Ryan Dale

improve gffwriter

1

How to write out to file is not currently obvious (xref #37, #88). Having a class or function to handle this will help with discoverability and will be an obvious...

spliced sequence extraction

2

xref https://github.com/mdshw5/pyfaidx/pull/127

add a mechanism for cleaning a database of features that have an annotated parent, but that parent does not exist.

Command-line interface for gffutils

7

What sort of functionality should be exposed to the CLI? For example a universal GTFGFFrefFlat conversion script would be useful.

See http://www.biostars.org/p/64363/#64463

Bulk branch is currently failing on macOS, which currently looks to be due to differences in how the `conda-forge-ci-setup` package behaves in recent versions. This PR is to help diagnose...

VCF output truncated, if blank line follows header

2

Hi Aaron - I have some VCF files with a blank line after the `#CHROM...` header line. BEDTools programs operating on these VCFs only report 2 columns (chrom, pos) rather...

v2.29.2: truncated bam output using bedpetobam

4

I'm making sure the pybedtools tests work with bedtools v2.29.2, and I'm seeing the following issue. It's been a while since I've updated the tests, so this may not be...

Add recipe for termseq-peaks ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). * If this PR adds or updates a recipe, use "Add" or...

# Overview As part of the recent migration that re-built many packages for Python 3.10, we encountered issues with recipes that either haven't been re-built in a while or that...