veg / flea-pipeline

A pipeline for long-read sequencing data.
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Compute copynumbers after editing alignment #53

Closed kemaleren closed 7 years ago

kemaleren commented 9 years ago

Deleting HQCSs during alignment editing should be reflected in the copynumbers, but currently it is not because they are done separately. Need to refactor so we do copynumber counting with the results of the edited alignment.