gamgee::IndexedVariantReader< ITERATOR > Class Template Reference

Utility class to read an indexed BCF file by intervals using an appropriate Variant iterator in a for-each loop. More...

#include <indexed_variant_reader.h>

Public Member Functions
	IndexedVariantReader (const std::string &filename, const std::vector< std::string > &interval_list)
	reads through all records in a file matching one of the given intervals, parsing them into Variant objects More...
	IndexedVariantReader (const IndexedVariantReader &other)=delete
	an IndexedVariantReader cannot be copied safely, as it is iterating over a stream. More...
IndexedVariantReader &	operator= (const IndexedVariantReader &other)=delete
	IndexedVariantReader (IndexedVariantReader &&other)=default
	an IndexedVariantReader can be moved More...
IndexedVariantReader &	operator= (IndexedVariantReader &&other)=default
ITERATOR	begin () const
ITERATOR	end () const
VariantHeader	header () const
	returns the variant header of the file being read More...

Detailed Description

template<class ITERATOR>
class gamgee::IndexedVariantReader< ITERATOR >

Utility class to read an indexed BCF file by intervals using an appropriate Variant iterator in a for-each loop.

NOTE: this will only parse BCF files with CSI indices

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

for (auto& record : IndexedVariantReader<IndexedVariantIterator>{filename, intervals})
  do_something_with_record(record);

Constructor & Destructor Documentation

template<class ITERATOR >

gamgee::IndexedVariantReader< ITERATOR >::IndexedVariantReader ( const std::string &  filename, const std::vector< std::string > &  interval_list  )

inline

reads through all records in a file matching one of the given intervals, parsing them into Variant objects

Parameters

filename	the name of the variant file
interval_list	a vector of intervals represented by strings. Empty vector for all intervals.

template<class ITERATOR >

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

delete

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

template<class ITERATOR >

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

default

an IndexedVariantReader can be moved

Member Function Documentation

template<class ITERATOR >

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

inline

template<class ITERATOR >

ITERATOR gamgee::IndexedVariantReader< ITERATOR >::end ( ) const

inline

template<class ITERATOR >

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

inline

returns the variant header of the file being read

template<class ITERATOR >

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

delete

template<class ITERATOR >

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

default

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

• gamgee/variant/indexed_variant_reader.h