Struct noodles_bam::record::data::Data

pub struct Data { /* private fields */ }

BAM record data.

This is also called optional fields.

Implementations

impl Data

pub fn len(&self) -> usize

Returns the number of data fields.

Examples

use noodles_bam::record::Data;
let data = Data::default();
assert_eq!(data.len(), 0);

pub fn is_empty(&self) -> bool

Returns whether there are any data fields.

Examples

use noodles_bam::record::Data;
let data = Data::default();
assert!(data.is_empty());

pub fn clear(&mut self)

Removes all fields from the data map.

This does not affect the capacity of the map.

Examples

use noodles_bam::record::Data;

let mut data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

assert_eq!(data.len(), 2);

data.clear();

assert!(data.is_empty());

pub fn get(&self, tag: Tag) -> Option<Result<Field>>

Returns a field by the given tag.

Examples

use noodles_bam::record::{data::{field::Value, Field}, Data};
use noodles_sam::record::data::field::Tag;

let data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

let rg = data.get(Tag::ReadGroup).transpose()?;
assert_eq!(rg, Some(Field::new(Tag::ReadGroup, Value::String(String::from("rg0")))));

assert!(data.get(Tag::AlignmentScore).is_none());

pub fn get_index(&self, i: usize) -> Option<Result<Field>>

Returns a field by an index.

Examples

use noodles_bam::record::{data::{field::Value, Field}, Data};
use noodles_sam::record::data::field::Tag;

let data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

let rg = data.get_index(1).transpose()?;
assert_eq!(rg, Some(Field::new(Tag::ReadGroup, Value::String(String::from("rg0")))));

assert!(data.get_index(2).is_none());

pub fn insert(&mut self, field: Field) -> Option<Result<Field>>

Inserts a field into the data map.

This uses the field tag as the key and field as the value.

If the tag already exists in the map, the existing field is replaced by the new one, and the existing field is returned.

Examples

use noodles_bam::record::{data::{field::Value, Field}, Data};
use noodles_sam::record::data::field::Tag;

let mut data = Data::default();

let nh = Field::new(Tag::AlignmentHitCount, Value::UInt8(1));
data.insert(nh.clone()).transpose()?;

assert_eq!(data.len(), 1);
assert_eq!(data.get_index(0).transpose()?, Some(nh));

pub fn fields(&self) -> Fields<&[u8]>

👎 Deprecated since 0.8.0:

Use Data::values instead.

Returns an iterator over data fields.

Examples

use noodles_bam::record::{data::{field::Value, Field}, Data};
use noodles_sam::record::data::field::Tag;

let data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

let mut fields = data.values();

assert_eq!(
    fields.next().transpose()?,
    Some(Field::new(Tag::AlignmentHitCount, Value::Int32(1)))
);

assert_eq!(
    fields.next().transpose()?,
    Some(Field::new(Tag::ReadGroup, Value::String(String::from("rg0"))))
);

assert!(fields.next().is_none());

pub fn keys(&self) -> impl Iterator<Item = Result<Tag>> + '_

Returns an iterator over all tags.

Examples

use noodles_bam::record::Data;
use noodles_sam::record::data::field::Tag;

let data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

let mut keys = data.keys();

assert_eq!(keys.next().transpose()?, Some(Tag::AlignmentHitCount));
assert_eq!(keys.next().transpose()?, Some(Tag::ReadGroup));
assert!(keys.next().is_none());

pub fn values(&self) -> Fields<&[u8]>

Returns an iterator over all fields.

Examples

use noodles_bam::record::{data::{field::Value, Field}, Data};
use noodles_sam::record::data::field::Tag;

let data = Data::try_from(vec![
    b'N', b'H', b'i', 0x01, 0x00, 0x00, 0x00, // NH:i:1
    b'R', b'G', b'Z', b'r', b'g', b'0', 0x00, // RG:Z:rg0
])?;

let mut values = data.values();

assert_eq!(
    values.next().transpose()?,
    Some(Field::new(Tag::AlignmentHitCount, Value::Int32(1)))
);

assert_eq!(
    values.next().transpose()?,
    Some(Field::new(Tag::ReadGroup, Value::String(String::from("rg0"))))
);

assert!(values.next().is_none());

Trait Implementations

impl AsMut<Vec<u8, Global>> for Data

fn as_mut(&mut self) -> &mut Vec<u8>

Performs the conversion.

impl AsRef<[u8]> for Data

fn as_ref(&self) -> &[u8]

Performs the conversion.

impl Clone for Data

fn clone(&self) -> Data

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Data

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

Formats the value using the given formatter.

impl Default for Data

fn default() -> Data

Returns the “default value” for a type.

impl PartialEq<Data> for Data

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

This method tests for self and other values to be equal, and is used by ==.

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

This method tests for !=.

impl TryFrom<&'_ Data> for Data

type Error = TryFromDataError

The type returned in the event of a conversion error.

fn try_from(data: &Data) -> Result<Self, Self::Error>

Performs the conversion.

impl TryFrom<Vec<Field, Global>> for Data

type Error = Error

The type returned in the event of a conversion error.

fn try_from(fields: Vec<Field>) -> Result<Self, Self::Error>

Performs the conversion.

impl TryFrom<Vec<u8, Global>> for Data

type Error = Error

The type returned in the event of a conversion error.

fn try_from(data: Vec<u8>) -> Result<Self, Self::Error>

Performs the conversion.

impl Eq for Data

impl StructuralEq for Data

impl StructuralPartialEq for Data