class ChimeraCheckRDP : public Chimera {
public:
- ChimeraCheckRDP(string, string);
+ ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir
~ChimeraCheckRDP();
int getChimeras(Sequence*);
- void print(ostream&);
- void doPrep();
+ Sequence* print(ostream&, ostream&);
- private:
+ #ifdef USE_MPI
+ Sequence* print(MPI_File&, MPI_File&);
+ #endif
+ private:
Sequence* querySeq;
AlignmentDB* templateDB;
vector<sim> IS; //IS is the vector of IS values for each window for query
string fastafile;
map<string, string> names;
+ string name;
+ bool svg;
+ int kmerSize, increment;
vector<sim> findIS();
int calcKmers(map<int, int>, map<int, int>);