Struct checkm::CheckMResult

pub struct CheckMResult<T: GenomeQuality> {
    pub genome_to_quality: BTreeMap<String, T>,
}

Fields

genome_to_quality: BTreeMap<String, T>

Implementations

impl<T: GenomeQuality + Copy + Debug> CheckMResult<T>

pub fn order_genomes_by_completeness_minus_4contamination(&self) -> Vec<&String>

pub fn order_genomes_by_completeness_minus_5contamination(&self) -> Vec<&String>

pub fn order_fasta_paths_by_completeness_minus_4contamination<'a>( &self, genome_fasta_files: &[&'a str], min_completeness: Option<f32>, max_contamination: Option<f32> ) -> Result<Vec<&'a str>, String>

Map paths to FASTA paths to CheckM qualities, and return paths ordered by their quality, where quality is completeness - 4*contamination. If not None, min_completeness and max_contamination specify thresholds as fractions e.g. 0.8 not 80.

pub fn order_fasta_paths_by_completeness_minus_5contamination<'a>( &self, genome_fasta_files: &[&'a str], min_completeness: Option<f32>, max_contamination: Option<f32> ) -> Result<Vec<&'a str>, String>

Map paths to FASTA paths to CheckM qualities, and return paths ordered by their quality, where quality is completeness - 5*contamination. If not None, min_completeness and max_contamination specify thresholds as fractions e.g. 0.8 not 80.

pub fn filter( &self, min_completeness: f32, max_contamination: f32 ) -> CheckMResult<T>

pub fn retrieve_via_fasta_path( &self, fasta_path: &str ) -> Result<T, CheckMRetrievalError>