#include <genesis/population/format/sam_variant_input_stream.hpp>

Detailed Description

Iterator over loci of the input sources.

This is the class that does the actual work of turning the underlying file data into our Variant and SampleCounts samples. Use the dereference operator*() and operator->() to get the Variant at the current locus of the iteration.

Definition at line 157 of file sam_variant_input_stream.hpp.

Public Member Functions
	Iterator (self_type &&)=default

	Iterator (self_type const &)=default

	~Iterator ()=default

bool	operator!= (self_type const &it) const

value_type &	operator* ()

const value_type &	operator* () const

self_type &	operator++ ()

value_type *	operator-> ()

const value_type *	operator-> () const

Iterator &	operator= (self_type &&)=default

Iterator &	operator= (self_type const &)=default

bool	operator== (self_type const &it) const
	Compare two iterators for equality. More...

std::vector< std::string >	rg_tags (bool all_header_tags=false) const
	Get the list of read group `RG` tags as used in the iteration, or as found in the SAM/BAM/CRAM file. More...

size_t	sample_size () const
	Return the size of the Variant::sample vector of SampleCounts that is produced by the iterator. More...

Public Types
using	iterator_category = std::input_iterator_tag

using	pointer = value_type const *

using	reference = value_type const &

using	self_type = SamVariantInputStream::Iterator

using	value_type = Variant

Public Attributes
friend	SamFileHandle

friend	SamVariantInputStream

Constructor & Destructor Documentation

◆ ~Iterator()

~Iterator ( )

default

◆ Iterator() [1/2]

Iterator ( self_type const & )

default

◆ Iterator() [2/2]

Iterator ( self_type && )

default

Member Function Documentation

◆ operator!=()

bool operator!= ( self_type const & it ) const

inline

Definition at line 242 of file sam_variant_input_stream.hpp.

◆ operator*() [1/2]

value_type& operator* ( )

inline

Definition at line 208 of file sam_variant_input_stream.hpp.

◆ operator*() [2/2]

const value_type& operator* ( ) const

inline

Definition at line 203 of file sam_variant_input_stream.hpp.

◆ operator++()

self_type& operator++ ( )

inline

Definition at line 217 of file sam_variant_input_stream.hpp.

◆ operator->() [1/2]

value_type* operator-> ( )

inline

Definition at line 198 of file sam_variant_input_stream.hpp.

◆ operator->() [2/2]

const value_type* operator-> ( ) const

inline

Definition at line 193 of file sam_variant_input_stream.hpp.

◆ operator=() [1/2]

Iterator& operator= ( self_type && )

default

◆ operator=() [2/2]

Iterator& operator= ( self_type const & )

default

◆ operator==()

bool operator== ( self_type const & it ) const

inline

Compare two iterators for equality.

Any two iterators that are created by calling begin() on the same SamVariantInputStream instance will compare equal, as long as neither of them is past-the-end. A valid (not past-the-end) iterator and an end() iterator will not compare equal.

Definition at line 237 of file sam_variant_input_stream.hpp.

◆ rg_tags()

std::vector< std::string > rg_tags ( bool all_header_tags = false ) const

Get the list of read group RG tags as used in the iteration, or as found in the SAM/BAM/CRAM file.

This function is useful when split_by_rg() is set to true, so that the reads are split by their read group tags. The function then returns the RG read group tag names, in the same order that the SampleCounts objects are stored in the resulting Variant of this iterator.

When additionally with_unaccounted_rg() is set to true, an additional RG tag "unaccounted" is added to the result as a last element, which is the same position that the unaccounted reads go in the Variant.

When using rg_tag_filter() to sub-set the RG tags (samples) being processed, this function by default only returnes those sample names (RG tags) that represent the final SampleCounts samples of the resulting Variant when iterating the data (and potentially including the "unaccounted" group).

If split_by_rg() is false, we are not splitting by read group tags, so then this function returns an empty vector. Note that the Variant that is produced during iteration still contains one SampleCounts sample, which collects all counts from all reads.

All of the above is ignored if the argument all_header_tags is set to true. In that case, the function instead simply returns those RG tags that are present in the SAM/BAM/CRAM header, without the "unaccounted", and without any filtering. Note that in this case, this function needs to fill the vector when called. Hence, if this list is needed often, it is recommended to call this function once and store the result.

Definition at line 698 of file sam_variant_input_stream.cpp.