Struct SequencingRecord 

pub struct SequencingRecord<'a> { /* private fields */ }

A zero-copy record used to write sequences to binary sequence files.

This struct provides a unified API for writing records to all binseq formats (BQ, VBQ, and CBQ). It uses borrowed references for zero-copy efficiency.

Example

use binseq::SequencingRecordBuilder;

let record = SequencingRecordBuilder::default()
    .s_seq(b"ACGTACGT")
    .s_qual(b"IIIIFFFF")
    .s_header(b"seq_001")
    .flag(42)
    .build()
    .unwrap();

Implementations

impl<'a> SequencingRecord<'a>

pub fn new( s_seq: &'a [u8], s_qual: Option<&'a [u8]>, s_header: Option<&'a [u8]>, x_seq: Option<&'a [u8]>, x_qual: Option<&'a [u8]>, x_header: Option<&'a [u8]>, flag: Option<u64>, ) -> Self

pub fn s_seq(&self) -> &'a [u8]

Returns the primary sequence

pub fn s_qual(&self) -> Option<&'a [u8]>

Returns the primary quality scores if present

pub fn s_header(&self) -> Option<&'a [u8]>

Returns the primary header if present

pub fn x_seq(&self) -> Option<&'a [u8]>

Returns the extended/paired sequence if present

pub fn x_qual(&self) -> Option<&'a [u8]>

Returns the extended quality scores if present

pub fn x_header(&self) -> Option<&'a [u8]>

Returns the extended header if present

pub fn flag(&self) -> Option<u64>

Returns the flag if present

pub fn configured_size_cbq( &self, is_paired: bool, has_flags: bool, has_headers: bool, has_qualities: bool, ) -> usize

Returns the configured size of this record for CBQ format.

CBQ uses columnar storage so there are no per-record length prefixes. This calculates the size based on writer configuration, ignoring any extra data in the record that the writer won’t use.

pub fn configured_size_vbq( &self, is_paired: bool, has_flags: bool, has_headers: bool, has_qualities: bool, bitsize: BitSize, ) -> usize

Returns the configured size of this record for VBQ format.

VBQ uses a row-based format with length prefixes for each field. This calculates the size based on writer configuration, ignoring any extra data in the record that the writer won’t use.

The VBQ record layout is:

• Flag (8 bytes, if has_flags)
• s_len (8 bytes)
• x_len (8 bytes)
• s_seq (encoded, rounded up to 8-byte words)
• s_qual (raw bytes, if has_qualities)
• s_header_len + s_header (8 + len bytes, if has_headers and s_header present)
• x_seq (encoded, rounded up to 8-byte words, if paired)
• x_qual (raw bytes, if has_qualities and paired)
• x_header_len + x_header (8 + len bytes, if has_headers and x_header present)

pub fn is_paired(&self) -> bool

pub fn has_flags(&self) -> bool

pub fn has_headers(&self) -> bool

pub fn has_qualities(&self) -> bool

Trait Implementations

impl<'a> Clone for SequencingRecord<'a>

fn clone(&self) -> SequencingRecord<'a>

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl<'a> Copy for SequencingRecord<'a>

impl<'a> Default for SequencingRecord<'a>

fn default() -> SequencingRecord<'a>

Returns the “default value” for a type.