1 #ifndef CHIMERASLAYER_H
2 #define CHIMERASLAYER_H
8 * Created by westcott on 9/25/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
18 //***********************************************************************/
19 //This class was modeled after the chimeraSlayer written by the Broad Institute
20 /***********************************************************************/
23 class ChimeraSlayer : public Chimera {
26 ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
29 int getChimeras(Sequence*);
30 int print(ostream&, ostream&);
31 void printHeader(ostream&);
35 int print(MPI_File&, MPI_File&);
43 map<int, int> spotMap;
44 Database* databaseRight;
45 Database* databaseLeft;
47 vector<data_struct> chimeraResults;
48 string chimeraFlags, searchMethod, fastafile;
50 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
53 void printBlock(data_struct, string, ostream&);
54 string getBlock(data_struct, string);
58 /************************************************************************/