Clint Valentine

Use allele info in VariantContext comparisons for stable sorts

5

TLDR: This PR will make coordinate VCF sorting in HTSJDK/Picard similar to bcftools. I tried to use Picard's [SortVcf](https://gatk.broadinstitute.org/hc/en-us/articles/360036858331-SortVcf-Picard) for a VCF comparison task, but I had difficulty because it's...

Add source classes for BED and generic Interval types

2

I need helpers for reading generic interval data, so I added these classes! `BedSource`: A source for BED input (similar to `IntervalListSource`). `IntervalSource`: A source for interval data that wraps...

Request for an optional implicit to provide Variant conversions?

2

Are you amendable to supporting the compatibility between `Variant` and `VariantContext` classes through an implicit import that provides some of the helper methods in: https://github.com/fulcrumgenomics/fgbio/blob/e7ac6078850f272183d786576c1694e3654ada67/src/main/scala/com/fulcrumgenomics/vcf/api/VcfConversions.scala#L46 Reason being, I want to...

There are now error-corrected NGS technologies that can produce base quality scores Q60+. To make those technologies compatible with the Manta program, we need to increase the maximum allowed base...

See #95

- [ ] Support inline barcodes - [ ] Confirm `ReadStructure` class supports all example read structures - https://github.com/nh13/read-structure-examples - https://github.com/samtools/hts-specs/issues/270 - [ ] Support `+` operator on last read...

I love this plugin, so first off, thanks for the time you took to create and publish it! --- Currently the `channels` parameter allows one to **append** channels to the...

Samtools: Add support for `markdup`

3

Closes https://github.com/MultiQC/MultiQC/issues/1862 This draft PR begins to implement a parser for the new `samtools markdup` statistics data: - https://www.htslib.org/doc/samtools-markdup.html#STATISTICS I have elements of this code working in a private repo,...