Tags

This section describes the tags that can be used in SeqAn algorithms and data structures.

Aggregates

BitPacked	Tag to mark a bit-packed specialization that avoids to waste bits.
Pack	Tag to mark a packed specialization that disables address alignment for members.

Alignments

Alignment Graph Combination	A tag to specify how to combine alignment graphs.
Distance Calculation	A tag to specify how to calculate distance matrices.
Join Strategies	Tags used for selecting journaling strategies when joining a Journaled String to a global reference sequence.
Pairwise Global Alignment Algorithms	Tags used for selecting pairwise global alignment algorithms.
Pairwise Local Alignment Algorithms	Tags used for selecting pairwise global alignment algorithms.
Segment Match Generation	A tag that specifies how to generate segment matches.
Upgma Configurator	A tag to configure the guide tree construction.

BAM I/O

Bam	Tag for identifying the BAM format.
Sam	Tag for identifying the SAM format.

Basic

Default	Tag that specifies default behavior.
HammingDistance	Switch to trigger Hamming distance, which is a measure of character substitutions.
LevenshteinDistance	Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions).
Move Switch	Switch to force move.
Nothing	Tag that represents an absent parameter or an absent type.
TagList	A structure to represent a list of tags.

Consensus

Consensus Calling

A tag that specifies how to call the consensus.

Fragment Store

sortAlignedRead Tags

Tag to select a specific field to stably sort the alignedReadStore by.

Fundamental

Tag	Template for tag definition.

Graph

Graph Iterator

A specification of the iterator to traverse a graph.

Index

CompressText	Tag 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 Fibres	Tag to select a specific fibre of a CompressedSA.
DFS Order	Pre/postorder selection for depth-first search.
ESA Index Fibres	Tag to select a specific fibre (e.g. table, object, ...) of an ESA index.
FM Index Fibres	Tag to select a specific fibre of a FMIndex.
Index Find Algorithm	Tag to specify the index search algorithm.
LF Table Fibres	Tag to select a specific fibre of a FMIndex.
Pizza & Chili Index Fibres	Tag to select a specific fibre (e.g. table, object, ...) of a Pizza & Chili Index index.
Pizza & Chili Index Tags	Tag specifying the Pizza & Chili library to use.
PrefixSumTable Fibres	Tag to select a specific fibre of a CompressedSA.
QGram Index Fibres	Tag to select a specific fibre (e.g. table, object, ...) of a q-gram Index.
RankSupportBitString Fibres	Tag to select a specific fibre (e.g. table, object, ...) of a RankSupportBitString.
SBM	Tag that specifies the FMIndex to use a StringSet of rank support bis strings as the occurrence table.
WOTD Index Fibres	Tag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index.
WT	Tag that specifies the FMIndex to use a wavelet tree as the occurrence table.

Input/Output

Alignment Graph Format	A file format to write an alignment graph.
DotDrawing	Switch to trigger drawing in dot format.
File Format	A file format.
Stream Feature	Tag to select a given feature for querying in HasStreamFeature.

Iteration

Iterator Spec

Specifies the kind of an iterator.

Memory

Allocator Usage

The purpose of an allocated memory block.

Metaprogramming

Case	Metaprogramming case expression.
Logical Values	Tag that represents true and false.
NilCase	Metaprogramming default: case expression.

Miscellaneous

IntervalTree Centers	Tag to select a specific way to compute the center of an interval tree node.
IntervalTree Node Types	Tags to select the node type for IntervalTree.

Motif Search

Omops	Represents the One or More Occurences Per Sequence model.
Oops	Represents the One Occurrence Per Sequence model.
Tcm	Represents the Two-Component-Mixture Sequence model.
Zoops	Represents the Zero or One Occurence Per Sequence model.

Random

Lognormal Construction

Specify parameters for lognormal distribution construction.

RightArrayBinaryTree

RightArrayBinaryTree Fibres

Tag to select a specific fibre (e.g. table, object, ...) of a RightArrayBinaryTree.

Searching

FindInfix	Find needle as a substring of haystack (infix search).
FindPrefix	Find needle as a prefix of the haystack (prefix serach)
Index Find Algorithm	Tag to specify the index search algorithm.

Seed Handling

Global Chaining	Tags for selecting the global chaining algorithm.
Local Chaining	The local chaining algorithms to use when adding a seed to a SeedSet.
Seed Extension	The algorithms used to extend a seed.

SentinelRankDictionary

SentinelRankDictionary Fibres

Tag to select a specific fibre (e.g. table, object, ...) of a SentinelRankDictionary.

Sequences

Overflow Strategy	The strategy for resizing containers.
Prefix Order	Specify whether less-than or greather-than comparison is meant.

Spec: WaveletTree

WaveletTree Fibres

Tag to select a specific fibre (e.g. table, object, ...) of a WaveletTree.

Strings

ExternalConfig	Standard configuration for the External String.
ExternalConfigLarge	Large size type configuration for the External String.
ExternalConfigSize	Arbitrary size type configuration for the External String.

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