Struct checkm::CheckMResult

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

Fields

genome_to_quality: BTreeMap<String, GenomeQuality>

Methods

impl CheckMResult

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: &Vec<&'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: &Vec<&'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

impl CheckMResult

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