batch hybrid: Use autobin for target and antitarget bin sizes

Open etal opened this issue 8 years ago • 1 comments

Currently the autobin step is skipped for -m hybrid and the hard-coded default values are used instead. Trust autobin. May need to restructure the code so autobin is run regardless of -m.

Jan 22 '18 22:01 etal

Hi @etal

Was this ever resolved.

I just used split the batch command into individual steps and this kind of fixed my noisy coverage I reported in #933.

Also looking at the documentation on the https://cnvkit.readthedocs.io/en/stable/pipeline.html

I thought this was supposed to be default way to run it? But then i looked at batch.py and apparently autobin is never run for hybrid mode?

https://github.com/etal/cnvkit/blob/dd834b0b5b482f174d1dcb7c35b358087309c6b3/cnvlib/batch.py#L86-L116

The whole part is under an if condition which is only vaild for mode wgs?

https://github.com/etal/cnvkit/blob/dd834b0b5b482f174d1dcb7c35b358087309c6b3/cnvlib/batch.py#L60

Dec 21 '24 14:12 shashwatsahay