Crate bamslice 

Extract byte ranges from BAM files and convert to interleaved FASTQ format.

This library provides efficient extraction of specific byte ranges from BAM (Binary Alignment/Map) files and converts them to interleaved FASTQ format. This enables parallel processing of large BAM files by splitting them into chunks that can be processed independently.

Key Features

• Block-aligned extraction: Automatically aligns to BGZF block boundaries for valid data
• Paired-read aware: Ensures read pairs are kept together across chunk boundaries
• Interleaved FASTQ output: Compatible with samtools fastq interleaved format
• Barcode support: Preserves BC tags in FASTQ headers

Example

use std::io::stdout;
use bamslice::process_blocks;

let mut output = stdout();
let read_count = process_blocks(
    "input.bam",
    0,           // start offset
    1_000_000,   // end offset (1MB chunk)
    &mut output
)?;
println!("Extracted {read_count} reads");

BGZF Block Format

BAM files use BGZF (Blocked GNU Zip Format) compression. Each block is independently compressed, allowing random access. This library scans for valid BGZF block headers using an 8-byte signature and validates blocks by decompressing and checking for valid BAM records.

Implementation Notes

• Read pairs are kept together by reading one extra record past the end boundary if needed

Functions

process_blocks

Process a byte range from a BAM file and output interleaved FASTQ.