Tags
This section describes the tags that can be used in SeqAn algorithms and data structures.
Aggregates
BitPackedTag to mark a bit-packed specialization that avoids to waste bits.
PackTag to mark a packed specialization that disables address alignment for members.
Alignments
Alignment Graph CombinationA tag to specify how to combine alignment graphs.
Distance CalculationA tag to specify how to calculate distance matrices.
Join StrategiesTags used for selecting journaling strategies when joining a Journaled String to a global reference sequence.
Pairwise Global Alignment AlgorithmsTags used for selecting pairwise global alignment algorithms.
Pairwise Local Alignment AlgorithmsTags used for selecting pairwise global alignment algorithms.
Segment Match GenerationA tag that specifies how to generate segment matches.
Upgma ConfiguratorA tag to configure the guide tree construction.
BAM I/O
BamTag for identifying the BAM format.
SamTag for identifying the SAM format.
Basic
DefaultTag that specifies default behavior.
HammingDistanceSwitch to trigger Hamming distance, which is a measure of character substitutions.
LevenshteinDistanceSwitch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Move SwitchSwitch to force move.
NothingTag that represents an absent parameter or an absent type.
TagListA structure to represent a list of tags.
Consensus
Consensus CallingA tag that specifies how to call the consensus.
Fragment Store
sortAlignedRead TagsTag to select a specific field to stably sort the alignedReadStore by.
Fundamental
TagTemplate for tag definition.
Graph
Graph IteratorA specification of the iterator to traverse a graph.
Index
BottomUpTag that specifies a VSTree Iterator to traverse the virtual string tree from the root towards the leafs.
CompressTextTag to select a FM index variant that can be used such that it is not necessary to store the text after index construction. This index is very space efficient.
CompressedSA FibresTag to select a specific fibre of a CompressedSA.
DFS OrderPre/postorder selection for depth-first search.
ESA Index FibresTag to select a specific fibre (e.g. table, object, ...) of an ESA index.
FM Index FibresTag to select a specific fibre of a FMIndex.
LF Table FibresTag to select a specific fibre of a FMIndex.
Pizza & Chili Index FibresTag to select a specific fibre (e.g. table, object, ...) of a Pizza & Chili Index index.
Pizza & Chili Index TagsTag specifying the Pizza & Chili library to use.
PrefixSumTable FibresTag to select a specific fibre of a CompressedSA.
QGram Index FibresTag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
RankSupportBitString FibresTag to select a specific fibre (e.g. table, object, ...) of a RankSupportBitString.
SBMTag that specifies the FMIndex to use a StringSet of rank support bis strings as the occurrence table.
SparseString FibresTag to select a specific fibre of a SparseString.
TopDownTag that specifies a VSTree Iterator to traverse the virtual string tree from the root towards the leafs.
WOTD Index FibresTag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index.
WTTag that specifies the FMIndex to use a wavelet tree as the occurrence table.
Input/Output
Alignment Graph FormatA file format to write an alignment graph.
DotDrawingSwitch to trigger drawing in dot format.
File FormatA file format.
Stream FeatureTag to select a given feature for querying in HasStreamFeature.
Iteration
Iterator SpecSpecifies the kind of an iterator.
Memory
Allocator UsageThe purpose of an allocated memory block.
Metaprogramming
CaseMetaprogramming case expression.
Logical ValuesTag that represents true and false.
NilCaseMetaprogramming default: case expression.
Miscellaneous
IntervalTree CentersTag to select a specific way to compute the center of an interval tree node.
IntervalTree Node TypesTags to select the node type for IntervalTree.
Motif Search
OmopsRepresents the One or More Occurences Per Sequence model.
OopsRepresents the One Occurrence Per Sequence model.
TcmRepresents the Two-Component-Mixture Sequence model.
ZoopsRepresents the Zero or One Occurence Per Sequence model.
Parallelism
ParallelTag to select a parallel implementation of an algorithm.
SerialTag to select a non-parallel implementation of an algorithm.
Random
Lognormal ConstructionSpecify parameters for lognormal distribution construction.
RightArrayBinaryTree
RightArrayBinaryTree FibresTag to select a specific fibre (e.g. table, object, ...) of a RightArrayBinaryTree.
Searching
FindInfixFind needle as a substring of haystack (infix search).
FindPrefixFind needle as a prefix of the haystack (prefix serach)
Index Find AlgorithmTags to specialise the search strategies.
Seed Handling
Global ChainingTags for selecting the global chaining algorithm.
Local ChainingThe local chaining algorithms to use when adding a seed to a SeedSet.
Seed ExtensionThe algorithms used to extend a seed.
SentinelRankDictionary
SentinelRankDictionary FibresTag to select a specific fibre (e.g. table, object, ...) of a SentinelRankDictionary.
Sequences
Overflow StrategyThe strategy for resizing containers.
Prefix OrderSpecify whether less-than or greather-than comparison is meant.
Spec: WaveletTree
WaveletTree FibresTag to select a specific fibre (e.g. table, object, ...) of a WaveletTree.
Strings
ExternalConfigStandard configuration for the External String.
ExternalConfigLargeLarge size type configuration for the External String.
ExternalConfigSizeArbitrary size type configuration for the External String.
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