Crate bamnado 

BamNado Library

bamnado is a high-performance Rust library for manipulating BAM files, designed specifically for specialized genomics workflows such as single-cell ATAC-seq (scATAC-seq) and Multi-modal Cellular Characterization (MCC).

Core Features

• Coverage Analysis: Efficient calculation of coverage signals across chromosomes.
• BAM Splitting: Tools for splitting BAM files based on various criteria.
• Read Filtering: Advanced filtering capabilities for BAM reads.
• Signal Normalization: Methods for normalizing genomic signals.
• Spike-in Analysis: Utilities for handling spike-in controls.

Modules

• bam_modifier: Tools for modifying BAM records.
• bam_splitter: Functionality for splitting BAM files.
• bam_utils: General utilities and statistics for BAM files.
• coverage_analysis: Core logic for generating coverage tracks.
• genomic_intervals: Handling of genomic coordinates and intervals.
• read_filter: Structures and traits for filtering reads.
• signal_normalization: Normalization strategies for coverage data.
• spike_in_analysis: Analysis tools for spike-in normalization.

Re-exports

pub use bam_utils::BamStats;

pub use bam_utils::CellBarcodes;

pub use bam_utils::CellBarcodesMulti;

pub use bam_utils::Strand;

Modules

bam_modifier

BAM Modifier Module

bam_splitter

BAM Splitter Module

bam_utils

BAM Utilities Module

bedgraph_utils

bigwig_compare

coverage_analysis

Coverage Analysis Module

genomic_intervals

Genomic Intervals Module

read_filter

Read Filter Module

signal_normalization

Signal Normalization Module

spike_in_analysis

Spike-in Analysis Module