Struct ReadStructure 

pub struct ReadStructure { /* private fields */ }

A read structure made up of one or more ReadSegments.

Internally, in addition to the segments themselves, we cache per-segment start offsets (signed) and enough summary information to resolve the indefinite-length (+) segment’s end position at extract time without another pass over the segments.

Implementations

impl ReadStructure

pub fn new(segments: Vec<ReadSegment>) -> Result<Self, ReadStructureError>

Builds a new ReadStructure from a vector of ReadSegments.

At most one segment may have an indefinite length (+); it may appear in any position.

Errors

• Returns Err if no elements exist.
• Returns Err if more than one segment has an indefinite length.

pub fn extract<'rs, 'b>( &'rs self, bases: &'b [u8], quals: &'b [u8], skip_handling: SkipHandling, ) -> Result<ExtractedSegments<'rs, 'b>, ReadStructureError>

Extracts the bases and quality scores for every segment in this read structure.

Returns a no-alloc iterator over (&ReadSegment, &[u8] bases, &[u8] quals) triples. All error conditions are checked up front, so the returned iterator is infallible and can be cheaply .collect()ed into a Vec when an owned collection is needed.

skip_handling controls whether SegmentType::Skip segments are emitted (SkipHandling::Include) or silently dropped (SkipHandling::Exclude).

Errors

• ReadStructureError::MismatchingBasesAndQualsLen if bases.len() != quals.len().
• ReadStructureError::ReadTooShort if the read cannot accommodate every fixed segment. When the structure also has a + segment, the read must be strictly longer than the sum of the fixed-segment lengths (since + means at least one base).
• ReadStructureError::ReadTooLong if the structure has no + segment and bases.len() does not exactly match length_of_fixed_segments. Silently truncating trailing bases is almost always a bug (wrong structure, stray adapter, etc.), so we require an exact match.

pub fn has_fixed_length(&self) -> bool

Returns true if the ReadStructure has a fixed (i.e. non-variable) length, false if any segment has an indefinite length.

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

Returns the fixed length if there is one.

pub fn number_of_segments(&self) -> usize

Returns the number of segments in this read structure.

pub fn segments(&self) -> &[ReadSegment]

Returns the underlying elements in this read structure.

pub fn iter(&self) -> impl Iterator<Item = &ReadSegment>

Returns an iterator over the read segments.

pub fn segments_by_type( &self, kind: SegmentType, ) -> impl Iterator<Item = &ReadSegment>

Returns the ReadSegments in this read structure of the given kind.

pub fn templates(&self) -> impl Iterator<Item = &ReadSegment>

Returns the template ReadSegments in this read structure.

pub fn sample_barcodes(&self) -> impl Iterator<Item = &ReadSegment>

Returns the sample barcode ReadSegments in this read structure.

pub fn molecular_barcodes(&self) -> impl Iterator<Item = &ReadSegment>

Returns the molecular barcode ReadSegments in this read structure.

pub fn skips(&self) -> impl Iterator<Item = &ReadSegment>

Returns the skip ReadSegments in this read structure.

pub fn cellular_barcodes(&self) -> impl Iterator<Item = &ReadSegment>

Returns the cellular barcode ReadSegments in this read structure.

pub fn first(&self) -> Option<&ReadSegment>

Returns the first ReadSegment in this read structure.

pub fn last(&self) -> Option<&ReadSegment>

Returns the last ReadSegment in this read structure.

Trait Implementations

impl Clone for ReadStructure

fn clone(&self) -> Self

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for ReadStructure

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

Formats the value using the given formatter.

impl Display for ReadStructure

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

Formats this read structure as a string.

impl From<ReadStructure> for String

fn from(rs: ReadStructure) -> Self

Renders the read structure to its canonical string form (e.g. "8B+M10T").

impl FromStr for ReadStructure

fn from_str(rs: &str) -> Result<Self, Self::Err>

Returns a new read structure from a string, or Err if parsing failed.

type Err = ReadStructureError

The associated error which can be returned from parsing.

impl Index<usize> for ReadStructure

fn index(&self, idx: usize) -> &Self::Output

Returns the ReadSegment at the given index in the read structure.

type Output = ReadSegment

The returned type after indexing.

impl IntoIterator for ReadStructure

type Item = ReadSegment

The type of the elements being iterated over.

type IntoIter = IntoIter<<ReadStructure as IntoIterator>::Item>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl PartialEq for ReadStructure

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

Equality operator ==.

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

Inequality operator !=.

impl StructuralPartialEq for ReadStructure

impl TryFrom<&[ReadSegment]> for ReadStructure

fn try_from(elements: &[ReadSegment]) -> Result<Self, Self::Error>

Builds a new read structure from a slice of elements.

type Error = ReadStructureError

The type returned in the event of a conversion error.

impl TryFrom<String> for ReadStructure

fn try_from(s: String) -> Result<Self, Self::Error>

Parses a read structure from an owned string; equivalent to [FromStr].

type Error = ReadStructureError

The type returned in the event of a conversion error.