genotyping module broken in master branch

whatshap / whatshap

Read-based phasing of genomic variants, also called haplotype assembly

https://whatshap.readthedocs.io

MIT License

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genotyping module broken in master branch #222

Open marcelm opened 4 years ago

marcelm commented 4 years ago

Original report by Peter Ebert (Bitbucket: ptrebert, GitHub: ptrebert).

WhatsHap version 0.19.dev99+g7289583 (Python 3.6.7)

The --debug log output is flooded (thousands) with entries of the form:

like = <class 'whatshap.core.PhredGenotypeLikelihoods'>
like = <class 'whatshap.core.PhredGenotypeLikelihoods'>

The jobs are reported with an exist status 1, so I assume they fail eventually, although I see a VCF output for some.

marcelm commented 4 years ago

Original comment by Tobias Marschall (Bitbucket: tobiasmarschall, GitHub: tobiasmarschall).

https://bitbucket.org/whatshap/whatshap/commits/0e9d4607045490015068c7404a196c1b335af083#Lwhatshap/cli/genotype.pyT344

marcelm commented 4 years ago

Original comment by Jana Ebler (Bitbucket: jana_ebler, ).

@{5c12225d9439134c517c847f} I pushed a fix to branch “issue222“. The only problem seems to be a print statement that I had used for debugging and later forgot to remove. Can you check if it works now on your data?