Per Unneberg

Fix erroneous links in snakemake report

WIP: Protect index

2

Add protected keyword to index output.

fastqc uses everything up to the fastq suffix as sample name. Unless the prefix matches the sample name, the fastqc rules will fail with a missing output file exception. Unfortunately,...

Currently the workflow report consists of the workflow rulegraph and the default content (statistics, configuration). Things to add could be: - krakenuniq summary - authentication results - ...

Efficiently summing coverage tracks from multiple d4 files

3

Hi, I'm running variant calling on non-model organisms, and for some of the downstream analyses (e.g., nucleotide diversity calculations), it is necessary to generate (possibly boolean) accessibility masks that classify...

Windowing fails for datasets where contigs lack variant sites

1

The function `sgkit.window_by_position` fails if the input dataset has contigs that lack variant sites, throwing an `IndexError`. Traceback ```python IndexError Traceback (most recent call last) Cell In[36], line 1 ---->...