gamgee::IndexedSamReader< ITERATOR > Class Template Reference

Utility class to read a BAM/CRAM file with an appropriate Sam iterator from an indexed file in a for-each loop. Intervals are passed in using a vector of string coordinates compatible with Samtools. When iteration begins, the iterations (re-)starts at the beginning of the first interval. More...

#include <indexed_sam_reader.h>

Public Member Functions
	IndexedSamReader (const std::string &filename, const std::vector< std::string > &interval_list)
	reads through all records in a file parsing them into Sam objects More...
	IndexedSamReader (IndexedSamReader &&other)=default
	iterators and readers can be moved More...
IndexedSamReader &	operator= (IndexedSamReader &&other)=default
	IndexedSamReader (const IndexedSamReader &other)=delete
	no copy construction/assignment allowed for input iterators and readers More...
IndexedSamReader &	operator= (IndexedSamReader &other)=delete
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 ()
	returns the header More...

Detailed Description

template<class ITERATOR>
class gamgee::IndexedSamReader< ITERATOR >

Utility class to read a BAM/CRAM file with an appropriate Sam iterator from an indexed file in a for-each loop. Intervals are passed in using a vector of string coordinates compatible with Samtools. When iteration begins, the iterations (re-)starts at the beginning of the first interval.

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

for (const auto& record : IndexedSamReader<IndexedSamIterator>{filename, interval_list})
  do_something_with_sam(record);

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

for (const auto& record : IndexedSingleSamReader{filename, interval_list})
  do_something_with_sam(record);

Constructor & Destructor Documentation

template<class ITERATOR >

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

inline

reads through all records in a file parsing them into Sam objects

Parameters

filename	the name of the bam/cram file
interval_list	Samtools style intervals to look for records

template<class ITERATOR >

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

default

iterators and readers can be moved

template<class ITERATOR >

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

delete

no copy construction/assignment allowed for input iterators and readers

Member Function Documentation

template<class ITERATOR >

ITERATOR gamgee::IndexedSamReader< 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::IndexedSamReader< 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::IndexedSamReader< ITERATOR >::header ( )

inline

returns the header

Returns

the header

template<class ITERATOR >

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

default

template<class ITERATOR >

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

delete

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

• gamgee/sam/indexed_sam_reader.h