (ArgumentParser) | Set tool category for ArgumentParser object.
setCategory (ToolDoc) | Set tool category for ToolDoc object.
setDate (ArgumentParser) | Sets date string of ArgumentParser.
setDate (ToolDoc) | Set date string for ToolDoc object.
setDefaultValue (ArgParseOption) | Sets the default value for the given option.
setHelpText | Sets the help text for an ArgParseArgument.
setManTitle (ToolDoc) | Set version string for ToolDoc object.
setMaxValue | Sets the maximum value of a ArgParseArgument object.
setMinValue | Sets the minimum value of a ArgParseArgument object.
setName (ToolDoc) | Set tool name for ToolDoc object.
setRequired (ArgParseOption) | Sets whether or not the option is mandatory.
setRequired (ArgumentParser) | Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory.
setShortDescription (ArgumentParser) | Sets short description of the ArgumentParser object.
setShortDescription (ToolDoc) | Set short description for ToolDoc object.
setValidValues | Sets the set of allowed values of a ArgParseArgument object.
setVersion (ArgumentParser) | Sets version string of ArgumentParser.
setVersion (ToolDoc) | Set version string for ToolDoc object.
shareResources | Determines whether two sequences share the same resource.
sum (Accumulator) | Return sum from an accumulator.
sum | Returns the sum of all elements in a sequence.
sysTime | Returns the system time in seconds.
write (ArgParseOption) | Writes the basic information about the ArgParseOption to the provided stream.
writeCTD | Exports the app's interface description to a .ctd file.
xmlEscape | Replaces invalid XML characters in the given sequence with their valid XML equivalent.

Modifier

complement | Complement a sequence or a StringSet in-place.
reverse | Reverse an object/container in-place.
reverseComplement | Reverse and complement a sequence or a StringSet in-place.
toLower | Convert characters in sequence or StringSet to lower case in-place.
toUpper | Convert characters in sequence or StringSet to lower case in-place.

Motif Search

absFreqOfLettersInSeq | Counts the number of times each residue of a fixed sequence alphabet occurs in a given sequence.
absFreqOfLettersInSetOfSeqs | Counts the number of times each residue of a fixed sequence alphabet occurs in a given set of sequences.
addValue | Adds a value of a specific type to each element of a given FrequencyDistribution object.
backgroundFrequency | Determines the background letter frequencies in a given dataset
binomialCoefficient | Calculates the binomial coefficient C(n,k).
completeProfile | Concatenates the background frequency with the profile for the motif component.
convertPatternToProfile | Converts a pattern into a profile which consists of a set of frequency distributions.
convertResidueToFrequencyDist | Coverts a residue to a frequency distribution (profile).
convertSetOfPatternsToProfile | Converts a set of sequence patterns into a profile.
determineConsensusSeq | Determines the consensus pattern of a given profile.
display | Displays a given set of strings.
displayResult | Displays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate.
em | Represents the EM algorithm as used by MEME.
factorial | Calculates the factorial value of any integer number.
findMotif | Represents the main function which is used to start the search for noticeable motif patterns.
getMotif | Gets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned.
hammingDistance | Determines the Hamming distance between two sequences.
inverseHash | Determines the corresponding sequence pattern given the hash value.
logarithmize | Logarithmizes each element of a given FrequencyDistribution object.
motifCount | Gets number of motifs in the MotifFinder.
normalize | Determines the normalized frequencies.
posOfMax | Determines the residue position in a given FrequencyDistribution object with the maximum frequency.
sum (FrequencyDistribution) | Determines the sum of all frequencies in a given FrequencyDistribution object.

Parallelism

computeSplitters | Compute splitters for a sequence of objects.

Pipelining

beginRead | Initiates a read process.
beginWrite | Initiates a write process.
bundle2 | Returns a bundle of two objects.
bundle3 | Returns a bundle of three objects.
bundle5 | Returns a bundle of five objects.
endRead | Terminates a read process.
endWrite | Terminates a write process.
front (Pipe) | Gets the first element of the remaining stream.
pop | Pops the first element of the remaining stream.
push | Appends an item at the end of an input stream.

ROI I/O

nameStore | Return reference to name store from RoiIOContext.
nameStoreCache | Return reference to name store cache from RoiIOContext.

Random

defaultRng | Default default random number generator object of a given type.
pickRandomNumber | Pick a random number using a random number generator object, possibly following the given distribution.
reSeed | Reset and re-seed MersenneTwister
shuffle | Shuffle the given container.

Scoring

score | Returns the score for aligning the entries entryH and entryV.
score | Returns the score for aligning the entries entryH and entryV.
scoreGapExtendHorizontal | Returns the score for extending a gap in horizontal direction.
scoreGapExtendVertical | Returns the score for extending a gap in vertical direction.
scoreGapHorizontal | Returns the score for a gap in horizontal direction.
scoreGapOpenHorizontal | Returns the score for opening a gap in horizontal direction.
scoreGapOpenVertical | Returns the score for opening a gap in vertical direction.
scoreGapVertical | Returns the score for a gap in vertical direction.
setDefaultScoreMatrix | Set the value of the given matrix to the default value.
setScore | Set the substitution score between two values.

