Struct noodles::cram::Record

pub struct Record { /* fields omitted */ }

A CRAM record.

Implementations

impl Record

pub fn try_into_sam_record(
    &self,
    reference_assembly: &[Record],
    reference_sequences: &IndexMap<String, ReferenceSequence, RandomState>,
    compression_header: &CompressionHeader
) -> Result<Record, Error>

Converts this CRAM record to a SAM record.

impl Record

pub fn builder() -> Builder

Returns a builder to create a record from each of its fields.

pub fn bam_flags(&self) -> Flags

Returns the BAM flags.

This is also called the BAM bit flags.

pub fn flags(&self) -> Flags

Returns the CRAM flags.

This is also called the CRAM bit flags or compression bit flags.

pub fn reference_sequence_id(&self) -> Option<ReferenceSequenceId>

Returns the reference sequence ID.

This is also called the reference ID. It is the position of the reference sequence in the SAM header.

pub fn read_length(&self) -> usize

Returns the read length.

pub fn alignment_start(&self) -> Option<Position>

Returns the alignment start position.

This value is 1-based.

pub fn alignment_end(&self) -> i32

Returns the alignment end position.

This value is 1-based.

pub fn read_group_id(&self) -> ReadGroupId

Returns the read group ID.

This is also simply called the read group. It is the position of the read group in the SAM header.

pub fn read_name(&self) -> &[u8]

Returns the read name.

This may be the original read name or a generated one.

pub fn next_mate_flags(&self) -> NextMateFlags

Returns the next mate flags.

This is also call the next mate bit flags.

pub fn next_fragment_reference_sequence_id(&self) -> Option<ReferenceSequenceId>

Returns the reference sequence ID of the next fragment.

It is the position of the reference sequence in the SAM header.

pub fn next_mate_alignment_start(&self) -> Option<Position>

Returns the alignment start position of the next mate.

This value is 1-based.

pub fn template_size(&self) -> i32

Returns the template size.

pub fn distance_to_next_fragment(&self) -> i32

Returns the distance to the next fragment.

This is the number of records to the next fragment within a slice.

pub fn tags(&self) -> &[Tag]

Returns the tag dictionary.

pub fn bases(&self) -> &[u8]

Returns the read bases.

pub fn features(&self) -> &[Feature]

Returns the read features.

pub fn mapping_quality(&self) -> MappingQuality

Returns the mapping quality.

pub fn quality_scores(&self) -> &[u8]

Returns the per-base quality scores.

Trait Implementations

impl Clone for Record

pub fn clone(&self) -> Record

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Debug for Record

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

Formats the value using the given formatter.

impl Default for Record

pub fn default() -> Record

Returns the “default value” for a type.

impl PartialEq<Record> for Record

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

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

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

This method tests for !=.

impl StructuralPartialEq for Record