40 #ifndef _PLINKOUTPUTMAFITERATOR_H_
41 #define _PLINKOUTPUTMAFITERATOR_H_
64 std::vector<std::string>
ped_;
93 const std::vector<std::string>& species,
94 const std::string& reference,
96 bool recodeChr =
false) :
Helper class for developping filter for maf blocks.
A synteny block data structure, the basic unit of a MAF alignement file.
Interface to loop over maf alignment blocks.
virtual MafBlock * nextBlock()=0
Get the next available alignment block.
This iterator outputs all biallelic SNPs in the PLINK format (ped and map files).
std::map< std::string, unsigned int > chrCodes_
MafBlock * analyseCurrentBlock_()
std::vector< std::string > ped_
std::vector< std::string > species_
void parseBlock_(std::ostream &out, const MafBlock &block)
std::ostream * outputMap_
PlinkOutputMafIterator(MafIterator *iterator, std::ostream *outPed, std::ostream *outMap, const std::vector< std::string > &species, const std::string &reference, bool map3=false, bool recodeChr=false)
Build a new PlinkOutputMafIterator object.
PlinkOutputMafIterator(const PlinkOutputMafIterator &iterator)
void writePedToFile_(std::ostream &out)
std::ostream * outputPed_
unsigned int currentCode_
PlinkOutputMafIterator & operator=(const PlinkOutputMafIterator &iterator)