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#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum AlignmentMode {
Global,
SemiGlobal,
}
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum ConsensusMode {
HeaviestPath,
MajorityFrequency,
}
#[derive(Debug, Clone)]
pub struct PoaConfig {
/// 0 = unbanded (full NW over DAG). Warn if reads exceed ~1 kb and this is 0.
pub band_width: usize,
/// Enable adaptive band width using the abPOA formula: w = b + f*L.
pub adaptive_band: bool,
/// Base component of the adaptive band formula (abPOA default: 10).
pub adaptive_band_b: usize,
/// Length-proportional component of the adaptive band formula (abPOA default: 0.01).
pub adaptive_band_f: f32,
pub match_score: i32,
pub mismatch_score: i32,
/// One-time penalty when a gap opens. Negative.
pub gap_open: i32,
/// Per-base penalty inside a gap. Negative.
pub gap_extend: i32,
/// Fraction of reads that must cover a node for it to appear in consensus.
pub min_coverage_fraction: f64,
/// Minimum fraction of reads supporting an allele for bubble detection.
pub min_allele_freq: f64,
/// Minimum number of reads required to build a consensus.
pub min_reads: usize,
pub alignment_mode: AlignmentMode,
pub consensus_mode: ConsensusMode,
/// Emit a warning to stderr when reads exceed ~1 kb with band_width = 0.
pub warn_on_long_unbanded: bool,
/// Minimum arm span (nodes) for a bubble to be considered a structural variant
/// for cross-bubble phasing. Bubbles below this threshold (SNPs, short indels)
/// use the existing single-bubble partitioning. Default 10.
pub phasing_bubble_min_span: usize,
/// Whether this graph is being built for **multi-allele** consensus.
///
/// Controls two mode-dependent behaviours whose correct setting differs
/// between single- and multi-allele consensus:
/// - the O(1) diagonal-skip fast path in alignment (kept in multi-allele
/// mode to lock reads onto their own length-allele track; disabled in
/// single-allele mode where its greedy forward-match over-calls periodic
/// repeats by matching reads through phantom units), and
/// - the whole-graph unbanded rebuild on band-retry (needed only for
/// multi-allele bubble-structure consistency).
///
/// The functional wrappers set this automatically ([`consensus_multi`]
/// builds with it `true`; single-allele paths leave it `false`). Stateful
/// callers ([`PoaGraph::new`]) who intend to call
/// [`PoaGraph::consensus_multi`] should set it `true` so alignment is built
/// in multi-allele mode. Default: `false` (single-allele).
///
/// [`consensus_multi`]: crate::consensus_multi
/// [`PoaGraph::new`]: crate::PoaGraph::new
/// [`PoaGraph::consensus_multi`]: crate::PoaGraph::consensus_multi
pub multi_allele: bool,
}
impl Default for PoaConfig {
fn default() -> Self {
PoaConfig {
band_width: 50,
adaptive_band: true,
adaptive_band_b: 10,
adaptive_band_f: 0.01,
match_score: 1,
mismatch_score: -1,
gap_open: -2,
gap_extend: -1,
min_coverage_fraction: 0.0,
min_allele_freq: 0.2,
min_reads: 1,
alignment_mode: AlignmentMode::SemiGlobal,
consensus_mode: ConsensusMode::HeaviestPath,
warn_on_long_unbanded: true,
phasing_bubble_min_span: 10,
multi_allele: false,
}
}
}