Struct varlociraptor::testcase::runner::common::version3::TestcaseVersion3

pub struct TestcaseVersion3 {
    pub inner: Vec<Yaml>,
    pub path: PathBuf,
}

Fields

inner: Vec<Yaml>

path: PathBuf

Trait Implementations

impl Debug for TestcaseVersion3

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Testcase for TestcaseVersion3

fn inner(&self) -> &[Yaml]

fn path(&self) -> &PathBuf

fn reference(&self) -> Result<Box<dyn AsRef<Path>>>

fn preprocess_options(&self, sample_name: &str) -> String

fn test_record_index(&self) -> usize

Index of record in the candidates.vcf to evaluate expressions for.

fn mode(&self) -> Mode

fn omit_strand_bias(&self) -> bool

fn omit_read_orientation_bias(&self) -> bool

fn omit_read_position_bias(&self) -> bool

fn omit_softclip_bias(&self) -> bool

fn omit_homopolymer_artifact_detection(&self) -> bool

fn omit_alt_locus_bias(&self) -> bool

fn yaml(&self) -> &Yaml

fn output(&self) -> PathBuf

fn candidates(&self) -> PathBuf

fn samples(&self) -> Vec<String>

fn sample_preprocessed_path( &self, sample_name: &str, temp_preprocess: &TempDir ) -> PathBuf

fn sample_observations_path(&self, sample_name: &str) -> PathBuf

fn sample(&self, sample_name: &str) -> &Yaml

fn sample_bam(&self, sample_name: &str) -> PathBuf

fn sample_alignment_properties(&self, sample_name: &str) -> String

fn scenario(&self) -> Option<PathBuf>

fn purity(&self) -> Option<f64>

fn run(&self, pairhmm_mode_override: &str) -> Result<()>

fn check(&self)

fn index_reference(&self, path: &dyn AsRef<Path>)

fn alignment_properties(&self, properties: &str) -> Result<NamedTempFile>