gtars-scoring

Wrapper around gtars-overlaprs for generating X-by-peak count matrices.

Purpose

This module wraps the core overlap infrastructure from gtars-overlaprs to produce count matrices for genomic analysis. It handles all use cases that need X-by-peak matrices where X can be cells, pseudobulk aggregations, or samples.

Design Philosophy

All overlap computation is delegated to gtars-overlaprs. This module focuses on:

• Matrix data structures and I/O
• Aggregation strategies
• Output formats (dense/sparse)

Use Cases

• Cell-by-peak matrices for single-cell ATAC-seq
• Sample-by-peak matrices for bulk ATAC-seq/ChIP-seq
• Pseudobulk-by-peak matrices for aggregated single-cell data

Main Components

• ConsensusSet: Wraps consensus peaks using gtars-overlaprs::Bits for overlap detection
• CountMatrix: Dense matrix storage for count data
• region_scoring_from_fragments: Main scoring function for file-based input

CLI Usage

# Score multiple fragment files against consensus peaks
gtars fscoring "fragments/*.bed.gz" peaks.bed --output matrix.csv.gz

Example

use gtars_scoring::{region_scoring_from_fragments, ConsensusSet, FragmentFileGlob, ScoringMode};

// Set up inputs
let mut fragments = FragmentFileGlob::new("fragments/*.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")?;