Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Regions index #37

Merged
merged 10 commits into from
Jul 29, 2024
Merged

Regions index #37

merged 10 commits into from
Jul 29, 2024

Commits on Jul 25, 2024

  1. Rewrite asserts in assert_vcfs_close to give better failure messages

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    b5399c0 View commit details
    Browse the repository at this point in the history

  2. Don't create a variant mask if no regions or targets are specified

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    3cf19a1 View commit details
    Browse the repository at this point in the history

  3. Add index command to create an index to support efficient region queries

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    a47f7a6 View commit details
    Browse the repository at this point in the history

  4. Update vcf writer to use variant_position_end rather than computing i… 

    …t ourselves
    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    4c17f5a View commit details
    Browse the repository at this point in the history

  5. Only load variant_contig/position chunks that overlap query region

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    4f97d6d View commit details
    Browse the repository at this point in the history

  6. Create index in tests

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    8339dbc View commit details
    Browse the repository at this point in the history

  7. Support complement (^) in targets

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    ee74315 View commit details
    Browse the repository at this point in the history

  8. refactor

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    8661998 View commit details
    Browse the repository at this point in the history

  9. Support both regions and targets at once

    @tomwhite
    tomwhite committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    b3a56aa View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2024

  1. Use variant_length field rather than variant_position_end

    @tomwhite
    tomwhite committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    b9c22e9 View commit details
    Browse the repository at this point in the history