noodles
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zaeleus
Bioinformatics I/O libraries in Rust
Problem: for noodles-fasta 0.13.0, query on bgzipped indexed fasta has not yet supported, right? Possible solution: implement `std::io::Seek` for `noodles_bgzf::Reader`. However, it will conflict with the original `fn seek(pos: VirtualPosition)`....
rust-htslib: ``` cat 0.00s user 0.01s system 1% cpu 0.568 total sudo cargo run --release -- > tandem_reads.bam 0.43s user 0.04s system 82% cpu 0.570 total ``` noodles: ``` cat...
I'd like to programmatically generate VCF records as part of my unit tests for various tools. In some cases I'll create new records then write them to disk to test...
When a user parses a bam file they sometimes either forget or don't realise that they have to call `read_header()`, `read_reference_sequences()` then `.records()`. If this not done, it results in...
Is there a general strategy for simultaneous random access to GZ blocks in an indexed gz file? For large files, i know the virtual positions and buffer sizes i want...
I'm attempting to write a small utility that process bam records and I can't figure out the aysnc API. I'm attempting to adapt the noodles-bam/examples/bam_reheader_async.rs example and I've been running...
Hi. Currently `Query` struct have no methods to get `RecordBuf`. To make a method for that, I tried to write some codes. This small PR has `QueriedReader`, which has methods...
Hi, Thanks for you package. Some data (Clinvar in my case) has a `ID` in header `##ID=` Minimal working example ``` ##fileformat=VCFv4.1 ##ID= #CHROM POS ID REF ALT QUAL FILTER...
The [glnexus](https://github.com/dnanexus-rnd/GLnexus) tool writes out a `FORMAT/RNC` field with the following header. ``` ##FORMAT= ``` In the data rows this looks as follows: ``` GT:RNC ./.:II 1/1:15:1,14:1:16,4,0:.. ``` In other...
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....
