Scoring Module

Fragment scoring functionality for genomic analysis (ATAC-seq and ChIP-seq data).

What it does

Counts overlaps between fragment files and consensus peak regions, producing a count matrix where:

• Rows = fragment files
• Columns = consensus regions
• Values = overlap counts

CLI Usage

gtars fscoring <fragments> <consensus> /
  --mode <atac|chip> /
  --output <output.csv.gz>

Arguments:

• fragments: Glob pattern for fragment files (e.g., "*.bed.gz")
• consensus: Path to consensus peak set (BED file)
• --mode: Scoring mode (atac or chip, default: atac)
• atac: Counts 5' and 3' cut sites with shifts (+4/-5 bp)
• chip: Counts full fragment overlaps
• --output: Output file path (default: count_matrix.csv.gz)

Example:

gtars fscoring "fragments/*.bed.gz" peaks.bed /
  --mode atac /
  --output counts.csv.gz

Rust Library Usage

use gtars::scoring::{
    region_scoring_from_fragments, 
    ConsensusSet, 
    FragmentFileGlob, 
    ScoringMode
};

// Set up inputs
let mut fragments = FragmentFileGlob::new("path/to/*.bed.gz")?;
let consensus = ConsensusSet::new("peaks.bed".into())?;

// Generate count matrix
let count_matrix = region_scoring_from_fragments(
    &mut fragments, 
    &consensus, 
    ScoringMode::Atac
)?;

// Write to file
count_matrix.write_to_file("output.csv.gz")?;

// Or access counts directly
let count = count_matrix.get(row, col);

Output Format

Gzipped CSV file with:

• Each row = one fragment file
• Each column = one consensus region
• Values = count of overlapping fragments