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#ifndef CHIMERASLAYER_H
#define CHIMERASLAYER_H
/*
* chimeraslayer.h
* Mothur
*
* Created by westcott on 9/25/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "mothurchimera.h"
#include "maligner.h"
#include "slayer.h"
//***********************************************************************/
//This class was modeled after the chimeraSlayer written by the Broad Institute
/***********************************************************************/
class ChimeraSlayer : public MothurChimera {
public:
ChimeraSlayer(string, string, bool, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, int);
ChimeraSlayer(string, string, bool, map<string, int>&, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, int);
ChimeraSlayer(string, string, bool, map<string, int>&, int, int, int, int, float, int, int, int, int, int, int, int, int, bool, int, bool);
~ChimeraSlayer();
int getChimeras(Sequence*);
Sequence print(ostream&, ostream&);
Sequence print(ostream&, ostream&, data_results, data_results);
void printHeader(ostream&);
int doPrep();
int getNumNoParents() { return numNoParents; }
data_results getResults() { return printResults; }
private:
Sequence querySeq;
Sequence trimQuery;
DeCalculator decalc;
SearchDatabase* databaseRight;
SearchDatabase* 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, fastafile;
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, vector<Sequence*>&);
vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
};
/************************************************************************/
#endif
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