Seth

[feature] Pileup Engine

3

This is a first draft of a pileup engine using `noodles` for the underlying IO. Is this something you would be interested in having in the `noodles` family? If you...

Performance Tracking

13

@Shnatsel I'm moving performance tracking for `crabz` related things to here. Run the same benchmarks as found here: https://github.com/zlib-ng/pigzbench with the different backends. The `zlib-ng` benchmarks pretty clearly indicate that...

The current regex fails to parse `11.0.9.1-internal` due to the `.1` "update" group. This version is coming from openjdk conda forge. See [here](https://github.com/nextflow-io/nextflow/issues/953#issuecomment-888365138) for more details. This change allows for...

This PR allows for explicit checking for binary existence when using the `associate` and `try_associate` methods on the `DecompressionMatcherBuilder`. I have tried to preserve the current `resolve_binary` api being a...

It looks like oni2 has the same issue described here: https://github.com/GitSquared/edex-ui/issues/1124 I'm using `Onivim 2 (0.5.9-nightly)` with only the rust-analyzer plugin installed and all commands I try to run in...

Given that `gzp` does have internal buffer, it should implement `BufRead` so that double buffering isn't required to do things like iterate over lines. https://github.com/sstadick/gzp/issues/28

Find minimum versions of deps

1

Currently libeflate conflicts with the version of libdeflate used by rust-htslib

Add Intel ISA-L

4

@ghuls have you ever done any benchmarking with ISA-L vs zlib-ng or libdeflate? I'm looking at wrapping GKL and thinking it may be a way to get ISA-L into gzp...

[bug] demuxFastqs does not throw error when a read is shorter than the specified template length

1

[This](https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/test/scala/com/fulcrumgenomics/fastq/DemuxFastqsTest.scala#L470) creates the read structure 17B139T. [The read](https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/test/scala/com/fulcrumgenomics/fastq/DemuxFastqsTest.scala#L569) used to test [here](https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala#L864) is only 17B39T. Looking at the ReadStructure code in fgbio it looks like this should thrown an error...