gamgee::FastqReader Class Reference

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...

#include <fastq_reader.h>

Public Member Functions
	FastqReader (const std::string &filename)
	reads through all records in a file (fasta or fastq) parsing them into Fastq objects More...
	FastqReader (const std::vector< std::string > &filenames)
	reads through all records in a file (fasta or fastq) parsing them into Fastq objects More...
	FastqReader (std::istream *const input)
	reads through all records in a stream (e.g. stdin) parsing them into Fastq objects More...
	FastqReader (FastqReader &&)=default
	move constructor for the FastqReader class simply transfers all objects with the state maintained. More...
FastqReader &	operator= (FastqReader &&)=default
	FastqReader (const FastqReader &)=delete
	a FastqReader cannot be copied safely, as it is iterating over a stream. More...
FastqReader &	operator= (const FastqReader &)=delete
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 )

explicit

reads 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 ( const std::vector< std::string > &  filenames )

explicit

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

Parameters

filenames

a vector containing a single element: the name of the fasta/fastq file

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

explicit

reads 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 ( FastqReader &&  )

default

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.

Member Function Documentation

FastqIterator gamgee::FastqReader::begin

(

)

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

Returns

a FastqIterator ready to start parsing the file

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

FastqReader& gamgee::FastqReader::operator= ( FastqReader &&  )

default

FastqReader& gamgee::FastqReader::operator= ( const FastqReader &  )

delete

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

• gamgee/fastq_reader.h
• gamgee/fastq_reader.cpp