Struct 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.