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

Mehari wrapper vcf preprocessing does not actually fix INFO-SVLEN header #450

Closed
Nicolai-vKuegelgen opened this issue Oct 11, 2023 · 0 comments · Fixed by #451
Closed

Mehari wrapper vcf preprocessing does not actually fix INFO-SVLEN header #450

Nicolai-vKuegelgen opened this issue Oct 11, 2023 · 0 comments · Fixed by #451

Comments

@Nicolai-vKuegelgen
Copy link
Contributor

Describe the bug
Mehari wrapper needs to preprocess vcf files and fix the header INFO entry for SVLEN. This is done on the unsotred instead of the sorted vcf files in the tmp folder of the wrapper.

To Reproduce
Steps to reproduce the behavior:

  1. Run snappy with current commit and try to use mehari.

Expected behavior
Fixing of the header should happen on the sorted files that get used as mehari input.
Nicolai-vKuegelgen added a commit that referenced this issue Oct 11, 2023
@Nicolai-vKuegelgen
Fix: #450 perform preprocessing on sorted vcf files
687c70d
@Nicolai-vKuegelgen Nicolai-vKuegelgen mentioned this issue Oct 11, 2023
Merged
@Nicolai-vKuegelgen Nicolai-vKuegelgen linked a pull request Oct 11, 2023 that will close this issue
fix: mehari wrapper vcf preprocessing does not actually fix info svlen header (#450) #451
Merged
Nicolai-vKuegelgen added a commit that referenced this issue Oct 11, 2023
@Nicolai-vKuegelgen
fix: mehari wrapper vcf preprocessing does not actually fix info svle…
55146c7 
…n header (#450) (#451)
@tedil tedil mentioned this issue Jun 28, 2024
Merged
This was referenced Dec 9, 2024
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
1 participant
@Nicolai-vKuegelgen