Chad Niederhuth

Reducing Open Files

9

I need to run a large analysis, however my university's cluster places a hard limit on the number of open files and is not exactly willing to alter this for...

get_structures.py & cross_correlation.py both use parameters that are now deprecated in scikit-image and scikit-learn. This results in failure when running chess extract and chess cross-correlate. Specifically in get_structures.py lines 130...

single-end mode is broken in v1.1.0

13

I recently updated my conda installation of pairtools to v1.1.0 and it appears that the --single-end mode no longer works for single-end reads in pairtools parse2: Comparing two versions: `pairtools...

bcftools csq: Change chromosome name requirement.

1

Could you please drop the requirement that chromosome start with "chr" from bcftools csq. This creates many headaches when working with other species where this is not the case.