Enum coverm::mosdepth_genome_coverage_estimators::CoverageEstimator

pub enum CoverageEstimator {
    MeanGenomeCoverageEstimator {
        total_count: u32,
        total_bases: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        total_mismatches: u32,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
        exclude_mismatches: bool,
    },
    TrimmedMeanGenomeCoverageEstimator {
        counts: Vec<u32>,
        observed_contig_length: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        min: f32,
        max: f32,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
    },
    PileupCountsGenomeCoverageEstimator {
        counts: Vec<u32>,
        observed_contig_length: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
    },
    CoverageFractionGenomeCoverageEstimator {
        total_bases: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
    },
    NumCoveredBasesCoverageEstimator {
        total_bases: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
    },
    VarianceGenomeCoverageEstimator {
        counts: Vec<u32>,
        observed_contig_length: u32,
        num_covered_bases: u32,
        num_mapped_reads: u64,
        min_fraction_covered_bases: f32,
        contig_end_exclusion: u32,
    },
    ReferenceLengthCalculator {
        observed_contig_length: u32,
        num_mapped_reads: u64,
    },
    ReadCountCalculator {
        num_mapped_reads: u64,
    },
    ReadsPerBaseCalculator {
        observed_contig_length: u32,
        num_mapped_reads: u64,
    },
}

Variants

MeanGenomeCoverageEstimator

Fields of MeanGenomeCoverageEstimator

total_count: u32total_bases: u32num_covered_bases: u32num_mapped_reads: u64total_mismatches: u32min_fraction_covered_bases: f32contig_end_exclusion: u32exclude_mismatches: bool

TrimmedMeanGenomeCoverageEstimator

Fields of TrimmedMeanGenomeCoverageEstimator

counts: Vec<u32>observed_contig_length: u32num_covered_bases: u32num_mapped_reads: u64min: f32max: f32min_fraction_covered_bases: f32contig_end_exclusion: u32

PileupCountsGenomeCoverageEstimator

Fields of PileupCountsGenomeCoverageEstimator

counts: Vec<u32>observed_contig_length: u32num_covered_bases: u32num_mapped_reads: u64min_fraction_covered_bases: f32contig_end_exclusion: u32

CoverageFractionGenomeCoverageEstimator

Fields of CoverageFractionGenomeCoverageEstimator

total_bases: u32num_covered_bases: u32num_mapped_reads: u64min_fraction_covered_bases: f32contig_end_exclusion: u32

NumCoveredBasesCoverageEstimator

Fields of NumCoveredBasesCoverageEstimator

total_bases: u32num_covered_bases: u32num_mapped_reads: u64min_fraction_covered_bases: f32contig_end_exclusion: u32

VarianceGenomeCoverageEstimator

Fields of VarianceGenomeCoverageEstimator

counts: Vec<u32>observed_contig_length: u32num_covered_bases: u32num_mapped_reads: u64min_fraction_covered_bases: f32contig_end_exclusion: u32

ReferenceLengthCalculator

Fields of ReferenceLengthCalculator

observed_contig_length: u32num_mapped_reads: u64

ReadCountCalculator

Fields of ReadCountCalculator

num_mapped_reads: u64

ReadsPerBaseCalculator

Fields of ReadsPerBaseCalculator

observed_contig_length: u32num_mapped_reads: u64

Methods

impl CoverageEstimator

pub fn column_headers(&self) -> Vec<&str>

impl CoverageEstimator

pub fn new_estimator_mean(
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32,
    exclude_mismatches: bool
) -> CoverageEstimator

pub fn new_estimator_trimmed_mean(
    min: f32,
    max: f32,
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32
) -> CoverageEstimator

pub fn new_estimator_pileup_counts(
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32
) -> CoverageEstimator

pub fn new_estimator_covered_fraction(
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32
) -> CoverageEstimator

pub fn new_estimator_covered_bases(
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32
) -> CoverageEstimator

pub fn new_estimator_variance(
    min_fraction_covered_bases: f32,
    contig_end_exclusion: u32
) -> CoverageEstimator

pub fn new_estimator_length() -> CoverageEstimator

pub fn new_estimator_read_count() -> CoverageEstimator

pub fn new_estimator_reads_per_base() -> CoverageEstimator

Trait Implementations

impl MosdepthGenomeCoverageEstimator for CoverageEstimator

fn setup(&mut self)

fn add_contig(
    &mut self,
    ups_and_downs: &Vec<i32>,
    num_mapped_reads_in_contig: u64,
    total_mismatches_in_contig: u32
)

fn calculate_coverage(&mut self, unobserved_contig_length: u32) -> f32

fn copy(&self) -> CoverageEstimator

fn print_coverage<T: CoverageTaker>(
    &self,
    coverage: &f32,
    coverage_taker: &mut T
)

fn print_zero_coverage<T: CoverageTaker>(
    &self,
    coverage_taker: &mut T,
    entry_length: u32
)

fn num_mapped_reads(&self) -> u64

impl Clone for CoverageEstimator

fn clone(&self) -> CoverageEstimator

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for CoverageEstimator

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

Formats the value using the given formatter.