FastqParser

Mojo struct 🡭

FastqParser

@memory_only
struct FastqParser[R: Reader, config: ParserConfig = ParserConfig(262144, 1073741824, False, False, False, Optional(None))]

Unified FASTQ parser over a Reader.

Parameters

• R (Reader)
• config (ParserConfig)

Fields

• buffer (BufferedReader[R])
• quality_schema (QualitySchema)
• validator (Validator)

Implemented traits

AnyType, ImplicitlyDestructible, Movable

Methods

__init__

fn __init__(out self, var reader: R)

Args:

• reader (R)
• self (Self)

Returns:

Self

Raises:

fn __init__(out self, var reader: R, quality_schema: String)

Args:

• reader (R)
• quality_schema (String)
• self (Self)

Returns:

Self

Raises:

fn __init__(out self, var reader: R, batch_size: Int, schema: String = "generic")

Args:

• reader (R)
• batch_size (Int)
• schema (String)
• self (Self)

Returns:

Self

Raises:

has_more

fn has_more(self) -> Bool

Args:

• self (Self)

Returns:

Bool

next_view

fn next_view(mut self) -> FastqView[MutExternalOrigin]

Args:

• self (Self)

Returns:

FastqView[MutExternalOrigin]

Raises:

next_view_memchr_seq

fn next_view_memchr_seq(mut self) -> FastqView[MutExternalOrigin]

Benchmark-only variant that scans record boundaries via sequential memchr.

Args:

• self (Self)

Returns:

FastqView[MutExternalOrigin]

Raises:

next_view_fused_old

fn next_view_fused_old(mut self) -> FastqView[MutExternalOrigin]

Benchmark-only variant that uses the original fused SIMD scan loop.

Args:

• self (Self)

Returns:

FastqView[MutExternalOrigin]

Raises:

next_record

fn next_record(mut self) -> FastqRecord

Args:

• self (Self)

Returns:

FastqRecord

Raises:

next_record_memchr_seq

fn next_record_memchr_seq(mut self) -> FastqRecord

Benchmark-only variant that scans record boundaries via sequential memchr.

Args:

• self (Self)

Returns:

FastqRecord

Raises:

next_record_fused_old

fn next_record_fused_old(mut self) -> FastqRecord

Benchmark-only variant that uses the original fused SIMD scan loop.

Args:

• self (Self)

Returns:

FastqRecord

Raises:

next_batch

fn next_batch(mut self, max_records: Int = 4096) -> FastqBatch

Args:

• self (Self)
• max_records (Int)

Returns:

FastqBatch

Raises:

views

fn views(ref self) -> _FastqParserViewIter[R, config, origin_of(self)]

Args:

• self (Self)

Returns:

_FastqParserViewIter[R, config, origin_of(self)]

records

fn records(ref self) -> _FastqParserRecordIter[R, config, origin_of(self)]

Args:

• self (Self)

Returns:

_FastqParserRecordIter[R, config, origin_of(self)]

batches

fn batches(ref self, max_records: Optional[Int] = None) -> _FastqParserBatchIter[R, config, origin_of(self)]

Args:

• self (Self)
• max_records (Optional[Int])

Returns:

_FastqParserBatchIter[R, config, origin_of(self)]