cusbf::detail::FastxReader Class Reference

Streaming FASTA/FASTQ parser. More...

#include <Fastx.hpp>

Public Member Functions
	FastxReader (std::istream &input, std::string_view source_name="<stream>")
	Constructs a reader over an open input stream.
Result< bool >	nextRecord (FastxRecord &record)
	Reads the next FASTA/FASTQ record into record.

Detailed Description

Streaming FASTA/FASTQ parser.

Reads one record at a time via nextRecord. Errors reading the stream are returned as error results.

Definition at line 297 of file Fastx.hpp.

Constructor & Destructor Documentation

FastxReader()

cusbf::detail::FastxReader::FastxReader ( std::istream &  input, std::string_view  source_name = "<stream>"  )

inlineexplicit

Constructs a reader over an open input stream.

Parameters

input	Input stream positioned at the first record.
source_name	Label used in parse error messages.

Definition at line 305 of file Fastx.hpp.

        : input_(input), source_name_(source_name) {}

Member Function Documentation

nextRecord()

Result< bool > cusbf::detail::FastxReader::nextRecord ( FastxRecord &  record )

inline

Reads the next FASTA/FASTQ record into record.

Parameters

record

Output record, cleared before fill.

Returns

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

Definition at line 314 of file Fastx.hpp.

                                                               {
        record.header.clear();
        record.sequence.clear();
 
        const auto header = readHeaderLine();
        if (!header) {
            return Err(header.error());
        }
        if (header->empty()) {
            return false;
        }
 
        const char headerTag = header->front();
 
        if (format_ == FastxFormat::unknown) {
            if (headerTag == '>') {
                format_ = FastxFormat::fasta;
            } else if (headerTag == '@') {
                format_ = FastxFormat::fastq;
            } else {
                return Err(
                    parseError("expected FASTA or FASTQ header", fastx_column_at(*header, 0))
                );
            }
        }
 
        const char expectedHeader = format_ == FastxFormat::fasta ? '>' : '@';
        if (headerTag != expectedHeader) {
            return Err(parseError(
                "mixed FASTA and FASTQ records are not supported", fastx_column_at(*header, 0)
            ));
        }
 
        record.header.assign(header->substr(1));
        if (format_ == FastxFormat::fasta) {
            CUSBF_TRY(readFastaSequence(record.sequence));
        } else {
            CUSBF_TRY(readFastqSequence(record.sequence));
        }
        return true;
    }

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

• Fastx.hpp