Struct libprosic::model::sample::Sample

pub struct Sample { /* private fields */ }

A sequenced sample, e.g., a tumor or a normal sample.

Implementations

impl Sample

pub fn new(
    bam: IndexedReader,
    pileup_window: u32,
    use_fragment_evidence: bool,
    use_secondary: bool,
    use_mapq: bool,
    alignment_properties: AlignmentProperties,
    likelihood_model: LatentVariableModel,
    prob_insertion_artifact: Prob,
    prob_deletion_artifact: Prob,
    prob_insertion_extend_artifact: Prob,
    prob_deletion_extend_artifact: Prob,
    indel_haplotype_window: u32
) -> Self

Create a new Sample.

Arguments

• bam - BAM file with the aligned and deduplicated sequence reads.
• pileup_window - Window around the variant that shall be searched for evidence (e.g. 5000).
• use_fragment_evidence - Whether to use read pairs that are left and right of variant.
• use_secondary - Whether to use secondary alignments.
• insert_size - estimated insert size
• prior_model - Prior assumptions about allele frequency spectrum of this sample.
• likelihood_model - Latent variable model to calculate likelihoods of given observations.
• max_indel_overlap - maximum number of bases a read may be aligned beyond the start or end of an indel in order to be considered as an observation
• indel_haplotype_window - maximum number of considered bases around an indel breakpoint

pub fn likelihood_model(&self) -> LatentVariableModel

Return likelihood model.

pub fn extract_observations(
    &mut self,
    start: u32,
    variant: &Variant,
    chrom: &[u8],
    chrom_seq: &[u8]
) -> Result<Vec<Observation>, Box<dyn Error>>

Extract observations for the given variant.