Expand description
A database for multiple targeted sequences.
§What is Reference
?
Reference
is a target of alignment, containing multiple sequences.- It is primarily used by the
Aligner
to perform alignments.
§Features
Reference
is designed to be agnostic to the storage and retrieval methods for sequences.- Sequences could be stored in memory, files, or remote physical locations accessible over a network.
- During alignment,
Reference
remains immutable.Aligner
manages theSequenceBuffer
defined inSequenceStorage
to store temporary sequences.Reference
only defines the how to access the target sequences.
- The target sequences’ range can be adjusted after building the
Reference
, unlike conventional “Reference” in bioinformatics. - Basically,
Reference
is simply built fromSequenceStorage
andPatternIndex::Option
insigalign-core
.
§Internal Traits
- SequenceStorage: Fetches a target sequence based on a given target index.
- PatternIndex: Accepts pattern bytes and returns the indices of the targets exactly matching the pattern. This is necessary for the SigAlign algorithm to exactly locate all patterns in the target sequences.
Modules§
- extensions
- Supplementary functionalities for the
Reference
.
Structs§
- Pattern
Location PatternLocation
holds the index of a pattern within a target.- Reference
- A database for multiple target sequences.