Vince Buffalo

This commit adds the function `fastx`, which behaves like `sprintf` for FASTA/FASTQ output. It simplifies FASTA/FASTQ output, as `fastx($name, $seq)` outputs a FASTA entry and `fastx($name, $seq, $qual)` outputs a...

Why are AD and DP > 0 but gt_depths all -1?

2

Here's another issue I've run into, perhaps because I'm misunderstanding something about VCFs. I have a per-basepair VCF (example attached as `small.gvcf.gz`). In ipython: ```python from cyvcf2 import VCF vcf...

is_indel treats "<NON_REF>" ALT as an indel

3

The [GVCF format](https://gatk.broadinstitute.org/hc/en-us/articles/360035531812-GVCF-Genomic-Variant-Call-Format) uses `` as a placeholder for a possible non-reference allele in the ALT column. Because cyvcf2 compares REF to ALT [length to determine if a variant is...

added parsing of FASTA/FASTQ comment (everything after space)

1

Minor change that adds parsing of comment.

weighted averages for bedtools map?

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I was looking at the documentation for [bedtools map](https://bedtools.readthedocs.io/en/latest/content/tools/map.html) and wondered about a possible improvement. From the illustration of the mean by overlapping features, it seems like the mean may...

Allow for expressions in Eidos event times

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I think a simple feature that could make Eidos a lot more extensible would be to allow for expressions in the generation that Eidos events are triggered. For example, (modifying...

issue when installing from yaml file

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Hey ncls folks, I really like ncls but am having a very odd issue when installing it from an environment YAML file, which I need to use to include it...

Iteration results differ between BasicCOITree and NeonCOITree

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I was using this library in a project and noticed a subtle potential bug: taking a `Vec` and creating both `BasicCOITree` and `NeonCOITree` objects, and then iterating over their intervals...

This is an issue to open up discussion on interleave support on Scythe. I have some time to work on my quality control pipeline components and I'd like to use...

Documentation is opaque on 0 vs 1 indexing, and whether regions are right-inclusive or not.

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Thank you for writing noodles! Really exciting to have great Rust interfaces to so many bioinformatic formats. I've noticed is it's currently hard to figure out from docs whether 1....