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

Detailed Description

template<class T = SimplePileupReader::Record>
class genesis::population::SimplePileupInputStream< T >

Iterate an input source and parse it as a (m)pileup file.

This simple wrapper allows easy iteration through the records/lines of an (m)pileup file line by line. See SimplePileupReader for details. The class is templated, so that it can be either used to produce SimplePileupReader::Record or Variant objects per line of the input mpileup file.

Basic usage:

auto it = SimplePileupInputStream<>( utils::from_file( infile ));
while( it ) {
    // work with it.record() or it->...
    ++it;
}

or

for( auto it = SimplePileupInputStream<Variant>( utils::from_file( infile )); it; ++it ) {
    // work with it
}

both allow to iterate each line in the file. The first instanciates an iterator over SimplePileupReader::Record, while the second over Variant.

Additionally, filtering of which samples (by index) to include can be provided, either as a vector of indices to consider, or as a bool vector that is true at the indices to consider. The latter filter does not need to contain the same number of values as the record has samples. If it is shorter, all samples after its last index will be ignored. If it is longer, the remaining entries are not used as a filter.

Definition at line 79 of file simple_pileup_input_stream.hpp.

Public Member Functions
	SimplePileupInputStream ()=default
	Create a default instance, with no input. More...

	SimplePileupInputStream (self_type &&)=default

	SimplePileupInputStream (self_type const &)=default

	SimplePileupInputStream (std::shared_ptr< utils::BaseInputSource > source, SimplePileupReader const &reader={})
	Create an instance that reads from an input source, and optionally take a SimplePileupReader with settings to be used. More...

	SimplePileupInputStream (std::shared_ptr< utils::BaseInputSource > source, std::vector< bool > const &sample_filter, SimplePileupReader const &reader={})
	Create an instance that reads from an input source, using only the samples at the indices where the `sample_filter` is true, and optionally take a SimplePileupReader with settings to be used. More...

	~SimplePileupInputStream ()=default

bool	good () const

void	increment ()

	operator bool () const
	Return true iff dereferencing is valid, i.e., iff there is a line/record available. More...

bool	operator!= (self_type const &it) const

T &	operator* ()

T const &	operator* () const

self_type &	operator++ ()

self_type &	operator++ (int)

T *	operator-> ()

T const *	operator-> () const

self_type &	operator= (self_type &&)=default

self_type &	operator= (self_type const &)=default

bool	operator== (self_type const &it) const

SimplePileupReader const &	reader () const

T &	record ()

T const &	record () const

Public Types
using	const_reference = value_type const &

using	difference_type = std::ptrdiff_t

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = SimplePileupInputStream

using	value_type = T

Constructor & Destructor Documentation

◆ SimplePileupInputStream() [1/5]

SimplePileupInputStream ( )

default

Create a default instance, with no input.

◆ SimplePileupInputStream() [2/5]

SimplePileupInputStream	(	std::shared_ptr< utils::BaseInputSource >	source,
		SimplePileupReader const &	reader = `{}`
	)

inlineexplicit

Create an instance that reads from an input source, and optionally take a SimplePileupReader with settings to be used.

Definition at line 108 of file simple_pileup_input_stream.hpp.

◆ SimplePileupInputStream() [3/5]

SimplePileupInputStream	(	std::shared_ptr< utils::BaseInputSource >	source,
		std::vector< bool > const &	sample_filter,
		SimplePileupReader const &	reader = `{}`
	)

inline

Create an instance that reads from an input source, using only the samples at the indices where the sample_filter is true, and optionally take a SimplePileupReader with settings to be used.

Definition at line 145 of file simple_pileup_input_stream.hpp.