Utility class to read many Fastq records from a stream (e.g. Fastq file, stdin, ...) in a for-each loop in a for-each loop. More...

Public Member Functions
	FastqReader (const std::string &filename)
	reades through all records in a file (fasta or fastq) parsing them into Fastq objects More...

	FastqReader (std::istream *const input)
	reades through all records in a stream (e.g. stdin) parsing them into Fastq objects More...

	~FastqReader ()
	closes the file stream if there is one (in case we are reading a fasta/fastq file) More...

	FastqReader (FastqReader &&)
	move constructor for the FastqReader class simply transfers all objects with the state maintained. More...

	FastqReader (const FastqReader &)=delete
	a FastqReader cannot be copied safely, as it is iterating over a stream. More...

FastqIterator	begin ()
	creates a FastqIterator pointing at the start of the input stream (needed by for-each loop) More...

FastqIterator	end ()
	creates a FastqIterator with a nullified input stream (needed by for-each loop) More...

Detailed Description

Utility class to read many Fastq records from a stream (e.g. Fastq file, stdin, ...) in a for-each loop in a for-each loop.

This class is designed to parse fastq files in for-each loops with the following signature:

for (auto& record : FastqReader(filename))

do_something_with_fastq(record);

You can also use it with the stdin or any other stream by simply giving the reference to the stream in the constructor, like so:

for (auto& record : FastqReader(&std::cin))

do_something_with_fastq(record);

Although one could use it as an iterator, if your goal is to do so, you should use the FastqIterator class

Constructor & Destructor Documentation

gamgee::FastqReader::FastqReader ( const std::string & filename )

reades through all records in a file (fasta or fastq) parsing them into Fastq objects

Parameters

filename the name of the fasta/fastq file

gamgee::FastqReader::FastqReader ( std::istream *const input )

reades through all records in a stream (e.g. stdin) parsing them into Fastq objects

Parameters

input a reference to the input stream (e.g. &std::cin)

gamgee::FastqReader::~FastqReader ( )

closes the file stream if there is one (in case we are reading a fasta/fastq file)

gamgee::FastqReader::FastqReader ( FastqReader && )

move constructor for the FastqReader class simply transfers all objects with the state maintained.

gamgee::FastqReader::FastqReader ( const FastqReader & )

delete

a FastqReader cannot be copied safely, as it is iterating over a stream.

FastqIterator gamgee::FastqReader::begin ( )

creates a FastqIterator pointing at the start of the input stream (needed by for-each loop)

FastqIterator gamgee::FastqReader::end ( )

creates a FastqIterator with a nullified input stream (needed by for-each loop)

Returns: a FastqIterator that will match the end status of the iterator at the end of the stream

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