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, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
27 ChimeraSlayer(string, string, bool, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
31 int getChimeras(Sequence*);
32 Sequence* print(ostream&, ostream&);
33 void printHeader(ostream&);
37 Sequence* print(MPI_File&, MPI_File&);
44 map<int, int> spotMap;
45 Database* databaseRight;
46 Database* databaseLeft;
47 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
49 vector<data_struct> chimeraResults;
50 string chimeraFlags, searchMethod, fastafile, includeAbunds;
51 bool realign, trimChimera;
52 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
55 void printBlock(data_struct, string, ostream&);
56 string getBlock(data_struct, string);
57 int readNameFile(string);
58 vector<Sequence*> getTemplate(Sequence*);
62 /************************************************************************/