gamgee::VariantReader< ITERATOR > Class Template Reference

Utility class to read a VCF/BCF file with an appropriate Variant iterator from a stream (e.g. file, stdin, ...) in a for-each loop. More...

#include <variant_reader.h>

Public Member Functions
	VariantReader (const std::string &filename)
	reads through all records in a file (vcf or bcf) parsing them into Variant objects More...
	VariantReader (const std::vector< std::string > &filenames)
	reads through all records in a file (vcf or bcf) parsing them into Variant objects More...
	VariantReader (const std::string &filename, const std::vector< std::string > &samples, const bool include=true)
	reads through all records in a file (vcf or bcf) parsing them into Variant objects but only including the selected samples. To create a sites only file, simply pass an empty vector of samples. More...
	VariantReader (const std::vector< std::string > &filenames, const std::vector< std::string > &samples, const bool include=true)
	reads through all records in a file (vcf or bcf) parsing them into Variant objects but only including the selected samples. To create a sites only file, simply pass an empty vector of samples. More...
	VariantReader (const VariantReader &other)=delete
	a VariantReader cannot be copied safely, as it is iterating over a stream. More...
VariantReader &	operator= (const VariantReader &other)=delete
	VariantReader (VariantReader &&other)=default
	a VariantReader can be moved More...
VariantReader &	operator= (VariantReader &&other)=default
ITERATOR	begin () const
	creates a ITERATOR pointing at the start of the input stream (needed by for-each loop) More...
ITERATOR	end () const
	creates a ITERATOR with a nullified input stream (needed by for-each loop) More...
VariantHeader	header () const
	returns the variant header of the file being read More...

Detailed Description

template<class ITERATOR>
class gamgee::VariantReader< ITERATOR >

Utility class to read a VCF/BCF file with an appropriate Variant 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 : VariantReader<VariantIterator>{filename})
  do_something_with_record(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& record : VariantReader<VariantIterator>{filename})
  do_something_with_record(record);

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

for (auto& record : SingleVariantReader{filename})
  do_something_with_record(record);

Constructor & Destructor Documentation

template<class ITERATOR >

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

inlineexplicit

reads through all records in a file (vcf or bcf) parsing them into Variant objects

Parameters

filename

the name of the variant file

template<class ITERATOR >

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

inlineexplicit

reads through all records in a file (vcf or bcf) parsing them into Variant objects

Parameters

filenames

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

template<class ITERATOR >

gamgee::VariantReader< ITERATOR >::VariantReader ( const std::string &  filename, const std::vector< std::string > &  samples, const bool  include = true  )

inline

reads through all records in a file (vcf or bcf) parsing them into Variant objects but only including the selected samples. To create a sites only file, simply pass an empty vector of samples.

Parameters

filename	the name of the variant file
samples	the list of samples you want included/excluded from your iteration
include	whether you want these samples to be included or excluded from your iteration. default = true (include)

template<class ITERATOR >

gamgee::VariantReader< ITERATOR >::VariantReader ( const std::vector< std::string > &  filenames, const std::vector< std::string > &  samples, const bool  include = true  )

inline

reads through all records in a file (vcf or bcf) parsing them into Variant objects but only including the selected samples. To create a sites only file, simply pass an empty vector of samples.

Parameters

filenames	a vector containing a single element: the name of the variant file
samples	the list of samples you want included/excluded from your iteration
include	whether you want these samples to be included or excluded from your iteration. default = true (include)

template<class ITERATOR >

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

delete

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

template<class ITERATOR >

gamgee::VariantReader< ITERATOR >::VariantReader ( VariantReader< ITERATOR > &&  other )

default

a VariantReader can be moved

Member Function Documentation

template<class ITERATOR >

ITERATOR gamgee::VariantReader< ITERATOR >::begin ( ) const

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::VariantReader< ITERATOR >::end ( ) const

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 >

VariantHeader gamgee::VariantReader< ITERATOR >::header ( ) const

inline

returns the variant header of the file being read

template<class ITERATOR >

VariantReader& gamgee::VariantReader< ITERATOR >::operator= ( const VariantReader< ITERATOR > &  other )

delete

template<class ITERATOR >

VariantReader& gamgee::VariantReader< ITERATOR >::operator= ( VariantReader< ITERATOR > &&  other )

default

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

• gamgee/variant/variant_reader.h