Fixes for Bamstats - Githubissues

cgat-developers / cgat-flow

cgat-flow repository

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Fixes for Bamstats #114

Closed jscaber closed 4 years ago

jscaber commented 4 years ago

Removed PicardInserts functions in pipeline_bamstats.py, these are duplicated and already part of CollectMultipleMetrics. Incidentally, CollectInsertMetrics fails with memory errors whereas it CollectMultipleMetrics which includes it does not.
Corrected header for loadpicardhistogram in bamstats.py- was empty in some circumstances resulting in function to fail.

Acribbs commented 4 years ago

Looks ok, but im just running testing to make sure nothing else is braking.

Acribbs commented 4 years ago

Have just tested with pipeline tests and all looks ok.

Acribbs commented 4 years ago

only works with the argparse fix from cgatcore though.

Acribbs commented 4 years ago

You happy to merge @jscaber ?

jscaber commented 4 years ago

only works with the argparse fix from cgatcore though.

I wrote these using the pre-argparse code and it also worked. I might actually see and take out the buildInsertSizes from the modulefile as well later as its now redundant, but will deal with this later. Will merge & close for now.

jscaber commented 4 years ago

Thanks for doing all the testing, Adam. I will re-set up the testing pipeline.