gamgee::SamReader< ITERATOR > Class Template Reference

Utility class to read a SAM/BAM/CRAM file with an appropriate Sam iterator from a stream (e.g. file, stdin, ...) in a for-each loop. More...

#include <sam_reader.h>

Public Member Functions
	SamReader (const std::string &filename)
	reads through all records in a file ( or sam) parsing them into Sam objects More...
	SamReader (const std::vector< std::string > &filenames)
	reads through all records in a file ( or sam) parsing them into Sam objects More...
	SamReader (const SamReader &other)=delete
	no copy construction/assignment allowed for iterators and readers More...
SamReader &	operator= (const SamIterator &)=delete
	SamReader (SamReader &&)=default
	a SamReader move constructor guarantees all objects will have the same state. More...
SamReader &	operator= (SamReader &&)=default
ITERATOR	begin ()
	creates a ITERATOR pointing at the start of the input stream (needed by for-each loop) More...
ITERATOR	end ()
	creates a ITERATOR with a nullified input stream (needed by for-each loop) More...
SamHeader	header ()

Detailed Description

template<class ITERATOR>
class gamgee::SamReader< ITERATOR >

Utility class to read a SAM/BAM/CRAM file with an appropriate Sam iterator from a stream (e.g. file, stdin, ...) in a for-each loop.

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

for (auto& record : SamReader<SamIterator>{filename})
  do_something_with_sam(record);

You can also use it with the stdin or any other stream by using the default constructor or passing in an empty string for a filename, like so:

for (auto& pair : SamReader<SamPairIterator>{filename})
  do_something_with_pair(pair);

Most iterators have aliases defined by this module so you can use it like so:

for (auto& pair : SingleSamReader{filename})
  do_something_with_pair(pair);

Constructor & Destructor Documentation

template<class ITERATOR >

gamgee::SamReader< ITERATOR >::SamReader ( const std::string &  filename )

inline

reads through all records in a file ( or sam) parsing them into Sam objects

Parameters

filename

the name of the sam file

template<class ITERATOR >

gamgee::SamReader< ITERATOR >::SamReader ( const std::vector< std::string > &  filenames )

inline

reads through all records in a file ( or sam) parsing them into Sam objects

Parameters

filenames

a vector containing a single element: the name of the sam file

template<class ITERATOR >

gamgee::SamReader< ITERATOR >::SamReader ( const SamReader< ITERATOR > &  other )

delete

no copy construction/assignment allowed for iterators and readers

template<class ITERATOR >

gamgee::SamReader< ITERATOR >::SamReader ( SamReader< ITERATOR > &&  )

default

a SamReader move constructor guarantees all objects will have the same state.

Member Function Documentation

template<class ITERATOR >

ITERATOR gamgee::SamReader< ITERATOR >::begin ( )

inline

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

Returns

a ITERATOR ready to start parsing the file

template<class ITERATOR >

ITERATOR gamgee::SamReader< ITERATOR >::end ( )

inline

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

Returns

a ITERATOR that will match the end status of the iterator at the end of the stream

template<class ITERATOR >

SamHeader gamgee::SamReader< ITERATOR >::header ( )

inline

template<class ITERATOR >

SamReader& gamgee::SamReader< ITERATOR >::operator= ( const SamIterator &  )

delete

template<class ITERATOR >

SamReader& gamgee::SamReader< ITERATOR >::operator= ( SamReader< ITERATOR > &&  )

default

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

• gamgee/sam/sam_reader.h