Struct noodles::cram::Record

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pub struct Record { /* private fields */ }

Expand description

A CRAM record.

Implementations

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impl Record

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pub fn try_from_alignment_record<R>(
 header: &Header,
 record: &R
) -> Result<Record, Error> where
 R: AlignmentRecord + ?Sized,

Converts an alignment record to a CRAM record.

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pub fn try_into_sam_record(&self, header: &Header) -> Result<Record, Error>

Converts this CRAM record to a SAM record.

This assumes this record is fully resolved.

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impl Record

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pub fn builder() -> Builder

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

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pub fn bam_flags(&self) -> Flags

Returns the BAM flags.

This is also called the BAM bit flags.

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pub fn cram_flags(&self) -> Flags

Returns the CRAM flags.

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

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

Returns the reference sequence ID.

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

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pub fn read_length(&self) -> usize

Returns the read length.

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pub fn read_group_id(&self) -> Option<usize>

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.

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pub fn next_mate_flags(&self) -> NextMateFlags

Returns the next mate flags.

This is also call the next mate bit flags.

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

Returns the reference sequence ID of the next fragment.

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

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

Returns the alignment start position of the next mate.

This value is 1-based.

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pub fn template_size(&self) -> i32

Returns the template size.

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pub fn distance_to_next_fragment(&self) -> Option<usize>

Returns the distance to the next fragment.

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

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pub fn tags(&self) -> &Data

Returns the tag dictionary.

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pub fn bases(&self) -> &Sequence

Returns the read bases.

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pub fn features(&self) -> &Features

Returns the read features.

Trait Implementations

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impl AlignmentRecord for Record

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fn read_name(&self) -> Option<&ReadName>

Returns the read name. Read more

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fn reference_sequence(
&self,
reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>
) -> Option<Result<&'rs ReferenceSequence, Error>>

Returns the associated reference sequence.

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fn flags(&self) -> Flags

Returns the flags.

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

Returns the start position.

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fn alignment_span(&self) -> usize

Calculates the alignment span over the reference sequence.

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fn mapping_quality(&self) -> Option<MappingQuality>

Returns the mapping quality.

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fn cigar(&self) -> &Cigar

Returns the CIGAR operations.

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fn mate_reference_sequence(
&self,
reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>
) -> Option<Result<&'rs ReferenceSequence, Error>>

Returns the associated reference sequence of the mate.

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fn mate_alignment_start(&self) -> Option<Position>

Returns the start position of the mate.

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fn template_length(&self) -> i32

Returns the template length.

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fn sequence(&self) -> &Sequence

Returns the sequence.

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fn quality_scores(&self) -> &QualityScores

Returns the quality scores.

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fn data(&self) -> &Data

Returns the data fields.

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fn alignment_end(&self) -> Option<Position>

Calculates the end position. Read more

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impl Clone for Record

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fn clone(&self) -> Record

Returns a copy of the value. Read more

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

Performs copy-assignment from source. Read more

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impl Debug for Record

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

Formats the value using the given formatter. Read more

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impl Default for Record

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fn default() -> Record

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

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impl PartialEq<Record> for Record

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

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

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

This method tests for !=.

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impl StructuralPartialEq for Record

Auto Trait Implementations

impl RefUnwindSafe for Record

impl Send for Record

impl Sync for Record

impl Unpin for Record

impl UnwindSafe for Record

Blanket Implementations

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impl<T> Any for T where
T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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impl<T> Borrow<T> for T where
T: ?Sized,

const: unstable · source

fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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impl<T> BorrowMut<T> for T where
T: ?Sized,

const: unstable · source

fn borrow_mut(&mut self) -> &mut T

Mutably borrows from an owned value. Read more

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impl<T> From<T> for T

const: unstable · source

fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Into for T where
U: From<T>,

const: unstable · source

fn into(self) -> U

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

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impl<T> Same<T> for T

type Output = T

Should always be Self

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impl<T> ToOwned for T where
T: Clone,

type Owned = T

The resulting type after obtaining ownership.

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fn to_owned(&self) -> T

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

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fn clone_into(&self, target: &mut T)

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

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

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impl<T, U> TryFrom for T where
U: Into<T>,

type Error = Infallible

The type returned in the event of a conversion error.

const: unstable · source

fn try_from(value: U) -> Result<T, <T as TryFrom>::Error>

Performs the conversion.

