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griffithlab / civicpy

A python interface for the CIViC db application
MIT License
9 stars 5 forks source link

Fix bug in VCF coordinate retrieval for complex indels #81

Closed susannasiebert closed 4 years ago

susannasiebert commented 4 years ago

We should take a very close look at whether this logic in how to translate CIViC coordinates to VCF coordinates are correct. 5 examples for different types of variants are given in the test file. Special attention should be paid to the POS for each.

susannasiebert commented 4 years ago

I'm pretty sure it's failing due to an outdated test cache but the new test cache file is too large to be uploaded to github directly.

ahwagner commented 4 years ago

We should address the underlying issue with the test file. It was a shortcut ahead of v1.0 release, but clearly is not sustainable.

@susannasiebert, what do you think about selecting / creating a fixed test cache from the CIViC production server and download it to the designated test directory ahead of pytest in our travis.yml config? It would require no changes to the codebase beyond the travis config and removing the existing cache file, and the infrastructure is already in place.

susannasiebert commented 4 years ago

@ahwagner I made the change to the .travis.yml to download the pkl file from CIViC. I also discovered a couple more bugs in the process. This is ready for re-review.