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Clinical-Genomics / chanjo

Chanjo provides a better way to analyze coverage data in clinical sequencing.
https://clinical-genomics.github.io/chanjo/
MIT License
49 stars 12 forks source link

calculate gene / interval is missing #190

Open mjlarsen opened 7 years ago

mjlarsen commented 7 years ago

Hi I can see that earlier versions of change the change calculate contained both gene and interval as subcommands, however in the recent version only contains "mean" as the only subcommand. Is that by purpose ?

Thank you for providing a version useful peace of software.

/Martin

robinandeer commented 7 years ago

Hey!

Happy you find Chanjo useful :) I'm sorry for being unresponsive.

My idea was to scale back on functionality in the latest major release and add back features one-by-one but haven't had time as of late :/

I will keep this issue open as a reminder that these features are requested!

moonso commented 7 years ago

Hi @mjlarsen ,

unfortunately calculate interval will not be possible with the current setup of chanjo. At the moment only the transcripts and some information about exons are stored, the database grew to much when storing coverage for each base. I have added functionality to calculate mean coverage for all transcripts in a gene which should give some indication on the average coverage in a gene.