#include "maligner.h"
#include "slayer.h"
-
-
//***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
-
class ChimeraSlayer : public Chimera {
public:
- ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
- ChimeraSlayer(string, string, string, string, 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);
+ ChimeraSlayer(string, string, bool, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
~ChimeraSlayer();
int getChimeras(Sequence*);
- int print(ostream&, ostream&);
+ Sequence* print(ostream&, ostream&);
+ Sequence* print(ostream&, ostream&, data_results, data_results);
void printHeader(ostream&);
int doPrep();
+ data_results getResults() { return printResults; }
#ifdef USE_MPI
- int print(MPI_File&, MPI_File&);
+ Sequence* print(MPI_File&, MPI_File&);
+ Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
#endif
private:
Sequence* querySeq;
+ Sequence* trimQuery;
DeCalculator* decalc;
map<int, int> spotMap;
Database* databaseRight;
map<string, vector<string> > nameMapRank; //sequence name to rank so you can construct a template of the abundant sequences if the user uses itself as template
vector<data_struct> chimeraResults;
+ data_results printResults;
string chimeraFlags, searchMethod, fastafile, includeAbunds;
- bool realign;
+ bool realign, trimChimera;
int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
float divR;
void printBlock(data_struct, string, ostream&);
+ void printBlock(data_results, data_results, bool, bool, string, ostream&);
string getBlock(data_struct, string);
+ string getBlock(data_results, data_results, bool, bool, string);
int readNameFile(string);
vector<Sequence*> getTemplate(Sequence*);