bpp-seq-omics  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::VcfOutputMafIterator Class Reference

This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF). More...

#include <Bpp/Seq/Io/Maf/VcfOutputMafIterator.h>

+ Inheritance diagram for bpp::VcfOutputMafIterator:
+ Collaboration diagram for bpp::VcfOutputMafIterator:

Public Member Functions

 VcfOutputMafIterator (MafIterator *iterator, std::ostream *out, const std::string &reference, const std::vector< std::string > &genotypes)
 Build a new VcfOutputMafIterator object. More...
 
MafBlock * analyseCurrentBlock_ () throw (Exception)
 
void setLogStream (OutputStream *logstream)
 
void addIterationListener (IterationListener *listener)
 
MafBlock * nextBlock () throw (Exception)
 Get the next available alignment block. More...
 
bool isVerbose () const
 
void setVerbose (bool yn)
 

Protected Member Functions

virtual void fireIterationStartSignal_ ()
 
virtual void fireIterationMoveSignal_ (const MafBlock &currentBlock)
 
virtual void fireIterationStopSignal_ ()
 

Protected Attributes

MafIterator * iterator_
 
MafBlock * currentBlock_
 
OutputStream * logstream_
 
std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Private Member Functions

 VcfOutputMafIterator (const VcfOutputMafIterator &iterator)
 
VcfOutputMafIterator & operator= (const VcfOutputMafIterator &iterator)
 
void writeHeader_ (std::ostream &out) const
 
void writeBlock_ (std::ostream &out, const MafBlock &block) const
 

Private Attributes

std::ostream * output_
 
std::string refSpecies_
 
std::vector< std::string > genotypes_
 

Detailed Description

This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF).

Only substitutions are supported for now.

Definition at line 57 of file VcfOutputMafIterator.h.

Constructor & Destructor Documentation

◆ VcfOutputMafIterator() [1/2]

bpp::VcfOutputMafIterator::VcfOutputMafIterator ( MafIterator *  iterator,
std::ostream *  out,
const std::string &  reference,
const std::vector< std::string > &  genotypes 
)
inline

Build a new VcfOutputMafIterator object.

Parameters
iteratorThe input iterator.
outThe output stream where to write the VCF file.
referenceThe species to use as a reference.
genotypesA list of species for which genotype information should be written in the VCF file. There will be one extra column per genotype, +1 format column.

Definition at line 74 of file VcfOutputMafIterator.h.

References output_, and writeHeader_().

◆ VcfOutputMafIterator() [2/2]

bpp::VcfOutputMafIterator::VcfOutputMafIterator ( const VcfOutputMafIterator &  iterator)
inlineprivate

Definition at line 82 of file VcfOutputMafIterator.h.

Member Function Documentation

◆ addIterationListener()

void bpp::AbstractMafIterator::addIterationListener ( IterationListener *  listener)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

◆ analyseCurrentBlock_()

MafBlock* bpp::VcfOutputMafIterator::analyseCurrentBlock_ ( )
throw (Exception
)
inlinevirtual

Implements bpp::AbstractMafIterator.

Definition at line 99 of file VcfOutputMafIterator.h.

References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), output_, and writeBlock_().

◆ fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock)
protectedvirtualinherited

Definition at line 57 of file MafIterator.cpp.

◆ fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )
protectedvirtualinherited

Definition at line 51 of file MafIterator.cpp.

◆ fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )
protectedvirtualinherited

Definition at line 63 of file MafIterator.cpp.

◆ isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

◆ nextBlock()

MafBlock* bpp::AbstractMafIterator::nextBlock ( )
throw (Exception
)
inlinevirtualinherited

Get the next available alignment block.

Returns
A maf alignment block, or a null pointer if no more block is available.

Implements bpp::MafIterator.

Definition at line 103 of file MafIterator.h.

◆ operator=()

VcfOutputMafIterator& bpp::VcfOutputMafIterator::operator= ( const VcfOutputMafIterator &  iterator)
inlineprivate

Definition at line 89 of file VcfOutputMafIterator.h.

References genotypes_, output_, and refSpecies_.

◆ setLogStream()

void bpp::AbstractFilterMafIterator::setLogStream ( OutputStream *  logstream)
inlineinherited

Definition at line 178 of file MafIterator.h.

◆ setVerbose()

void bpp::AbstractMafIterator::setVerbose ( bool  yn)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

◆ writeBlock_()

void VcfOutputMafIterator::writeBlock_ ( std::ostream &  out,
const MafBlock &  block 
) const
private

Definition at line 81 of file VcfOutputMafIterator.cpp.

References bpp::MafBlock::getAlignment(), bpp::MafSequence::getChromosome(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::getSequencesForSpecies(), and bpp::MafSequence::start().

Referenced by analyseCurrentBlock_().

◆ writeHeader_()

void VcfOutputMafIterator::writeHeader_ ( std::ostream &  out) const
private

Definition at line 58 of file VcfOutputMafIterator.cpp.

Referenced by VcfOutputMafIterator().

Member Data Documentation

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_
protectedinherited

Definition at line 154 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), analyseCurrentBlock_(), and bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_().

◆ genotypes_

std::vector<std::string> bpp::VcfOutputMafIterator::genotypes_
private

Definition at line 63 of file VcfOutputMafIterator.h.

Referenced by operator=().

◆ iterationListeners_

std::vector<IterationListener*> bpp::AbstractMafIterator::iterationListeners_
protectedinherited

Definition at line 89 of file MafIterator.h.

◆ iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_
protectedinherited

Definition at line 153 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ logstream_

OutputStream* bpp::AbstractFilterMafIterator::logstream_
protectedinherited

Definition at line 155 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ output_

std::ostream* bpp::VcfOutputMafIterator::output_
private

Definition at line 61 of file VcfOutputMafIterator.h.

Referenced by analyseCurrentBlock_(), operator=(), and VcfOutputMafIterator().

◆ refSpecies_

std::string bpp::VcfOutputMafIterator::refSpecies_
private

Definition at line 62 of file VcfOutputMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protectedinherited

Definition at line 91 of file MafIterator.h.

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