noodles
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zaeleus
Bioinformatics I/O libraries in Rust
In many cases, we want to iterate over all bases in a FASTA, for example when looking for repeats, STRs, and other genomic features. Currently, this requires reading a contig...
I wanted to use rayon to parallelize some of my processing, but found that I need to have the [`Send + Sync`](https://doc.rust-lang.org/nomicon/send-and-sync.html) traits for key structs, like a Bed record...
Hi -- for my line of work I often have to (de-)serialize bioinformatic file formats into more common formats, and I'm curious if there are any recommendations for how to...
Hello, After upgrading from 0.23.0 to 0.24.0, I'm seeing a lot of these errors with code that worked before: ``` invalid genotypes: invalid genotype: empty input ``` I'm using a...
I'm curious about the design choices for the sam/bam/cram modules and whether there is a relatively easy (though perhaps) less efficient way to transparently work with the three formats interchangeably?...
To avoid writing corrupt or incompatible SAM/BAM files an extra validation step is applied before writing. This makes sure: - The number of base qualities is equal to the sequence...
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...
This is a tracking issue for CRAM 3.1 write support. The CRAM 3.1 format is still [a draft](https://github.com/samtools/hts-specs/pull/433), but [there is interest](https://github.com/zaeleus/noodles/issues/78#issuecomment-1220668241) in having noodles-cram demonstrate a second implementation. The...
I have headers with: PL:illumina 'Could not parse header: InvalidReadGroup(InvalidPlatform(Invalid))' A non strict mode for header parsing would be great. I really don't care about the header, just give me...
See #108, the key is to `impl Seek for bgzf::Reader`. My draft implementation has three steps: 1. Rename all `fn seek(&mut self, pos: VirtualPosition)` to `fn seek_virtual_position(&mut self, pos: VirtualPosition)`....
