Handle TIDDIT style SV type names #128
Draft
+70
−0
Conversation
This file contains hidden or 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
henrikstranneheim
approved these changes
Dec 22, 2023
| coordinates["end"] = end | ||
|
|
||
| sv_type = variant.INFO.get("SVTYPE").split(":")[0] | ||
| sv_type = variant.INFO.get("SVTYPE") |
| def test_format_old_tiddit_dup_tandem(duptandem_old_tiddit_variant, case_obj): | ||
| ## GIVEN a dup with older TIDDIT notation (TDUP, IDUP, ...) | ||
| variant = duptandem_variant | ||
| variant = duptandem_old_tiddit_variant |
Contributor
There was a problem hiding this comment.
Suggested change
| variant = duptandem_old_tiddit_variant | |
| variant: str = duptandem_tiddit_variant_legacy_format |
| def test_format_tiddit_dup_tandem(duptandem_tiddit_variant, case_obj): | ||
| ## GIVEN a TIDDIT style notation, ie both SVTYPE info and alt field tag has subtype, eg DUP:TANDEM | ||
| variant = duptandem_variant | ||
| variant = duptandem_tiddit_variant |
Contributor
There was a problem hiding this comment.
Suggested change
| variant = duptandem_tiddit_variant | |
| variant: str = duptandem_tiddit_variant |
Collaborator
|
Should we try to merge these changes @dnil? |
Member
Author
You are asking such good questions! I had the same one last week, but didn't spend the time trying to answer it. Probably, if it was an issue 2023. On the other hand we seem to have lived without. Again, whoever has time to figure out the current status (checking files that go for upload for variants like this etc etc). |
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Outdated suggestions cannot be applied.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.
This PR adds | fixes:
How to prepare for test:
sshto ...bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]How to test:
Expected outcome:
Review:
This version is a: