Struct Record 

pub struct Record { /* private fields */ }

A base BED record

It can be used as starting point to construct records for other file types like .narrowPeak, .broadPeak, ecc..

With the the derefable crate you can write a wrapper around common::Record that maintains its methods, while giving you the possibility of expanding them.

use bio::io::common;
use derefable::Derefable;
use serde::{Deserialize, Serialize};

type Reader<R> = common::Reader<R, BedRecord>;

#[derive(
    Debug, Default, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Serialize, Deserialize,
    Derefable
)]
pub struct BedRecord(#[deref(mutable)] common::Record);

/// Add new methods specific for a BED Record
impl BedRecord {
    /// Create a new Record
    pub fn new() -> Self {
        Self::default()
    }

    /// Name of the feature.
    pub fn name(&self) -> Option<&str> {
        self.aux(3)
    }

    /// Set name.
    pub fn set_name(&mut self, name: &str) {
        self.set_aux(3, name)
    }
}

fn main() {
    let src = b"chr1\t2\t3\tname1";
    let mut reader = Reader::new(&src[..]);
    for record in reader.records() {
        let rec: BedRecord = record.unwrap();
        assert_eq!(rec.chrom(), "chr1");
        assert_eq!(rec.start(), 2);
        assert_eq!(rec.end(), 3);
        assert_eq!(rec.name(), Some("name1"));
    }
}

Implementations

impl Record

pub fn set_start(&mut self, val: u64) -> &mut Self

pub fn set_end(&mut self, val: u64) -> &mut Self

impl Record

pub fn with_chrom(self, val: String) -> Self

pub fn with_start(self, val: u64) -> Self

pub fn with_end(self, val: u64) -> Self

impl Record

pub fn chrom_mut(&mut self) -> &mut String

pub fn start_mut(&mut self) -> &mut u64

pub fn end_mut(&mut self) -> &mut u64

impl Record

pub fn start(&self) -> u64

pub fn end(&self) -> u64

impl Record

pub fn new() -> Self

Create new record.

pub fn chrom(&self) -> &str

Chromosome of the feature.

pub fn aux(&self, i: usize) -> Option<&str>

Access auxilliary fields after the end field by index (counting first field (chromosome) as 0).

impl Record

pub fn set_chrom(&mut self, chrom: &str)

Set chromosome.

pub fn set_aux(&mut self, i: usize, field: &str)

Set auxiliary field after the end field by index. If the index is bigger than the current auxiliary vector, empty strings will be pushed into the vector until the index is reached. (counting first field (chromosome) as 0).

pub fn push_aux(&mut self, field: &str)

Add auxilliary field.

Trait Implementations

impl Clone for Record

fn clone(&self) -> Record

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

fn default() -> Record

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for Record

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Hash for Record

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for Record

fn cmp(&self, other: &Record) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for Record

fn eq(&self, other: &Record) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for Record

fn partial_cmp(&self, other: &Record) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Serialize for Record

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Eq for Record

impl StructuralPartialEq for Record