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raphael-group / chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
BSD 3-Clause "New" or "Revised" License
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Hardcoded list of chromosomes #4

Closed ivanov-v-v closed 4 years ago

ivanov-v-v commented 4 years ago

Seems like you are not forwarding a list of chromosomes to the RDREstimator.py, despite the fact that you allow passing those to the chisel.py. This causes a lot of confusion because it's not always chr1 ... chr22 in 10x BAMs and the script fails to detect any cells due to that. I can make a pull request that fixes this issue if you don't mind

simozacca commented 4 years ago

Thank you for this very useful feedback and for pointing out an actual bug: the list of chromosomes should be indeed forwarded to RDREstimator.py. Please feel free to initiate a pull request and I will be very happy to review it.

In the coming version the chromosome names, as well as the chromosome lengths will be read directly from the reference dictionary. Until this integration will be completed I keep this issue open.

simozacca commented 4 years ago

The integration is complete and all these information are now read from the human-reference dictionary.