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yhoogstrate / fuma

:dash::leopard: FuMa: reporting overlap in RNA-seq detected fusion genes
GNU General Public License v3.0
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Fix bug when GTF line has no gene/transcript id #50

Closed Redmar-van-den-Berg closed 6 months ago

Redmar-van-den-Berg commented 2 years ago

This pull request contains two main changes:

  1. Fix a crash when a GTF line has no gene/transcript id
  2. Enable github-CI to automatically run the tests.

The background is that I am trying to generate a bed file to use with FuMa, as per https://github.com/yhoogstrate/fuma#obtain-bed-file---fuma-gencode-gtf-to-bed. I tried using the "comprehensive gene annotations" from https://www.gencodegenes.org/human/, but fuma-gencode-gtf-to-bed crashed because not all GTF lines had a gene/transcript id. Do you have any advice on which gencode GTF file is best to use? I can add that to the readme as well if you want.

yhoogstrate commented 6 months ago

@Redmar-van-den-Berg you're probably not working on this anymore, but if you like you can proceed and get CI working ..