Tags
This section describes the tags that can be used in SeqAn algorithms and data structures.
Tags
Alignment Graph CombinationA tag to specify how to combine alignment graphs.
Alignment Graph FormatA file format to write an alignment graph.
Allocator UsageThe purpose of an allocated memory block.
Consensus CallingA tag that specifies how to call the consensus.
DefaultTag that specifies default behavior.
Distance CalculationA tag to specify how to calculate distance matrices.
DotDrawingSwitch to trigger drawing in dot format.
File FormatA file format.
FindInfixFind needle as a substring of haystack (infix search).
FindPrefixFind needle as a prefix of the haystack (prefix serach)
Global Alignment AlgorithmsGlobal alignment algorithm used by globalAlignment.
Graph IteratorA specification of the iterator to traverse a graph.
HammingDistanceSwitch to trigger Hamming distance, which is a measure of character substitutions.
Iterator SpecSpecifies the kind of an iterator.
LevenshteinDistanceSwitch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Local Alignment AlgorithmsLocal alignment algorithm used by localAlignment.
Logical ValuesTag that represents true and false.
Move SwitchSwitch to force move.
NothingTag that represents an absent parameter or an absent type.
Overflow StrategyThe strategy for resizing containers.
Prefix OrderSpecify whether less-than or greather-than comparison is meant.
Segment Match GenerationA tag that specifies how to generate segment matches.
TagListA structure to represent a list of tags.
Upgma ConfiguratorA tag to configure the guide tree construction.
Fragment Store
sortAlignedRead TagsTag to select a specific field to stably sort the alignedReadStore by.
Index
ESA Index FibresTag to select a specific fibre (e.g. table, object, ...) of an ESA index.
EmptyEdgesConsider a suffix tree with leaves for every suffix.
HideEmptyEdgesConsider a suffix tree with no empty edges (default behaviour).
Index Find AlgorithmTag to specify the index search algorithm.
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.
PostorderPostorder depth-first search.
PostorderEmptyEdgesPostorder depth-first search in a suffix tree with leaves for every suffix.
PreorderPreorder depth-first search.
PreorderEmptyEdgesPreorder depth-first search in a suffix tree with leaves for every suffix.
QGram Index FibresTag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
WOTD Index FibresTag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index.
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.
Random
MeanStdDevTag to specify that the given parameters are mean an standard deviation of the lognormal distribution.
MuSigmaTag to specify that the given parameters are mu and sigma of the underlying normal distribution for lognormal distributions.
Scoring
SimpleTag for the Score to mark it as a simple score.
Searching
Index Find AlgorithmTag to specify the index search algorithm.
Seed Handling
Seed AddingThe algorithm used to add a seed to a SeedSet.
Seed ExtensionThe algorithms used to extend a seed.
SeedSet Tags for the behaviour of a SeedSet
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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