Struct ConditionSummary

pub struct ConditionSummary {

    pub name: String,
    pub total_reads: usize,
    pub mean_read_lengths: MeanReadLengths,
    pub off_target_read_count: usize,
    pub on_target_read_count: usize,
    pub off_target_percent: f64,
    pub off_target_yield: usize,
    pub on_target_yield: usize,
    pub off_target_mean_read_quality: f64,
    pub on_target_mean_read_quality: f64,
    pub n50: usize,
    pub on_target_n50: usize,
    pub off_target_n50: usize,
    pub contigs: HashMap<String, ContigSummary>,
}

Represents a summary of sequencing data, including various metrics related to the output of the experiment.

Fields

name: String

The name or identifier of the sequencing data.

total_reads: usize

The total number of reads in the sequencing data.

mean_read_lengths: MeanReadLengths

Mean read lengths

off_target_read_count: usize

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

on_target_read_count: usize

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

off_target_percent: f64

The percentage of off-target reads in the sequencing data.

off_target_yield: usize

The total yield (base pairs) of off-target reads in the sequencing data.

on_target_yield: usize

The total yield (base pairs) of on-target reads in the sequencing data.

off_target_mean_read_quality: f64

The mean read quality of off-target reads.

on_target_mean_read_quality: f64

The mean read quality of on-target reads.

n50: usize

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

on_target_n50: usize

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

off_target_n50: usize

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

contigs: HashMap<String, ContigSummary>

A vector of ContigSummary representing summaries of individual contigs or sequences in the sequencing data.

Implementations

impl ConditionSummary

pub fn update( &mut self, paf: PafRecord, on_target: bool, ) -> Result<(), Box<dyn Error + 'static>>

Update the ConditionSummary with information from the provided PafRecord.

This method updates the fields of the ConditionSummary based on the information from the given PafRecord. It increments the appropriate read counts (on-target or off-target), calculates the mean read lengths and read qualities, updates the total reads count, and calculates the off-target percentage.

Arguments

• paf - The PafRecord containing the information about the alignment.
• on_target - A boolean flag indicating whether the alignment is on-target or off-target.

Returns

This function returns a [DynResult] (a dynamic result that can contain any error). If the operation is successful, the DynResult will hold an Ok(()). Otherwise, it will hold an Err containing a helpful error message.

pub fn new(name: String) -> Self

Create a new Summary instance with default values for all fields except name.

Arguments

• name - The name of the summary.

pub fn name(&self) -> &str

Get the name or identifier of the sequencing data.

pub fn set_name(&mut self, name: String)

Set the name or identifier of the sequencing data.

pub fn total_reads(&self) -> usize

Get the total number of reads in the sequencing data.

pub fn add_total_reads(&mut self, total_reads: usize)

Set the total number of reads in the sequencing data.

pub fn off_target_read_count(&self) -> usize

Get the count of reads that are mapped off the target regions (off-target reads).

pub fn set_off_target_read_count(&mut self, off_target_read_count: usize)

Set the count of reads that are mapped off the target regions (off-target reads).

pub fn on_target_read_count(&self) -> usize

Get the count of reads that are mapped to the target regions (on-target reads).

pub fn set_on_target_read_count(&mut self, on_target_read_count: usize)

Set the count of reads that are mapped to the target regions (on-target reads).

pub fn off_target_percent(&self) -> f64

Get the percentage of off-target reads in the sequencing data.

pub fn set_off_target_percent(&mut self, off_target_percent: f64)

Set the percentage of off-target reads in the sequencing data.

pub fn off_target_yield(&self) -> usize

Get the total yield (base pairs) of off-target reads in the sequencing data.

pub fn set_off_target_yield(&mut self, off_target_yield: usize)

Set the total yield (base pairs) of off-target reads in the sequencing data.

pub fn on_target_yield(&self) -> usize

Get the total yield (base pairs) of on-target reads in the sequencing data.

pub fn set_on_target_yield(&mut self, on_target_yield: usize)

Set the total yield (base pairs) of on-target reads in the sequencing data.

pub fn mean_read_length(&self) -> usize

Get the mean read length of all reads

pub fn off_target_mean_read_length(&self) -> usize

Get the mean read length of off-target reads.

pub fn on_target_mean_read_length(&self) -> usize

Get the mean read length of on-target reads.

pub fn off_target_mean_read_quality(&self) -> f64

Get the mean read quality of off-target reads.

pub fn set_off_target_mean_read_quality( &mut self, off_target_mean_read_quality: f64, )

Set the mean read quality of off-target reads.

pub fn on_target_mean_read_quality(&self) -> f64

Get the mean read quality of on-target reads.

pub fn set_on_target_mean_read_quality( &mut self, on_target_mean_read_quality: f64, )

Set the mean read quality of on-target reads.

pub fn n50(&self) -> usize

Get the N50 metric for the entire dataset.

pub fn set_n50(&mut self, n50: usize)

Set the N50 metric for the entire dataset.

pub fn on_target_n50(&self) -> usize

Get the N50 metric for on-target reads.

pub fn set_on_target_n50(&mut self, on_target_n50: usize)

Set the N50 metric for on-target reads.

pub fn off_target_n50(&self) -> usize

Get the N50 metric for off-target reads.

pub fn set_off_target_n50(&mut self, off_target_n50: usize)

Set the N50 metric for off-target reads.

pub fn contigs(&self) -> &HashMap<String, ContigSummary>

Get a reference to the vector of ContigSummary.

pub fn contigs_mut(&mut self) -> &mut HashMap<String, ContigSummary>

Get a mutable reference to the vector of ContigSummary.

pub fn get_or_add_contig( &mut self, contig: &str, length: usize, ) -> &mut ContigSummary

Get the ContigSummary associated with the given contig name or add a new ContigSummary with the specified name and length if it doesn’t exist.

Arguments

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

Returns

A reference to the ContigSummary associated with the contig name.

Example

use std::collections::HashMap;
use your_crate::ContigSummary;

let mut contig_map: HashMap<String, ContigSummary> = HashMap::new();

// Get an existing contig or add a new one if it doesn't exist
let contig_name = "chr1".to_string();
let contig_length = 1000;
let contig_summary = contig_map.get_or_add_contig(contig_name.clone(), contig_length);

// Now you can modify the ContigSummary fields or access its properties
println!("Contig name: {}", contig_summary.name);
println!("Contig length: {}", contig_summary.length);

pub fn total_yield(&self) -> usize

get the total yield

Trait Implementations

impl Debug for ConditionSummary

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

Formats the value using the given formatter.

impl Display for ConditionSummary

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

Formats the value using the given formatter.