Struct SampleGroup 

pub struct SampleGroup {
    pub samples: Vec<Sample>,
}

Struct for storing information about multiple samples and for defining functions associated with groups of Samples, rather than individual structs.

Fields

samples: Vec<Sample>

A group of samples

Implementations

impl SampleGroup

pub fn from_samples(samples: &[Sample]) -> Result<Self>

Validates a group of Samples and instantiates a Self struct if they are valid. Will clone the Sample structs and change the number on the ordinal field on those cloned to match the order in which they are stored in this Self.

Per-sample read structures may differ in their per-input (T, B, M, C) segment counts across samples (which lets each sample produce a different set of output files), but the total length of all sample-barcode (B) segments per sample must equal the barcode column for that sample (and barcodes are required to be the same length).

Errors

• Will error if no samples are provided.
• Will error if there are duplicate sample names provided.
• Will error if there are duplicate barcodes provided.
• Will error if barcodes don’t all have the same length.
• Will error if any sample’s per-sample sample-barcode (B) segment is not fixed length.
• Will error if any sample’s per-sample sample-barcode (B) segment lengths don’t sum to that sample’s barcode column length.

pub fn from_file<P: AsRef<Path>>( path: P, globals: &[ReadStructure], ) -> Result<SampleGroup>

Attempts to load a Self object from a tab-delimited file. The file must have a header row containing at least the columns sample_id and barcode. Optional additional columns read_structure_1, read_structure_2, …, read_structure_<N> attach per-sample read structures to each sample (one per input FASTQ in the order given to --inputs). When these columns are present:

• globals (the --read-structures argument) must have exactly N entries, one per input FASTQ.
• A blank cell in read_structure_<i> falls back to globals[i-1] for that sample.
• A row whose read_structure_<n> cells are all blank uses globals entirely (i.e. is equivalent to omitting the per-sample columns for that sample only).

When no read_structure_<n> columns are present, globals is unused and every sample uses the global structures.

Errors

• Will error if the file cannot be read.
• Will error if the header row is missing required columns.
• Will error if read_structure_<n> columns are non-contiguous or don’t match globals.len() (when present).
• Will error if any read_structure_<n> cell has a value that fails to parse.
• Will error if SampleGroup::from_samples rejects the parsed records (e.g. duplicate names/barcodes, inconsistent barcode lengths, or barcode/B-segment length mismatch).

pub fn has_per_sample_read_structures(&self) -> bool

Returns true if this group has per-sample read structures (i.e. at least one sample carries custom read structures that override --read-structures).

pub fn matching_prefix_lens( &self, default_structures: &[ReadStructure], ) -> Result<Vec<usize>>

Returns the per-input matching prefix lengths needed to demultiplex this sample group. For each input FASTQ index, this is the maximum across samples of the number of bases before the first Template segment in that sample’s read structure. Falls back to the corresponding entry in default_structures for samples without per-sample read structures.

Errors

• Returns an error if any non-Template segment in the matching window has a non-fixed length.
• Returns an error if a sample’s per-sample read-structure count differs from default_structures.len().

pub fn build_matching_patterns( &self, default_structures: &[ReadStructure], prefix_lens: &[usize], ) -> Result<Vec<Vec<u8>>>

Builds the matching pattern bytes for each sample. The pattern is a fixed-length byte sequence (concatenated across all input FASTQs) of total length prefix_lens.iter().sum(). For each input, the sample’s read structure is walked position-by-position; B (sample-barcode) segment positions are filled from sample.barcode (taken in order across inputs), and M/S/C/T segment positions and any trailing positions up to the prefix length are filled with N (treated as a wildcard by the matcher).

Errors

• Returns an error if any sample’s read structure has a non-fixed-length non-template segment in the matching window.
• Returns an error if a sample-barcode (B) segment crosses the matching window boundary, since silently truncating a barcode would corrupt matching.

Trait Implementations

impl Clone for SampleGroup

fn clone(&self) -> SampleGroup

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for SampleGroup

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

Formats the value using the given formatter.

impl Display for SampleGroup

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

Formats the value using the given formatter.

impl PartialEq for SampleGroup

fn eq(&self, other: &SampleGroup) -> 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 SampleGroup