cuddl::detail::fastx_fastq_reader Class Reference

FASTQ parser over a contiguous in-memory buffer. More...

#include <fastx_sequence_file.hpp>

Public Member Functions
	fastx_fastq_reader (std::string_view data, std::string source_name="<buffer>")
	Constructs a reader over a contiguous in-memory FASTQ buffer.
Result< bool >	append_next_record (std::string &sequence)
	Appends the next record's sequence bytes to sequence.

Detailed Description

FASTQ parser over a contiguous in-memory buffer.

Accumulates multiline sequence lines and validates multiline qualities against the sequence length, exactly as the FASTA path's record scan excludes header bytes: only sequence bytes reach the caller. The first header fixes the format; a later header of the other kind is a mixed-format error.

Definition at line 455 of file fastx_sequence_file.hpp.

Constructor & Destructor Documentation

fastx_fastq_reader()

cuddl::detail::fastx_fastq_reader::fastx_fastq_reader ( std::string_view  data, std::string  source_name = "<buffer>"  )

inlineexplicit

Constructs a reader over a contiguous in-memory FASTQ buffer.

Parameters

data	Entire file or decompressed payload.
source_name	Label used in parse error messages.

Definition at line 463 of file fastx_sequence_file.hpp.

        : data_(data), source_name_(std::move(source_name)) {}

Member Function Documentation

append_next_record()

Result< bool > cuddl::detail::fastx_fastq_reader::append_next_record ( std::string &  sequence )

inline

Appends the next record's sequence bytes to sequence.

Returns

false at end-of-buffer, true when a record was read, or an error.

Definition at line 471 of file fastx_sequence_file.hpp.

                                                                       {
        auto header = CUDDL_TRY(read_header_line());
        if (header.empty()) {
            return false;
        }
 
        char const tag = header.front();
        if (format_ == fastx_format::unknown) {
            if (tag == '>') {
                format_ = fastx_format::fasta;
            } else if (tag == '@') {
                format_ = fastx_format::fastq;
            } else {
                return Err(parse_error("expected FASTA or FASTQ header"));
            }
        }
 
        char const expected = format_ == fastx_format::fasta ? '>' : '@';
        if (tag != expected) {
            return Err(parse_error("mixed FASTA and FASTQ records are not supported"));
        }
        if (format_ != fastx_format::fastq) {
            return Err(parse_error("mixed FASTA and FASTQ records are not supported"));
        }
        auto const base = sequence.size();
        CUDDL_TRY(read_fastq_sequence(sequence, base));
        return true;
    }

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The documentation for this class was generated from the following file:

• fastx_sequence_file.hpp