Alan Boyle

Yes, this makes sense - I will compute these and share them in the repo.

The smaller genomes use a different overlap parameter. I recommend using 5kb instead of 20kb like was done for human. You can change this in the code here: https://github.com/Boyle-Lab/Blacklist/blob/master/blacklist.cpp#L469

Have you been able to work out the discrepancy? Perhaps we can compare md5 hashs of the bam files to make sure that we are working with the same data?

10.2.1 Here is my env: ``` # packages in environment at /home/apboyle/.conda/envs/b529: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge anyio 4.2.0 pyhd8ed1ab_0 conda-forge...

Can you provide a link to the bed file? One thought is that there is an aberrant read position throwing things off because it is much larger than the chromosome....

To avoid this error you will need to use an older version of Java.