Trait varlociraptor::testcase::runner::common::Testcase

source · 
pub trait Testcase {

Show 27 methods    fn inner(&self) -> &[Yaml];
    fn path(&self) -> &PathBuf;

    fn test_record_index(&self) -> usize { ... }
    fn preprocess_options(&self, sample_name: &str) -> String { ... }
    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 reference(&self) -> Result<Box<dyn AsRef<Path>>> { ... }
    fn index_reference(&self, path: &dyn AsRef<Path>) { ... }
    fn alignment_properties(&self, properties: &str) -> Result<NamedTempFile> { ... }

}

Required Methods

Provided Methods

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

Implementors