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BlazeSeq

FastqParser

Mojo struct 🡭

FastqParser

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

Unified FASTQ parser over a Reader.

Parameters

Section titled “Parameters”
  • R (Reader)
  • config (ParserConfig)

Fields

Section titled “Fields”
  • buffer (BufferedReader[R])
  • quality_schema (QualitySchema)
  • validator (Validator)

Implemented traits

Section titled “Implemented traits”

AnyType, ImplicitlyDestructible, Movable

Methods

Section titled “Methods”

__init__

Section titled “__init__”
def __init__(out self, var reader: R)

Args:

  • reader (R)
  • self (Self)

Returns:

Self

Raises:

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

Args:

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

Returns:

Self

Raises:

def __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

Section titled “has_more”
def has_more(self) -> Bool

Args:

  • self (Self)

Returns:

Bool

next_view

Section titled “next_view”
def next_view(mut self) -> FastqView[MutExternalOrigin]

Args:

  • self (Self)

Returns:

FastqView

Raises:

next_view_memchr_seq

Section titled “next_view_memchr_seq”
def next_view_memchr_seq(mut self) -> FastqView[MutExternalOrigin]

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

Args:

  • self (Self)

Returns:

FastqView

Raises:

next_record

Section titled “next_record”
def next_record(mut self) -> FastqRecord

Args:

  • self (Self)

Returns:

FastqRecord

Raises:

next_record_memchr_seq

Section titled “next_record_memchr_seq”
def next_record_memchr_seq(mut self) -> FastqRecord

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

Args:

  • self (Self)

Returns:

FastqRecord

Raises:

next_batch

Section titled “next_batch”
def next_batch(mut self, max_records: Int = 4096) -> FastqBatch

Args:

  • self (Self)
  • max_records (Int)

Returns:

FastqBatch

Raises:

views

Section titled “views”
def views(ref self) -> _FastqParserViewIter[R, config, origin_of(self)]

Args:

  • self (Self)

Returns:

_FastqParserViewIter

records

Section titled “records”
def records(ref self) -> _FastqParserRecordIter[R, config, origin_of(self)]

Args:

  • self (Self)

Returns:

_FastqParserRecordIter

batches

Section titled “batches”
def batches(ref self, max_records: Optional[Int] = None) -> _FastqParserBatchIter[R, config, origin_of(self)]

Args:

  • self (Self)
  • max_records (Optional)

Returns:

_FastqParserBatchIter