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rust-bio/rust-htslib
How to add new INFO fileds into VCF

Hi, Thank you for this nice rust crate. In my use, I want to read a vcf file, then add some custom fields into the INFO column, and then write back as an output vcf. I understand that any record you push ...
  • AuroUTU
  • Opened 
    on May 4
  • #475

rust-bio/rust-htslib
dealing with mixed ploidy

As made clear in the documentation, this crate does not support anything other than diploid calls. Being able to deal with mixed ploidy would be super useful, e.g., on the mammalian X chromosome. I have ...
  • esrice
  • Opened 
    on Apr 30
  • #474

rust-bio/rust-htslib
Add public constructor for public structs

Hi, I m using rust_htslib to parse XA tags and wanted to use IterAlignedBlocks to find where the alt alignments pointed. Unfortunately the fields are private so it s not possible to construct that struct ...
  • TedBrookings
  • Opened 
    on Apr 10
  • #472

rust-bio/rust-htslib
Support for using Cursor?

https://doc.rust-lang.org/std/io/struct.Cursor.html It seems that bam::IndexedReader can be made with path only. It would be good that we can use Cursor for IndexedReader to reduce I/O bottleneck when ...
  • Crispy13
  • Opened 
    on Mar 23
  • #471

rust-bio/rust-htslib
Performance degradation with VCF Reader Apple Silicon

Hello, I observed a serious performance degradation between 0.48 and 0.49.0 0.48.0 RUSTFLAGS= -Ctarget-cpu=native cargo run --release 10.28s user 0.55s system 127% cpu 8.463 total 0.49.0 RUSTFLAGS= ...
  • mwiewior
  • 1
  • Opened 
    on Jan 27
  • #464

rust-bio/rust-htslib
Question about bam::IndexedReader::fetch()

Before I start, I just wanted to thank you for this library; It s a staple of the software I m writing. I had a question about the fetch() method of the IndexedReader, for use with indexed .bam files: ...
  • epiliper
  • Opened 
    on Jan 26
  • #463

rust-bio/rust-htslib
Question about building rust-htslib with conda-installed dependencies

I m currently working on a bioconda recipe for a tool depending on rust-htslib. I ve got a working version, but it seems the rust compilation chain still pulls in lots of C sources, via hts-sys I guess, ...
  • wm75
  • 1
  • Opened 
    on Jan 16
  • #462

rust-bio/rust-htslib
[deps] idna currently used is impacted by RUSTSEC-2024-0421

cargo deny raised the issue that the current version of rust-htslib is impacted by RUSTSEC-2024-0421 which is a dependency of url versions 2.5.3 and earlier. Uprevving url to version 2.5.4 should fix ...
  • sjlangley
  • Opened 
    on Dec 10, 2024
  • #460

rust-bio/rust-htslib
Multiple unsound problems in bcf crate

https://github.com/rust-bio/rust-htslib/blob/da6278f1b2da36b8404633b0d2fa1675c97e5937/src/bcf/header.rs#L288 Hello, thank you for your contribution in thin project. Currently, I m scnning rust project ...
  • lwz23
  • 7
  • Opened 
    on Dec 5, 2024
  • #459

rust-bio/rust-htslib
Is there any way to tell where in the file the reader is ?

Title basically is the question. I need a way to know where in the file the reader is. Ideally id want the file offset (in bytes) of the current record, as well as where that record ends . I have not found ...
  • JulianDicken
  • Opened 
    on Nov 27, 2024
  • #456
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