Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

WhatsHap polyphasegenetic throws an error about indel usage #523

Open
schrins opened this issue Mar 19, 2024 · 0 comments
Open

WhatsHap polyphasegenetic throws an error about indel usage #523

schrins opened this issue Mar 19, 2024 · 0 comments
Assignees

Comments

@schrins
Copy link
Collaborator

schrins commented Mar 19, 2024

WhatsHap polyphase genetic is currently not usable, because the module complains about an indels_used. Adding an --only-snvs flag or the deprecated --indels flag does not change the behavior.

Traceback (most recent call last):
  File "/srv/homes/schrinner/polyphase-pipeline/whatshap-polyphase-experiments/polyploid_human/evaluation/.snakemake/conda/d6c9a753ce0b321feabdd11be95d2e4f_/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/srv/homes/schrinner/polyphase-pipeline/whatshap-polyphase-experiments/polyploid_human/evaluation/.snakemake/conda/d6c9a753ce0b321feabdd11be95d2e4f_/lib/python3.10/site-packages/whatshap/__main__.py", line 64, in main
    module.main(args)
  File "/srv/homes/schrinner/polyphase-pipeline/whatshap-polyphase-experiments/polyploid_human/evaluation/.snakemake/conda/d6c9a753ce0b321feabdd11be95d2e4f_/lib/python3.10/site-packages/whatshap/cli/polyphasegenetic.py", line 642, in main
    run_polyphasegenetic(**vars(args))
TypeError: run_polyphasegenetic() got an unexpected keyword argument 'indels_used'
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant