Fastq Filter

Problem Description

Build a CLI tool fastq_filter that filters a gzipped fastq file based on length and gc content. The output should be a filtered and gzipped fastq file.

Expected command:

fastq_filter --fastq <file.fastq.gz> --outfile <filtered.fastq.gz> --min_len <usize> --max_len <usize> --min_gc <f32> --max_gc <f32>

Checklist

• Figure out how to read a gzipped file using Flate2.
• Figure out out how write a needletail SequenceRecord to a target output.fastq.gz file.

Suggested Rust Crates

• Clap - argument parsing.
• Needletail - reading fastq files.
• Flate2 - compression/decompression.

Code Examples

• fastq_rs

Extra Credit

• Add functionality to also filter on mean error rate.
• Handle only files with extensions .fastq.gz, .fq.gz.
• Graceful error handling.