TileDB-Inc / TileDB-VCF

Efficient variant-call data storage and retrieval library using the TileDB storage library.
https://tiledb-inc.github.io/TileDB-VCF/
MIT License
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More robust handling of info END fields #672

Closed gspowley closed 3 months ago

gspowley commented 3 months ago

This PR introduces two changes related to the info END field:

  1. The info END field is normally defined as an integer in VCF headers. This PR handles the case where END is defined as a string in a VCF header.
  2. The info_END attribute in the TileDB array now contains the original value of END from the VCF, including missing values.

The pos_end TileDB attribute has not changed. If info END is defined, pos_end holds the value of info END. Otherwise, pos_end holds the value POS + length(REF) - 1.

shortcut-integration[bot] commented 3 months ago

This pull request has been linked to Shortcut Story #43060: Unexpected END values in VCF dataset.

jdblischak commented 3 months ago

You can rebase onto main to fix the failing CI. I fixed the dask-expr error in #673

jdblischak commented 3 months ago

Something went wrong with the Azure jobs. They aren't even in the queue

github-actions[bot] commented 3 months ago

The backport to release-0.29 failed:

The process '/usr/bin/git' failed with exit code 128

To backport manually, run these commands in your terminal:

# Fetch latest updates from GitHub
git fetch
# Create a new working tree
git worktree add .worktrees/backport-release-0.29 release-0.29
# Navigate to the new working tree
cd .worktrees/backport-release-0.29
# Create a new branch
git switch --create backport-672-to-release-0.29
# Cherry-pick the merged commit of this pull request and resolve the conflicts
git cherry-pick --mainline 1 28c5e5d7e920b83b24759915a739e683fc685fc7
# Push it to GitHub
git push --set-upstream origin backport-672-to-release-0.29
# Go back to the original working tree
cd ../..
# Delete the working tree
git worktree remove .worktrees/backport-release-0.29

Then, create a pull request where the base branch is release-0.29 and the compare/head branch is backport-672-to-release-0.29.