Struct noodles_bcf::Record[][src]

pub struct Record(_);
Expand description

A BCF record.

A bcf::Record wraps a raw byte buffer, and the fields should be considered immutable.

Implementations

Converts a VCF record to a BCF record.

Examples

use noodles_bcf as bcf;
use noodles_vcf::{self as vcf, record::Position};

let raw_header = "##fileformat=VCFv4.3\n##contig=<ID=sq0>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
let header: vcf::Header = raw_header.parse()?;
let string_map = raw_header.parse()?;

let record = bcf::Record::from(vec![
    0x00, 0x00, 0x00, 0x00, // chrom = sq0
    0x00, 0x00, 0x00, 0x00, // pos = 0 (base 0)
    0x01, 0x00, 0x00, 0x00, // rlen = 1
    0x01, 0x00, 0x80, 0x7f, // qual = Float::Missing
    0x00, 0x00, // n_info = 0
    0x01, 0x00, // n_allele = 1
    0x00, // n_sample = 0
    0x00, 0x00, 0x00, // n_fmt = 0
    0x07, // id = [missing]
    0x17, 0x41, // ref = A
    0x00, // filter = []
]);

let actual = record.try_into_vcf_record(&header, &string_map)?;

let expected = vcf::Record::builder()
    .set_chromosome("sq0".parse()?)
    .set_position(Position::try_from(1)?)
    .set_reference_bases("A".parse()?)
    .build()?;

assert_eq!(actual, expected);

Returns the chromosome ID of the record.

The chromosome ID is the index of the associated contig in the VCF header.

Examples

use noodles_bcf as bcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    // ...
]);

assert_eq!(record.chromosome_id()?, 8);

Returns the start position of this record.

Despite the BCF format using 0-based positions, this normalizes the value as a 1-based position.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    0x0c, 0x00, 0x00, 0x00, // POS
    // ...
]);

assert_eq!(record.position().map(i32::from)?, 13);

Returns the end position of this record.

This value is 1-based.

Examples

use noodles_bcf as bcf;
use noodles_vcf as vcf;

let record = bcf::Record::from(vec![
    0x08, 0x00, 0x00, 0x00, // CHROM
    0x0c, 0x00, 0x00, 0x00, // POS
    0x05, 0x00, 0x00, 0x00, // rlen
    // ...
]);

assert_eq!(record.end().map(i32::from)?, 17);

Trait Implementations

Returns a copy of the value. Read more

Performs copy-assignment from source. Read more

Returns the “default value” for a type. Read more

The resulting type after dereferencing.

Dereferences the value.

Mutably dereferences the value.

Performs the conversion.

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

This method tests for !=.

Auto Trait Implementations

Blanket Implementations

Gets the TypeId of self. Read more

Immutably borrows from an owned value. Read more

Mutably borrows from an owned value. Read more

Converts self into T using Into<T>. Read more

Converts self into a target type. Read more

Compare self to key and return true if they are equal.

Causes self to use its Binary implementation when Debug-formatted.

Causes self to use its Display implementation when Debug-formatted. Read more

Causes self to use its LowerExp implementation when Debug-formatted. Read more

Causes self to use its LowerHex implementation when Debug-formatted. Read more

Causes self to use its Octal implementation when Debug-formatted.

Causes self to use its Pointer implementation when Debug-formatted. Read more

Causes self to use its UpperExp implementation when Debug-formatted. Read more

Causes self to use its UpperHex implementation when Debug-formatted. Read more

Performs the conversion.

Performs the conversion.

Pipes by value. This is generally the method you want to use. Read more

Borrows self and passes that borrow into the pipe function. Read more

Mutably borrows self and passes that borrow into the pipe function. Read more

Borrows self, then passes self.borrow() into the pipe function. Read more

Mutably borrows self, then passes self.borrow_mut() into the pipe function. Read more

Borrows self, then passes self.as_ref() into the pipe function.

Mutably borrows self, then passes self.as_mut() into the pipe function. Read more

Borrows self, then passes self.deref() into the pipe function.

Mutably borrows self, then passes self.deref_mut() into the pipe function. Read more

Pipes a value into a function that cannot ordinarily be called in suffix position. Read more

Pipes a trait borrow into a function that cannot normally be called in suffix position. Read more

Pipes a trait mutable borrow into a function that cannot normally be called in suffix position. Read more

Pipes a trait borrow into a function that cannot normally be called in suffix position. Read more

Pipes a trait mutable borrow into a function that cannot normally be called in suffix position. Read more

Pipes a dereference into a function that cannot normally be called in suffix position. Read more

Pipes a mutable dereference into a function that cannot normally be called in suffix position. Read more

Pipes a reference into a function that cannot ordinarily be called in suffix position. Read more

Pipes a mutable reference into a function that cannot ordinarily be called in suffix position. Read more

Immutable access to a value. Read more

Mutable access to a value. Read more

Immutable access to the Borrow<B> of a value. Read more

Mutable access to the BorrowMut<B> of a value. Read more

Immutable access to the AsRef<R> view of a value. Read more

Mutable access to the AsMut<R> view of a value. Read more

Immutable access to the Deref::Target of a value. Read more

Mutable access to the Deref::Target of a value. Read more

Calls .tap() only in debug builds, and is erased in release builds.

Calls .tap_mut() only in debug builds, and is erased in release builds. Read more

Calls .tap_borrow() only in debug builds, and is erased in release builds. Read more

Calls .tap_borrow_mut() only in debug builds, and is erased in release builds. Read more

Calls .tap_ref() only in debug builds, and is erased in release builds. Read more

Calls .tap_ref_mut() only in debug builds, and is erased in release builds. Read more

Calls .tap_deref() only in debug builds, and is erased in release builds. Read more

Calls .tap_deref_mut() only in debug builds, and is erased in release builds. Read more

Provides immutable access for inspection. Read more

Calls tap in debug builds, and does nothing in release builds.

Provides mutable access for modification. Read more

Calls tap_mut in debug builds, and does nothing in release builds.

Provides immutable access to the reference for inspection.

Calls tap_ref in debug builds, and does nothing in release builds.

Provides mutable access to the reference for modification.

Calls tap_ref_mut in debug builds, and does nothing in release builds.

Provides immutable access to the borrow for inspection. Read more

Calls tap_borrow in debug builds, and does nothing in release builds.

Provides mutable access to the borrow for modification.

Calls tap_borrow_mut in debug builds, and does nothing in release builds. Read more

Immutably dereferences self for inspection.

Calls tap_deref in debug builds, and does nothing in release builds.

Mutably dereferences self for modification.

Calls tap_deref_mut in debug builds, and does nothing in release builds. Read more

The resulting type after obtaining ownership.

Creates owned data from borrowed data, usually by cloning. Read more

🔬 This is a nightly-only experimental API. (toowned_clone_into)

recently added

Uses borrowed data to replace owned data, usually by cloning. Read more

Attempts to convert self into T using TryInto<T>. Read more

Attempts to convert self into a target type. Read more

The type returned in the event of a conversion error.

Performs the conversion.

The type returned in the event of a conversion error.

Performs the conversion.