| Title: | Parsing GFA and GAF Alignment Files |
| Version: | 0.1.2 |
| Maintainer: | Camille R. Mazurek <camillemazurek23@gmail.com> |
| 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. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| Suggests: | testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| URL: | https://github.com/cromazurek/MatchAlign |
| BugReports: | https://github.com/cromazurek/MatchAlign/issues |
| Config/roxygen2/version: | 8.0.0 |
| NeedsCompilation: | no |
| Packaged: | 2026-09-03 21:10:48 UTC; camillemazurek2025 |
| Author: | Camille R. Mazurek [aut, cre], Michael J. Tisza [ctb] |
| Repository: | CRAN |
| Date/Publication: | 2026-09-12 15:00:12 UTC |
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)