John St. John

Hi Adam! Forgive my slow reply. Please dig into the notebook https://github.com/lucidrains/enformer-pytorch/blob/main/evaluate_enformer_pytorch_correlation.ipynb to see how I got to those numbers. I did not use the function you're using for computing...

So now to your question, how is correlation calculated in forward? I didn't write that part. If you look at the code in forward, and you pass one hot sequences...

Here's the code for the correlation function: def pearson_corr_coef(x, y, dim = 1, reduce_dims = (-1,)): x_centered = x - x.mean(dim = dim, keepdim = True) y_centered = y -...

Quite possibly. I would for sure play around with parameters. When I wrote this years ago 150bp paired end data was not a common occurrence. On September 28, 2016 at...

what OS/gcc version are you using? I just tried on my mac, and the default `gcc` which goes to `clang` does not work, however I have `gcc-mp-4.8` installed through macports...

Maybe the gcc arguments in the makefile are screwing things up somehow for your system? On Sep 10, 2014, at 7:57 PM, Guangchuang Yu [email protected] wrote: > ygc@SPH:cUtils$ cat test.c...

My PR https://github.com/hammerlab/guacamole/pull/394 has the filters you mentioned in the mutect-like somatic caller. Eventually these filters need to be tested and refactored out in such a way that the joint...

I am getting this error too with my fork of the `SomaticStandardMutationCaller` @ankushreddy. It works fine for certain variants/loci, but when I run on larger files this happens sometimes. I...

The serializable issue seems to be fixed with the suggested `with Serializable` addition to `Arguments`. I have also gone through and updated many of the function names/added docs to the...

Just realized something, one Mutect filter is the distance between an allele and an indel in a read. So for example a read with an indel may be filtered out...