feat: added wrapper for using tabix to query an indexed file #203
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
johanneskoester
requested changes
Nov 30, 2020
|
I added test cases and reformatted a few of these old PRs, but there are merge conflicts because my test.py files are out of date. I'm not sure of the least complicated way to straighten this out. |
|
I've updated this and added a test case. It's ready for review. |
johanneskoester
approved these changes
Jan 26, 2022
johanneskoester
changed the title
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Outdated suggestions cannot be applied.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.
The current tabix wrapper can only be used to index a file, but tabix can also be used to query an indexed file, like
tabix -h my.vcf.gz chr1 > chr1.vcf.gzortabix coverage.bed.gz chr20 > chr20.bed.gz. Added this as a separate wrapper.