Struct ColumnarDNA 

pub struct ColumnarDNA { /* private fields */ }

Implementations

impl ColumnarDNA

pub const fn new() -> Self

pub fn with_capacity(capacity: usize) -> Self

pub const fn len(&self) -> usize

Examples found in repository

examples/histogram.rs (line 27)

fn main() {
    let path = std::env::args().nth(1).expect("No input file given");

    // create a parser with the desired options
    let mut parser = FastxParser::<CONFIG>::from_file(&path).expect("Cannot open file");
    let mut num_a = 0;
    let mut num_c = 0;
    let mut num_t = 0;
    let mut num_g = 0;

    while let Some(_event) = parser.next() {
        let cdna = parser.get_dna_columnar();
        let (high_bits, hi) = cdna.high_bits();
        let (low_bits, lo) = cdna.low_bits();
        let rem = cdna.len() % 64;
        for (&hi, &lo) in high_bits.iter().zip(low_bits) {
            num_a += (!hi & !lo).count_ones() as usize;
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
        if rem > 0 {
            num_a += (!hi & !lo).count_ones() as usize - (64 - rem);
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
    }

    println!("a: {num_a}");
    println!("c: {num_c}");
    println!("t: {num_t}");
    println!("g: {num_g}");
}

pub const fn is_empty(&self) -> bool

pub const fn capacity(&self) -> usize

pub fn clear(&mut self)

pub fn append(&mut self, high: u64, low: u64, size: usize)

pub fn high_bits(&self) -> (&[u64], u64)

Examples found in repository

examples/histogram.rs (line 25)

fn main() {
    let path = std::env::args().nth(1).expect("No input file given");

    // create a parser with the desired options
    let mut parser = FastxParser::<CONFIG>::from_file(&path).expect("Cannot open file");
    let mut num_a = 0;
    let mut num_c = 0;
    let mut num_t = 0;
    let mut num_g = 0;

    while let Some(_event) = parser.next() {
        let cdna = parser.get_dna_columnar();
        let (high_bits, hi) = cdna.high_bits();
        let (low_bits, lo) = cdna.low_bits();
        let rem = cdna.len() % 64;
        for (&hi, &lo) in high_bits.iter().zip(low_bits) {
            num_a += (!hi & !lo).count_ones() as usize;
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
        if rem > 0 {
            num_a += (!hi & !lo).count_ones() as usize - (64 - rem);
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
    }

    println!("a: {num_a}");
    println!("c: {num_c}");
    println!("t: {num_t}");
    println!("g: {num_g}");
}

pub fn low_bits(&self) -> (&[u64], u64)

Examples found in repository

examples/histogram.rs (line 26)

fn main() {
    let path = std::env::args().nth(1).expect("No input file given");

    // create a parser with the desired options
    let mut parser = FastxParser::<CONFIG>::from_file(&path).expect("Cannot open file");
    let mut num_a = 0;
    let mut num_c = 0;
    let mut num_t = 0;
    let mut num_g = 0;

    while let Some(_event) = parser.next() {
        let cdna = parser.get_dna_columnar();
        let (high_bits, hi) = cdna.high_bits();
        let (low_bits, lo) = cdna.low_bits();
        let rem = cdna.len() % 64;
        for (&hi, &lo) in high_bits.iter().zip(low_bits) {
            num_a += (!hi & !lo).count_ones() as usize;
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
        if rem > 0 {
            num_a += (!hi & !lo).count_ones() as usize - (64 - rem);
            num_c += (!hi & lo).count_ones() as usize;
            num_t += (hi & !lo).count_ones() as usize;
            num_g += (hi & lo).count_ones() as usize;
        }
    }

    println!("a: {num_a}");
    println!("c: {num_c}");
    println!("t: {num_t}");
    println!("g: {num_g}");
}

pub fn get(&self, i: usize) -> (bool, bool)

pub fn get_char(&self, i: usize) -> char

Trait Implementations

impl Clone for ColumnarDNA

fn clone(&self) -> ColumnarDNA

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Default for ColumnarDNA

fn default() -> ColumnarDNA

Returns the “default value” for a type.

impl Display for ColumnarDNA

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

Formats the value using the given formatter.