class ChimeraSlayer : public Chimera {
public:
- ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
- ChimeraSlayer(string, string, bool, map<string, int>&, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+ ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+ ChimeraSlayer(string, string, bool, map<string, int>&, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int);
+ ChimeraSlayer(string, string, bool, map<string, int>&, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, string, int, bool);
~ChimeraSlayer();
Sequence print(ostream&, ostream&, data_results, data_results);
void printHeader(ostream&);
int doPrep();
+ int getNumNoParents() { return numNoParents; }
data_results getResults() { return printResults; }
#ifdef USE_MPI
Sequence print(MPI_File&, MPI_File&);
- Sequence print(MPI_File&, MPI_File&, data_results, data_results);
+ Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&);
#endif
private:
Database* databaseLeft;
map<string, int> priority; //for template=self, seqname, seqAligned, abundance
set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
+ int numNoParents, threadID;
vector<data_struct> chimeraResults;
data_results printResults;
- string chimeraFlags, searchMethod, fastafile;
+ string chimeraFlags, searchMethod, fastafile, blastlocation;
bool realign, trimChimera;
int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
float divR;