Struct BamConfig 

pub struct BamConfig {
    pub min_mapq: u8,
    pub include_secondary: bool,
    pub include_supplementary: bool,
    pub partial: bool,
    pub min_partial_coverage: f64,
    pub min_region_quality: f64,
}

Filter and extraction settings for BAM reads.

This is the library equivalent of the CLI Opts fields that affect BAM extraction. Construct with BamConfig::default for permissive defaults (no filters, spanning reads only), then override individual fields as needed.

Fields

min_mapq: u8

Minimum mapping quality (MAPQ) a read must have to be included. Reads whose MAPQ is below this threshold are skipped. Default: 0 (no filter).

include_secondary: bool

Whether to include secondary alignments (SAM flag 0x100). Default: false (secondary alignments are skipped).

include_supplementary: bool

Whether to include supplementary alignments (SAM flag 0x800). Default: false (supplementary alignments are skipped).

partial: bool

Whether to include reads that only partially overlap the BED region. When false (the default), only reads whose alignment spans the entire region — from region_start to region_end — are returned. When true, reads that overlap any part of the region are included; the extracted subsequence is clipped to whatever portion the read covers.

min_partial_coverage: f64

Minimum fraction (0.0-1.0) of the requested (region ± flanks) window a partial read must cover to be included. Reads/alignments below this threshold are discarded, similar to liftOver’s -minMatch. Default: 0.0 (no filter — any overlap is accepted). Only meaningful when partial is true; non-partial reads always cover the full window by construction, so this is a no-op otherwise.

min_region_quality: f64

Minimum mean Phred quality of the extracted subsequence. After the CIGAR walk, the quality string of the extracted slice is scored with crate::utils::calculate_qscore; reads below this threshold are discarded. Default: 0.0 (no filter). Applies to BAM/CRAM input regardless of output format — the read’s quality scores are always present, whether or not --fastq is used for output.

Trait Implementations

impl Clone for BamConfig

fn clone(&self) -> BamConfig

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for BamConfig

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for BamConfig

fn default() -> Self

Returns the “default value” for a type.