Searching

find | Search for a Pattern in a Finder object.
findBegin | Search the begin of an approximate match.
getBeginScore | Score of the last match found by findBegin during approximate searching.
getMaxDeviationOfOrder | Returns the maximal out-of-order distance of adjacent hits.
getScore | Score of the last found match in approximate searching.
getWindowFindHits | Returns the string of hits from the finder.
haystack | Returns the haystack of a Finder object.
needle | Returns the needle of a Pattern object (not implemented for some online-algorithms).
positionRange | Returns a pair of the begin and end position in the haystack or needle for the last hit found.
positionRangeNoClip | Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
scoreLimit | The minimal score a match must reach in approximate searching.
scoringScheme | The scoring scheme used for finding or aligning.
setHaystack | Sets the haystack of a Finder object.
setNeedle | Sets the needle of a Pattern object and optionally induces preprocessing.
setPosition | Sets the position of a finder.
setScoreLimit | Sets the minimal score a match must reach in approximate searching.
setScoringScheme | Sets the scoring scheme used for finding or aligning.
windowFindBegin | Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it in the finder. Used together with windowFindBegin and windowFindEnd.
windowFindEnd | Flushes the pattern. Used together with windowFindBegin and windowFindNext.
windowFindNext | Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd.

Seed Handling

addSeed (SeedSet) | Adds a seed to an existing SeedSet using different algorithms for local chaining.
appendDiagonal | Adds diagonal to the Chained Seed.
beginDiagonal (Seed) | Returns the diagonal of the start point.
beginPositionH (Seed) | Returns the begin position of the seed in the database.
beginPositionV (Seed) | Returns the begin position of the seed in the query.
endDiagonal (Seed) | Returns the diagonal of the end point.
endPositionH (Seed) | Returns the end position of the seed in the database.
endPositionV (Seed) | Returns the end position of the seed in the query.
extendSeed | Extends a seed.
lowerDiagonal (Seed) | Returns the leftmost diagonal of the seed (minimum diagonal value).
minScore (SeedSet) | Returns the threshold to distinguish between high-scoring and low-scoring seeds.
score (Seed) | Returns the score of the seed.
setBeginPositionH (Seed) | Sets the begin position of the seed in the database.
setBeginPositionV (Seed) | Sets the begin position of the seed in the query.
setEndPositionH (Seed) | Sets the end position of the seed in the database.
setEndPositionV (Seed) | Returns the end position of the seed in the query.
setLowerDiagonal (Seed) | Sets a new value for the leftmost diagonal.
setMinScore (SeedSet) | Sets the threshold at which seeds are considered high-scoring.
setScore (Seed) | Set the score value of a seed.
setUpperDiagonal (Seed) | Sets a new value for the rightmost diagonal.
truncateDiagonals | Removes diagonals from the given first one to the end of the seed's diagonals.
upperDiagonal (Seed) | Returns the rightmost diagonal of the seed (maximum diagonal value).

Sequences

assignValueById | Adds a new string to the StringSet and returns an id.
atEndOfSequence | Returns true if the iterator is at the end of a sequence.
concat | Returns the concatenation sequence of all sequences in a StringSet.
createGlobalReference | Creates the global reference of a Journaled Set.
flatten | Apply the journal to the underlying string, destructively on the underlying string.
getSeqNo | Returns the sequence number of a position.
getSeqOffset | Returns the local sequence offset of a position.
getValueById | Retrieves a string from the StringSet given an id.
globalReference | Returns the global reference sequence of a Journaled Set.
idToPosition | Retrieves the position of a string in the StringSet given an id.
isFlat (Journaled String) | Returns whether journaled string has modifications.
join | Joins a Journaled String to a Journaled Set by computing and journaling differences to the global reference sequence.
mmapAdvise | Call advise function for memory mapped files.
posAdd | Returns a position where the local offset is increased by a value delta.
posAddAndCheck | Increases the local offset of a position by a value delta and check for overflow.
posGlobalize | Converts a local/global to a global position.
posInc | Increments the local offset of a position type.
posLocalToX | Converts a local to a local/global position.
posLocalize | Converts a local/global to a local position.
posNext | Returns a position where the local offset is increased by one.
posPrev | Returns a position where the local offset is decreased by one.
posSub | Returns a position where the local offset is decreased by a value delta.
positionToId | Retrieves the id of a string in the StringSet given a position.
prependValue | Prepend a value to a container.
removeValueById | Removes a string from the StringSet given an id.
setGlobalReference | Sets the global reference of a Journaled Set.
stringSetLimits | Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
stringSplit | Append a list of the words in the string, using sep as the delimiter string StringSet.
valueById | Retrieves a string from the StringSet given an id.

Statistics

expectation | Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
variance | Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel
zscore | Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel

Testing & Debugging

printDebugLevel | Print the current SeqAn debug level and the compiler flags to the given stream.

VCF I/O

atEnd (VcfStream) | Query a VcfStream for being at the end of the file.
clear (VcfRecord) | Clear a VcfRecord.
close (VcfStream) | Closes a VcfStream
flush (VcfStream) | Flush to a VcfStream
isGood (VcfStream) | Query a VcfStream for errors.
open (VcfStream) | Open a VcfStream.
read (VCF I/O) | Read a VcfHeader.
readRecord (VCF I/O) | Read a VcfRecord from a Single-Pass RecordReader.
readRecord (VcfStream) | Read a record from a VcfStream
write (VCF I/O) | Write a VcfHeader.
writeRecord (VCF I/O) | Write a VcfRecord.
writeRecord (VcfStream) | Write a record to a VcfStream

internal

alignment | Returns an alignment of the occurrences of the representative substring in the index text.

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