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impl<T, U> TryInto for T where
U: TryFrom<T>,

type Error = >::Error

The type returned in the event of a conversion error.

const: unstable · source

fn try_into(self) -> Result<U, >::Error>

Performs the conversion.

Struct noodles::cram::Record

Implementations

impl Record

pub fn try_from_alignment_record<R>( header: &Header, record: &R) -> Result<Record, Error> where R: AlignmentRecord + ?Sized,

pub fn try_into_sam_record(&self, header: &Header) -> Result<Record, Error>

impl Record

pub fn builder() -> Builder

pub fn bam_flags(&self) -> Flags

pub fn cram_flags(&self) -> Flags

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

pub fn read_length(&self) -> usize

pub fn read_group_id(&self) -> Option<usize>

pub fn next_mate_flags(&self) -> NextMateFlags

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

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

pub fn template_size(&self) -> i32

pub fn distance_to_next_fragment(&self) -> Option<usize>

pub fn tags(&self) -> &Data

pub fn bases(&self) -> &Sequence

pub fn features(&self) -> &Features

Trait Implementations

impl AlignmentRecord for Record

fn read_name(&self) -> Option<&ReadName>

fn reference_sequence( &self, reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>) -> Option<Result<&'rs ReferenceSequence, Error>>

fn flags(&self) -> Flags

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

fn alignment_span(&self) -> usize

fn mapping_quality(&self) -> Option<MappingQuality>

fn cigar(&self) -> &Cigar

fn mate_reference_sequence( &self, reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>) -> Option<Result<&'rs ReferenceSequence, Error>>

fn mate_alignment_start(&self) -> Option<Position>

fn template_length(&self) -> i32

fn sequence(&self) -> &Sequence

fn quality_scores(&self) -> &QualityScores

fn data(&self) -> &Data

fn alignment_end(&self) -> Option<Position>

impl Clone for Record

fn clone(&self) -> Record

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

impl Debug for Record

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

impl Default for Record

fn default() -> Record

impl PartialEq<Record> for Record

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

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

impl StructuralPartialEq for Record

Auto Trait Implementations

impl RefUnwindSafe for Record

impl Send for Record

impl Sync for Record

impl Unpin for Record

impl UnwindSafe for Record

Blanket Implementations

impl<T> Any for T where T: 'static + ?Sized,

fn type_id(&self) -> TypeId

impl<T> Borrow<T> for T where T: ?Sized,

fn borrow(&self) -> &T

impl<T> BorrowMut<T> for T where T: ?Sized,

fn borrow_mut(&mut self) -> &mut T

impl<T> From<T> for T

fn from(t: T) -> T

impl<T, U> Into<U> for T where U: From<T>,

fn into(self) -> U

impl<T> Same<T> for T

type Output = T

impl<T> ToOwned for T where T: Clone,

type Owned = T

fn to_owned(&self) -> T

fn clone_into(&self, target: &mut T)

impl<T, U> TryFrom<U> for T where U: Into<T>,

type Error = Infallible

fn try_from(value: U) -> Result<T, <T as TryFrom<U>>::Error>

impl<T, U> TryInto<U> for T where U: TryFrom<T>,

type Error = <U as TryFrom<T>>::Error

fn try_into(self) -> Result<U, <U as TryFrom<T>>::Error>

pub fn try_from_alignment_record<R>(
header: &Header,
record: &R
) -> Result<Record, Error> where
R: AlignmentRecord + ?Sized,

fn reference_sequence(
&self,
reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>
) -> Option<Result<&'rs ReferenceSequence, Error>>

fn mate_reference_sequence(
&self,
reference_sequences: &'rs IndexMap<String, ReferenceSequence, RandomState>
) -> Option<Result<&'rs ReferenceSequence, Error>>

impl<T> Any for T where
T: 'static + ?Sized,

impl<T> Borrow<T> for T where
T: ?Sized,

impl<T> BorrowMut<T> for T where
T: ?Sized,

impl<T, U> Into<U> for T where
U: From<T>,

impl<T> ToOwned for T where
T: Clone,

impl<T, U> TryFrom<U> for T where
U: Into<T>,

impl<T, U> TryInto<U> for T where
U: TryFrom<T>,