A library for working with phylogenetic data.
v0.25.0
SyncReader Class Reference

#include <genesis/population/formats/sync_reader.hpp>

Detailed Description

Reader for PoPoolation2's "synchronized" files.

These files are a simple tally of the counts at each position and sample in a (m)pileup file. See https://sourceforge.net/p/popoolation2/wiki/Tutorial/ for the format description.

Definition at line 54 of file sync_reader.hpp.

Public Member Functions

 SyncReader ()=default
 
 SyncReader (SyncReader &&)=default
 
 SyncReader (SyncReader const &)=default
 
 ~SyncReader ()=default
 
SyncReaderoperator= (SyncReader &&)=default
 
SyncReaderoperator= (SyncReader const &)=default
 
bool parse_line (utils::InputStream &input_stream, Variant &sample_set) const
 
bool parse_line (utils::InputStream &input_stream, Variant &sample_set, std::vector< bool > const &sample_filter) const
 
std::vector< Variantread (std::shared_ptr< utils::BaseInputSource > source) const
 
std::vector< Variantread (std::shared_ptr< utils::BaseInputSource > source, std::vector< bool > const &sample_filter) const
 

Constructor & Destructor Documentation

◆ SyncReader() [1/3]

SyncReader ( )
default

◆ ~SyncReader()

~SyncReader ( )
default

◆ SyncReader() [2/3]

SyncReader ( SyncReader const &  )
default

◆ SyncReader() [3/3]

SyncReader ( SyncReader &&  )
default

Member Function Documentation

◆ operator=() [1/2]

SyncReader& operator= ( SyncReader &&  )
default

◆ operator=() [2/2]

SyncReader& operator= ( SyncReader const &  )
default

◆ parse_line() [1/2]

bool parse_line ( utils::InputStream input_stream,
Variant sample_set 
) const

Definition at line 76 of file sync_reader.cpp.

◆ parse_line() [2/2]

bool parse_line ( utils::InputStream input_stream,
Variant sample_set,
std::vector< bool > const &  sample_filter 
) const

Definition at line 83 of file sync_reader.cpp.

◆ read() [1/2]

std::vector< Variant > read ( std::shared_ptr< utils::BaseInputSource source) const

Definition at line 47 of file sync_reader.cpp.

◆ read() [2/2]

std::vector< Variant > read ( std::shared_ptr< utils::BaseInputSource source,
std::vector< bool > const &  sample_filter 
) const

Definition at line 61 of file sync_reader.cpp.


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