here is a straightforward translation of the genotyping functionality, plus some mild error checking. Not the prettiest or most performance optimized code yet but it should do as a first version. I compiled it successfully under Linux using
g++ -std=c++11 genotyper.cpp
In order to use the Genotyper class with your WIP implementation of the container class under SV.cpp you might want to add a list of "reads" spanning the potential SV as a member of the SV class in the format of:
std::vector<std:tuple<int,int> > my_vec_of_reads;
s.t. _my_vec_ofreads is a C++ vector of tuples where each "read" in that vector is a tuple with index 0 being the indication whether the read has a SFS supporting the variant or not and index 1 being the predicted haplotype of that read. More details in the doxygen header of the _posterior_sv_genotype_givereads() function within genotyper.cpp.
Hey @ldenti ,
here is a straightforward translation of the genotyping functionality, plus some mild error checking. Not the prettiest or most performance optimized code yet but it should do as a first version. I compiled it successfully under Linux using
In order to use the Genotyper class with your WIP implementation of the container class under SV.cpp you might want to add a list of "reads" spanning the potential SV as a member of the SV class in the format of:
s.t. _my_vec_ofreads is a C++ vector of tuples where each "read" in that vector is a tuple with index 0 being the indication whether the read has a SFS supporting the variant or not and index 1 being the predicted haplotype of that read. More details in the doxygen header of the _posterior_sv_genotype_givereads() function within genotyper.cpp.