Struct rosella::coverage::coverage_table::CoverageTable

pub struct CoverageTable {
    pub table: Array2<f64>,
    pub average_depths: Vec<f64>,
    pub contig_names: Vec<String>,
    pub contig_lengths: Vec<usize>,
    pub sample_names: Vec<String>,
    pub output_path: String,
}

Fields

table: Array2<f64>

average_depths: Vec<f64>

contig_names: Vec<String>

contig_lengths: Vec<usize>

sample_names: Vec<String>

output_path: String

Implementations

impl CoverageTable

pub fn new( table: Array2<f64>, average_depths: Vec<f64>, contig_names: Vec<String>, contig_lengths: Vec<usize>, sample_names: Vec<String>, output_path: String ) -> Self

pub fn filter_by_length( &mut self, min_contig_size: usize ) -> Result<HashSet<String>>

pub fn get_contig_names(&self, indices: &HashSet<usize>) -> HashSet<String>

pub fn filter_by_index( &mut self, indices_to_remove: &HashSet<usize> ) -> Result<HashSet<String>>

pub fn from_file<P: AsRef<Path>>( file_path: P, mode: MappingMode ) -> Result<Self>

read a coverage table from a file we specify the mode as a parameter as coverm has different output formats for different modes depending on short/long read inputs

pub fn merge(&mut self, other: Self) -> Result<()>

pub fn merge_many(coverage_tables: Vec<CoverageTable>) -> Result<Self>

merge multiple coverage tables into one Make sure that the tables have the same contig names in the same order. We also want to be aware of sample name order. We will also need to recalculate average depths

pub fn write<P: AsRef<Path>>(&mut self, output_path: P) -> Result<()>

Write the coverage table to a file The file will be a tab delimited file with the following columns: contig_name, contig_length, sample1_coverage, sample1_variance, sample2_coverage, sample2_variance, … The first row will be a header row with the sample names

pub fn set_output_path(&mut self, output_path: String)