Question regarding queryAbundance(node) function. #19
Description
Hello all,
I am using GATB library for my work. I have a naive question which I have not been able to find an answer for. While using one of the functions to find the abundance of a node (queryAbundance(node)) in the initial dataset, I always get the abundance as 255 for any kmer having abundance greater than 255. Upon looking at the gatb-core source code I found the following template in Graph.cpp:
template<typename Node, typename Edge, typename GraphDataVariant>
struct queryAbundance_visitor : public boost::static_visitor {
Node& node;
queryAbundance_visitor (Node& node) : node(node){}
template<size_t span> int operator() (const GraphData& data) const
{
unsigned long hashIndex = getNodeIndex(data, node);
if(hashIndex == ULLONG_MAX) return 0; // node was not found in the mphf
unsigned char value = (*(data._abundance)).at(hashIndex);
return value;
}
};
The template is returning an unsigned char value which has a range of 0 to 255. This might be a reason why the value is always 255. But even if I change it to "unsigned int", I still get the same result. Inspired from the snippet given in GATB library (deBruijn26.cpp), I am using the query abundance function as follows:
std::string s = model.toString (itKmer->value()); //itkmer->value is the kmer of length 21 from a read
const char* sq = s.c_str();
Node node = graph.buildNode(sq);
auto abund = graph.queryAbundance(node);
Am I making a mistake here in my above code?
regards
Dilip