Add agat sp alignment output style #124
Draft
+251
−0
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
dorien-er
reviewed
Aug 29, 2024
| issue_tracker: https://github.com/NBISweden/AGAT/issues | ||
| repository: https://github.com/NBISweden/AGAT | ||
| references: | ||
| doi: 10.5281/zenodo.3552717 |
There was a problem hiding this comment.
Suggested change
| doi: 10.5281/zenodo.3552717 | |
| doi: https://doi.org/10.5281/zenodo.3552717 |
dorien-er
reviewed
Aug 29, 2024
Comment on lines
+4
to
+6
| The script takes a normal gtf/gff annotation format file and convert it | ||
| to gff3 alignment format. It means it add a structure of match / | ||
| match_part as relationship between the different features. |
There was a problem hiding this comment.
Suggested change
| The script takes a normal gtf/gff annotation format file and convert it | |
| to gff3 alignment format. It means it add a structure of match / | |
| match_part as relationship between the different features. | |
| The script takes a normal gtf/gff annotation format file and converts it to gff3 alignment format, adding a structure of match / match_part as relationship between the different features. |
dorien-er
reviewed
Aug 29, 2024
| arguments: | ||
| - name: --verbose | ||
| alternatives: [-v] | ||
| description: Verbose option to see the warning messages when parsing the gff file. |
There was a problem hiding this comment.
Suggested change
| description: Verbose option to see the warning messages when parsing the gff file. | |
| description: Add verbosity. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Added agat_sp_alignment_output_style:
-vargumentIssue ticket number
Closes #xxxx
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: