Package 'MatchAlign'

Title: Parsing GFA and GAF Alignment Files
Description: Provides tools for extracting segment paths from Graphical Fragment Assembly ('GFA') and Graph Alignment Format ('GAF') files. parse_paths_gfa() reads P (path) and W (walk) records and returns a named list of segment identifiers for each accession. parse_paths_gaf() parses the path string from each alignment and returns a named list of segments traversed by each query. parse_segment_lengths_gfa() reads S records and returns a named list of segment lengths keyed by segment identifier. These tools are intended to simplify downstream interpretation and analysis of pangenome graphs.
Authors: Camille R. Mazurek [aut, cre], Michael J. Tisza [ctb]
Maintainer: Camille R. Mazurek <[email protected]>
License: MIT + file LICENSE
Version: 0.1.2
Built: 2026-10-14 08:06:49 UTC
Source: https://github.com/cromazurek/matchalign

Help Index

Create a list where each alignment is an element with an associated list of the segments used

Description

Create a list where each alignment is an element with an associated list of the segments used

Usage

parse_paths_gaf(gaf_file)

Arguments

gaf_file

A gaf file

Value

A list where each alignment is an element with an associated list of segments used

Examples

example_gaf <- system.file("extdata", "example.gaf", package = "MatchAlign")
alignment_paths <- parse_paths_gaf(example_gaf)

Create a list where each accession is an element with an associated list of the segments

Description

Create a list where each accession is an element with an associated list of the segments

Usage

parse_paths_gfa(gfa_file)

Arguments

gfa_file

A gfa file

Value

A list where each accession is an element with an associated list of segments

Examples

example_gfa <- system.file("extdata", "example.gfa", package = "MatchAlign")
accession_paths <- parse_paths_gfa(example_gfa)

Create a list of segment lengths from a GFA file

Description

Create a list of segment lengths from a GFA file

Usage

parse_segment_lengths_gfa(gfa_file)

Arguments

gfa_file

A gfa file

Value

A named list where each segment is an element with its length

Examples

example_gfa <- system.file("extdata", "example.gfa", package = "MatchAlign")
segment_lengths <- parse_segment_lengths_gfa(example_gfa)