Struct FastqSet 

pub struct FastqSet {
    pub header: Vec<u8>,
    pub segments: Vec<FastqSegment>,
    pub skip_reason: Option<SkipReason>,
}

A FASTQ record parsed into its component segments according to a read structure.

When reading FASTQ files with complex structures (e.g., containing UMIs, barcodes, and template sequences), this structure holds the parsed segments along with the original header. Each segment is classified by type (template, molecular barcode, sample barcode, etc.).

Fields

• header - The original FASTQ header line (without the ‘@’ prefix)
• segments - Vector of parsed segments in order
• skip_reason - If Some, indicates why this read should be skipped during processing

Fields

header: Vec<u8>

The FASTQ header line (without ‘@’ prefix)

segments: Vec<FastqSegment>

Ordered list of parsed segments from this read

skip_reason: Option<SkipReason>

Reason for skipping this read, or None if the read should be processed

Implementations

impl FastqSet

pub fn template_segments( &self, ) -> Filter<Iter<'_, FastqSegment>, fn(&&FastqSegment) -> bool>

Returns an iterator over template segments.

Template segments contain the actual biological sequence to be analyzed (as opposed to barcodes or UMIs).

Returns

Iterator over references to template segments in this read set

pub fn sample_barcode_segments( &self, ) -> Filter<Iter<'_, FastqSegment>, fn(&&FastqSegment) -> bool>

Returns an iterator over sample barcode segments.

Sample barcodes identify which sample/library a read belongs to in multiplexed sequencing runs.

Returns

Iterator over references to sample barcode segments

pub fn molecular_barcode_segments( &self, ) -> Filter<Iter<'_, FastqSegment>, fn(&&FastqSegment) -> bool>

Returns an iterator over molecular barcode (UMI) segments.

Molecular barcodes (UMIs) uniquely tag individual molecules for duplicate detection and quantification.

Returns

Iterator over references to molecular barcode segments

pub fn cell_barcode_segments( &self, ) -> Filter<Iter<'_, FastqSegment>, fn(&&FastqSegment) -> bool>

Returns an iterator over cell barcode segments.

Cell barcodes identify which cell a read originated from in single-cell sequencing experiments.

Returns

Iterator over references to cell barcode segments

pub fn combine_readsets(readsets: Vec<Self>) -> Self

Combines multiple FastqSet instances into a single set.

Merges the segments from multiple read sets, preserving the header from the first set. Useful for combining segments from multiple FASTQ files that represent different parts of the same read (e.g., R1, R2, I1, I2).

Arguments

• readsets - Vector of read sets to combine

Returns

A new FastqSet with all segments combined

Panics

Panics if the input vector is empty or contains no segments

pub fn from_record_with_structure( header: &[u8], sequence: &[u8], quality: &[u8], read_structure: &ReadStructure, skip_reasons: &[SkipReason], ) -> Self

Creates a FastqSet from raw FASTQ record data and a read structure.

This method applies the read structure to segment the sequence and quality data, producing a FastqSet with appropriately typed segments.

Arguments

• header - The FASTQ header/name (without ‘@’ prefix)
• sequence - The full sequence bases
• quality - The full quality scores
• read_structure - The read structure describing segment layout
• skip_reasons - List of reasons to skip reads gracefully instead of failing

Returns

A FastqSet with segments parsed according to the read structure. If the read doesn’t have enough bases and TooFewBases is in skip_reasons, returns a FastqSet with skip_reason set.

Panics

Panics if the read has too few bases and TooFewBases is not in skip_reasons.

Trait Implementations

impl Clone for FastqSet

fn clone(&self) -> FastqSet

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for FastqSet

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

Formats the value using the given formatter.

impl PartialEq for FastqSet

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

Tests for self and other values to be equal, and is used by ==.

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

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl StructuralPartialEq for FastqSet