Struct ContigSummary

pub struct ContigSummary {
    pub name: String,
    pub length: usize,
    pub mean_read_lengths: MeanReadLengths,
    pub mean_read_quality: f64,
    pub total_bases: usize,
    pub n50: usize,
    pub on_target_read_count: usize,
    pub off_target_read_count: usize,
    pub yield_on_target: usize,
    pub yield_off_target: usize,
}

Represents a summary of a contig or sequence from a sequencing experiment. It includes various metrics related to the contig’s characteristics and read mapping.

Fields

name: String

The name or identifier of the contig.

length: usize

The length of the contig in base pairs.

mean_read_lengths: MeanReadLengths

The mean read length of the mapped reads associated with this contig.

mean_read_quality: f64

The mean read quality of the mapped reads associated with this contig.

total_bases: usize

Yield of mapped reads

n50: usize

The N50 metric for the contig, representing the length at which the cumulative sum of contig lengths reaches half of the total assembly length.

on_target_read_count: usize

The count of reads that are mapped on the target region (on-target reads).

off_target_read_count: usize

The count of reads that are mapped off the target region (off-target reads).

yield_on_target: usize

The total yield (base pairs) of on-target reads for this contig.

yield_off_target: usize

The total yield (base pairs) of off-target reads for this contig.

Implementations

impl ContigSummary

pub fn new(name: String, length: usize) -> Self

Create a new ContigSummary instance with default values for all fields except name and length.

Arguments

• name - The name of the contig.
• length - The length of the contig.

pub fn total_reads(&self) -> usize

Get the total number of reads on the contig.

pub fn mean_read_length(&self) -> usize

Mean read length of all reads on the contig.

pub fn on_target_mean_read_length(&self) -> usize

On target mean read length of all reads on the contig.

pub fn off_target_mean_read_length(&self) -> usize

Off target mean read length of all reads on the contig.

Trait Implementations

impl Debug for ContigSummary

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

Formats the value using the given formatter.