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...

Deprecated parameters in scikit-image & scikit-learn

2

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

17

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.

bcftools stats --samples-file give wrong results if sample order is different than vcf

1

I'm using bcftools v1.21 If I run bcftools stats with --sample-files, I've noticed that the per-sample statistics will be incorrect if the sample order in the input list of samples...