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cortes-ciriano-lab / savana

Somatic structural variant caller for long-read data
Apache License 2.0
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--cn_binsize is a required argument for the main/default savana process #43

Closed TBradley27 closed 1 month ago

TBradley27 commented 1 month ago

Hello,

Firstly, congrats to the Cortes Ciriano team for getting v1.2.0 and the preprint released! I am looking forward to using.

I am just writing about the following minor issue:

--cn_binsize is listed as not being a required argument for the CNA subcommand:

https://github.com/cortes-ciriano-lab/savana/blob/9cea04122a31136f47a6f128c419555b8f62e6e8/savana/savana.py#L353

However, it is listed as a required argument for the main savana process:

https://github.com/cortes-ciriano-lab/savana/blob/9cea04122a31136f47a6f128c419555b8f62e6e8/savana/savana.py#L448

It is also not listed as a required argument in the README:

https://github.com/cortes-ciriano-lab/savana/blob/9cea04122a31136f47a6f128c419555b8f62e6e8/README.md?plain=1#L104-L106

cmsauer commented 1 month ago

Hi Thomas, Good catch, thank you for spotting and reporting this, will fix! Carolin