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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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segmetrics: apply --drop-low-coverage option as skip_low in the API #694

Closed etal closed 2 years ago

etal commented 2 years ago

Via #646 : Adding --drop-low-coverage to segmetrics is a good idea, and it should match batch and the other commands.

etal commented 2 years ago

This option has been an option in the segmetrics command since 2015: 6cb1b09b

But it was applied in the command, not the library layer, so batch did not pass this option through when using segmetrics internally through the cnvlib API.

Exit: move the filter from the command layer to the library layer in segmetrics, and pass the option through from batch.