Skip to content

Add support for csi index - #407

Merged
daler merged 5 commits into
daler:v0.12.1rcfrom
liyao001:master
Aug 26, 2026
Merged

Add support for csi index#407
daler merged 5 commits into
daler:v0.12.1rcfrom
liyao001:master

Conversation

@liyao001

Copy link
Copy Markdown
Contributor

Hi there,

I've made an enhancement to pybedtools that adds support for the CSI index. The default TBI index fails for chromosomes larger than 512 Mbp, such as barley's chromosome 2H, which spans more than 665 Mbp. This update ensures that users can handle larger genomic regions without encountering indexing failures.

Thanks for considering this enhancement.

Best,
Li

@daler

daler commented Apr 27, 2024

Copy link
Copy Markdown
Owner

Thanks! Can you please add a test to this PR?

@liyao001

Copy link
Copy Markdown
Contributor Author

Certainly! I've extended one of the existing tests (test_tabix) to cover both the default TBI and the new CSI indexes. Additionally, considering the impact on the tabix_contigs function from the previous commit, I've introduced a new test case (test_tabix_contigs_csi) inspired by test_issues::test_issue_180 to ensure comprehensive coverage of the changes. Let me know if there are any further adjustments needed or if you have any other suggestions.

@daler
daler changed the base branch from master to v0.12.1rc August 26, 2026 18:43
@daler
daler merged commit 97b6541 into daler:v0.12.1rc Aug 26, 2026
0 of 5 checks passed
@daler daler mentioned this pull request Aug 26, 2026
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants