Skip to content

Fix LDpred2 error with uppercase chromosome column header#180

Merged
espenhgn merged 4 commits intomainfrom
fix-179
Jun 7, 2023
Merged

Fix LDpred2 error with uppercase chromosome column header#180
espenhgn merged 4 commits intomainfrom
fix-179

Conversation

@espenhgn
Copy link
Contributor

@espenhgn espenhgn commented Jun 5, 2023

Fixes #179

Changes proposed in this pull request:

  • Adds test and fix of LDpred2 crash occurring if sumstats column header is uppercase (e.g., CHR), and column also encodes chromosomes using characters (e.g., X)

Before submitting

  • I've read and followed all steps in the Making a pull request
    section of the CONTRIBUTING docs.
  • I've updated or added any relevant docstrings following the syntax described in the
    Writing docstrings section of the CONTRIBUTING docs.
  • If this PR fixes a bug, I've added a test that will fail without my fix.
  • If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

@espenhgn espenhgn changed the title Fix 179 Fix LDpred2 error with uppercase chromosome column header Jun 5, 2023
@espenhgn espenhgn requested a review from deepchocolate June 6, 2023 07:33
@espenhgn espenhgn added the bug-fix fixes a bug label Jun 6, 2023
Copy link
Contributor

@deepchocolate deepchocolate left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good! Many thanks!

@espenhgn espenhgn merged commit a195c98 into main Jun 7, 2023
@espenhgn espenhgn deleted the fix-179 branch June 7, 2023 07:14
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

bug-fix fixes a bug

Projects

None yet

Development

Successfully merging this pull request may close these issues.

LDpred2: Error when filtering characters in chromosome column

2 participants