Struct FastqChunkConfig 

#[non_exhaustive]
pub struct FastqChunkConfig {
    pub target_bases: u64,
    pub min_records: usize,
    pub max_bases: u64,
}

Chunking policy for FastqReader::next_chunk_with_sink.

Fields (Non-exhaustive)

Non-exhaustive structs could have additional fields added in future. Therefore, non-exhaustive structs cannot be constructed in external crates using the traditional Struct { .. } syntax; cannot be matched against without a wildcard ..; and struct update syntax will not work.

target_bases: u64

Target number of sequence bases to emit before returning a chunk.

A value of zero disables the target limit.

min_records: usize

Minimum number of records required before the target-base limit may stop a chunk.

Values below one are raised to one.

max_bases: u64

Hard maximum number of sequence bases to emit before returning a chunk.

A value of zero disables the hard limit. Unlike target_bases, this limit is not gated by min_records.

Implementations

impl FastqChunkConfig

pub fn new(target_bases: u64) -> Self

Create a chunking policy with a target base count.

Examples found in repository

examples/fastq_chunk_sink.rs (line 48)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

pub fn min_records(self, min_records: usize) -> Self

Return a copy with a minimum record count.

Examples found in repository

examples/fastq_chunk_sink.rs (line 48)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

pub fn max_bases(self, max_bases: u64) -> Self

Return a copy with a hard maximum base count.

pub fn target_bases(self) -> u64

Target bases per chunk. Zero means no target-base limit.

pub fn min_records_value(self) -> usize

Minimum records required before the target-base limit may stop a chunk.

pub fn max_bases_value(self) -> u64

Hard maximum bases per chunk. Zero means no hard limit.

pub fn estimated_records(self, read_len: usize) -> usize

Estimate records per chunk for a fixed or representative read length.

Examples found in repository

examples/fastq_chunk_sink.rs (line 51)

fn main() -> Result<()> {
    let stdin = io::stdin();
    let mut reader = FastqReader::new(stdin.lock());
    let config = FastqChunkConfig::new(10_000_000).min_records(40_000);
    let mut sink = ReadBuffer::default();

    sink.reserve_records(config.estimated_records(150));
    while let Some(stats) = reader.next_chunk_with_sink(config, &mut sink)? {
        let checksum: usize = sink
            .reads
            .iter()
            .map(|read| read.name.len() ^ read.seq.len() ^ read.qual.len())
            .sum();
        eprintln!(
            "chunk first_record={} records={} bases={} checksum={}",
            stats.first_record_index(),
            stats.records(),
            stats.bases(),
            checksum
        );

        // Downstream tools typically hand `sink.reads` to alignment or another
        // processing stage here, then reuse the allocation for the next chunk.
        sink.clear();
        sink.reserve_records(config.estimated_records(150));
    }

    Ok(())
}

Trait Implementations

impl Clone for FastqChunkConfig

fn clone(&self) -> FastqChunkConfig

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Copy for FastqChunkConfig

impl Debug for FastqChunkConfig

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

Formats the value using the given formatter.

impl Eq for FastqChunkConfig

impl PartialEq for FastqChunkConfig

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