[IO] Parsing for genome alignment formats (MAF and HAL)

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#2,903 6 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
5/5
Estimated time
Over a week
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
cpp
Domain
bioinformatics

Research direction

Start by reviewing Seqan3’s existing MSA parser and how it represents alignment formats. Investigate the MAF and HAL format requirements and determine the scope needed for both parsers. Done means Seqan3 can parse genome alignments in both formats, with the expected behavior covered by tests.

Written by the indexing model from the issue text.

Description

feature/proposal

Big fan of the Seqan3 library, thanks for all of your hard work! I have been using the MSA parser recently and it has worked quite well, however, the majority of my work centers around genome alignments. It would be extremely useful if there were parsers for MAF and HAL alignment formats.

Dominant language
C++
Stars
463
Forks
90
Avg merge
1h 11m
Merged PRs (30d)
3

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Open the contributing guide

First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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