An amplicon record for VarDictJava's amplicon-mode

amplicon_record.rs

/// A record of output from VarDict/VarDictJava run in amplicon-aware mode.
#[derive(Debug, Deserialize)]
struct AmpliconVariant<'a> {
    pub sample: &'a str,
    pub interval_name: &'a str,
    pub contig: &'a str,
    pub start: u64,
    pub end: u64,
    pub ref_allele: &'a str,
    pub alt_allele: &'a str,
    pub depth: u32,
    pub alt_depth: u32,
    pub ref_forward: u32,
    pub ref_reverse: u32,
    pub alt_forward: u32,
    pub alt_reverse: u32,
    pub gt: &'a str,
    pub af: f32,
    pub strand_bias: &'a str,
    pub mean_position_in_read: f32,
    pub stdev_position_in_read: f32,
    pub mean_base_quality: f32,
    pub stdev_base_quality: f32,
    pub strand_bias_p_value: f32,
    #[serde(deserialize_with = "maybe_infinite_f32")]
    pub strand_bias_odds_ratio: f32,
    pub mean_mapping_quality: f32,
    pub signal_to_noise: u32,
    pub af_high_quality_bases: f32,
    pub af_adjusted: f32,
    pub num_bases_3_prime_shift_for_deletions: u32,
    pub microsatellite: u32,
    pub microsatellite_length: u32,
    pub mean_mismatches_in_reads: f32,
    pub high_quality_variant_reads: u32,
    pub high_quality_total_reads: u32,
    pub flank_seq_5_prime: &'a str,
    pub flank_seq_3_prime: &'a str,
    // Position format, unused in VCF.
    pub segment: &'a str,
    pub variant_type: &'a str,
    pub num_amplicons_supporting_variant: u32,
    pub total_amplicons_overlapping: u32,
    pub num_amplicons_rare: u32,
    // A zero or one, need a custom deserializer.
    pub top_variant_in_amplicon_does_not_match: bool,
}

impl<'a> AbstractInterval for AmpliconVariant<'a> {
    fn contig(&self) -> &str {
        &self.contig
    }
    fn range(&self) -> Range<Position> {
        Range { start: self.start, end: self.end }
    }
}