angelovangel / faster

A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust

• 💻 Mostly R, Shiny, nextflow & shell
• 📚 Learning Rust, awk
• 🧬 Interested in bioinformatics

faster's Issues

use regex pattern to search by read name

Currently only the read description is searched for

Expected @ at record start.

I am getting the following error:

faster -t 20240327-54345-2B1-LAB5262-L144596.bam_dcc.fastq.gz > faster_results.tsv 
thread 'main' panicked at src/main.rs:404:14:
Failed to parse fastq record!: Custom { kind: Other, error: "Expected @ at record start." }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

So it seems as if the fastq file is corrupt? However, other programs had no problem with this file (e.g. assembled with hifiasm without hitch). Any ideas?

Thank you

Add header only one time

Hi,

Do you think it is possible to add the header only once. The -s argument controls whether to have no header or one header per fastq file.

example command I am using:
parallel faster -ts ::: /path/to/fastq/*.fastq.gz > out.tsv

thank you

count and output Ns in table

Warning with cargo build

Hi,

Great tool. I receive this warning with cargo build. The tool still works well.

warning: function `phred_gm` is never used
  --> src/modules.rs:87:8
   |
87 | pub fn phred_gm(q: &[u8]) -> f64 {
   |        ^^^^^^^^
   |
   = note: `#[warn(dead_code)]` on by default