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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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VCF input requires bgzip and tabix index #229

Closed LeahRoberts closed 1 year ago

LeahRoberts commented 1 year ago

I ran into an error running pyseer with VCF input:

File "pysam/libcbcf.pyx", line 4466, in pysam.libcbcf.VariantFile.fetch
ValueError: fetch requires an index

We realised it was because my VCF was not bgzipped (and indexed). Running bgzip and tabix fixed this error. I'm not sure if there was something in the docs I missed about this file format requirement, but might be nice to implement this (or check for it) within pyseer.

mgalardini commented 1 year ago

Thanks for pointing this out. Might be worth mentioning it in the docs, though giving a more informative error message should be something the pysam library should do