Tags
This section describes the tags that can be used in SeqAn algorithms and data structures.
Tags
Tag to select a FM index variant that can be used such that it is not necessary to store the text after index construction. |
Aggregates
Tag to mark a bit-packed specialization that avoids to waste bits. | |
Tag to mark a packed specialization that disables address alignment for members. |
Alignments
A tag to specify how to combine alignment graphs. | |
A tag to specify how to calculate distance matrices. | |
Tags used for selecting journaling strategies when joining a Journaled String to a global reference sequence. | |
Tags used for selecting pairwise global alignment algorithms. | |
Tags used for selecting pairwise global alignment algorithms. | |
A tag that specifies how to generate segment matches. | |
A tag to configure the guide tree construction. |
BAM I/O
Tag for identifying the BAM format. |
Basic
Tag that specifies default behavior. | |
Switch to trigger Hamming distance, which is a measure of character substitutions. | |
Switch to trigger Levenshtein distance, which is a measure of edit operations (character substitutions, deletions or insertions). | |
Switch to force move. | |
Tag that represents an absent parameter or an absent type. | |
A structure to represent a list of tags. |
Consensus
A tag that specifies how to call the consensus. |
Fragment Store
Tag for identifying the SAM format. | |
Tag to select a specific field to stably sort the alignedReadStore by. |
Fundamental
Template for tag definition. |
Graph
A specification of the iterator to traverse a graph. |
Index
Tag to select a specific fibre (e.g. table, object, ...) of an ESA index. | |
Consider a suffix tree with leaves for every suffix. | |
Tag to select a specific fibre (e.g. table, object, ...) of a FMIndex. | |
Consider a suffix tree with no empty edges (default behaviour). | |
Tag to specify the index search algorithm. | |
Tag to select a specific fibre (e.g. table, object, ...) of a Pizza & Chili Index index. | |
Tag specifying the Pizza & Chili library to use. | |
Postorder depth-first search. | |
Postorder depth-first search in a suffix tree with leaves for every suffix. | |
Preorder depth-first search. | |
Preorder depth-first search in a suffix tree with leaves for every suffix. | |
Tag to select a specific fibre (e.g. table, object, ...) of a q-gram Index. | |
Tag to select a specific fibre (e.g. table, object, ...) of a RankSupportBitString. | |
Tag to select a specific fibre (e.g. table, object, ...) of an IndexWotd index. | |
Tag that specifies the FMIndex to use a wavelet tree as the occurrence table. |
Input/Output
A file format to write an alignment graph. | |
Switch to trigger drawing in dot format. | |
A file format. | |
Tag to select a given feature for querying in HasStreamFeature. |
Iteration
Specifies the kind of an iterator. |
Memory
The purpose of an allocated memory block. |
Metaprogramming
Metaprogramming | |
Tag that represents true and false. | |
Metaprogramming |
Miscellaneous
Tag to select a specific way to compute the center of an interval tree node. | |
Tags to select the node type for IntervalTree. |
Motif Search
Represents the One or More Occurences Per Sequence model. | |
Represents the One Occurrence Per Sequence model. | |
Represents the Two-Component-Mixture Sequence model. | |
Represents the Zero or One Occurence Per Sequence model. |
Random
Tag to specify that the given parameters are mean an standard deviation of the lognormal distribution. | |
Tag to specify that the given parameters are mu and sigma of the underlying normal distribution for lognormal distributions. |
RightArrayBinaryTree
Tag to select a specific fibre (e.g. table, object, ...) of a RightArrayBinaryTree. |
Searching
Find needle as a substring of haystack (infix search). | |
Find needle as a prefix of the haystack (prefix serach) | |
Tag to specify the index search algorithm. |
Seed Handling
The algorithm used to add a seed to a SeedSet. | |
The algorithms used to extend a seed. | |
Tags for the behaviour of a SeedSet |
Sequences
The strategy for resizing containers. | |
Specify whether less-than or greather-than comparison is meant. |
Strings
Standard configuration for the External String. | |
Large size type configuration for the External String. | |
Arbitrary size type configuration for the External String. |
WaveletTree
Tag to select a specific fibre (e.g. table, object, ...) of a WaveletTree. |
SeqAn - Sequence Analysis Library - www.seqan.de