Type Alias varlociraptor::variants::evidence::observations::read_observation::ProcessedReadObservation

source · 
pub type ProcessedReadObservation = ReadObservation<ReadPosition, AltLocus>;

Aliased Type§

struct ProcessedReadObservation {
Show 19 fields
    pub fragment_id: Option<u64>,
    pub prob_alt: LogProb,
    pub prob_ref: LogProb,
    pub prob_missed_allele: LogProb,
    pub prob_sample_alt: LogProb,
    pub prob_double_overlap: LogProb,
    pub prob_single_overlap: LogProb,
    pub prob_hit_base: LogProb,
    pub strand: Strand,
    pub read_orientation: SequenceReadPairOrientation,
    pub softclipped: bool,
    pub paired: bool,
    pub read_position: ReadPosition,
    pub prob_observable_at_homopolymer_artifact: Option<LogProb>,
    pub prob_observable_at_homopolymer_variant: Option<LogProb>,
    pub homopolymer_indel_len: Option<i8>,
    pub is_max_mapq: bool,
    pub alt_locus: AltLocus,
    pub third_allele_evidence: Option<u32>,
    /* private fields */

}

Fields§

§fragment_id: Option<u64>§prob_alt: LogProb

Probability that the read/read-pair comes from the alternative allele.

§prob_ref: LogProb

Probability that the read/read-pair comes from the reference allele.

§prob_missed_allele: LogProb

Probability that the read/read-pair comes from an unknown allele at an unknown true locus (in case it is mismapped). This should usually be set as the product of the maxima of prob_ref and prob_alt per read.

§prob_sample_alt: LogProb

Probability to sample the alt allele

§prob_double_overlap: LogProb

Probability to overlap with both strands

§prob_single_overlap: LogProb

Probability to overlap with one strand only (1-prob_double_overlap)

§prob_hit_base: LogProb§strand: Strand

Strand evidence this observation relies on

§read_orientation: SequenceReadPairOrientation

Read orientation support this observation relies on

§softclipped: bool

True if obervation contains s

§paired: bool§read_position: ReadPosition

Read position of the variant in the read (for SNV and MNV)

§prob_observable_at_homopolymer_artifact: Option<LogProb>

Probability to make this observation at a homopolymer artifact

§prob_observable_at_homopolymer_variant: Option<LogProb>§homopolymer_indel_len: Option<i8>

Homopolymer indel length (None if there is no homopolymer indel compared to reference)

§is_max_mapq: bool§alt_locus: AltLocus§third_allele_evidence: Option<u32>

Edit distance of the read against the alt allele. Only recorded if it is higher than the expected number of sequencing errors of each type.