seqwish fails when `--output-dir` contains commas

pangenome / pggb

the pangenome graph builder

https://doi.org/10.1038/s41592-024-02430-3

MIT License

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seqwish fails when `--output-dir` contains commas #356

Open kdm9 opened 10 months ago

kdm9 commented 10 months ago

Hi folks,

Seqwish interprets commas in a PAF file path as multiple PAF files. This causes havoc when one uses commas in the --output-dir of PGGB (for example I used a dir like pggb_s5000_p90_G700,1000 encoding the pggb params in the dir name).

I'd suggest adding a check to the pggb script to ensure that output & tmp paths don't contain commas. Happy to implement this if you need.

best, K

subwaystation commented 6 months ago

If you really need this, please make a PR @kdm9, thanks!