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 /***********************************************************************/
22 class ChimeraSlayer : public Chimera {
25 ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
26 ChimeraSlayer(string, string, bool, map<string, int>&, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
30 int getChimeras(Sequence*);
31 Sequence* print(ostream&, ostream&);
32 Sequence* print(ostream&, ostream&, data_results, data_results);
33 void printHeader(ostream&);
35 data_results getResults() { return printResults; }
38 Sequence* print(MPI_File&, MPI_File&);
39 Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
46 Database* databaseRight;
47 Database* databaseLeft;
48 map<string, int> priority; //for template=self, seqname, seqAligned, abundance
49 set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
51 vector<data_struct> chimeraResults;
52 data_results printResults;
53 string chimeraFlags, searchMethod, fastafile;
54 bool realign, trimChimera;
55 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
58 void printBlock(data_struct, string, ostream&);
59 void printBlock(data_results, data_results, bool, bool, string, ostream&);
60 string getBlock(data_struct, string);
61 string getBlock(data_results, data_results, bool, bool, string);
62 //int readNameFile(string);
63 vector<Sequence*> getTemplate(Sequence*, vector<Sequence*>&);
64 vector<Sequence*> getRefSeqs(Sequence*, vector<Sequence*>&, vector<Sequence*>&);
65 vector<Sequence*> getBlastSeqs(Sequence*, vector<Sequence*>&, int);
66 vector<Sequence*> getKmerSeqs(Sequence*, vector<Sequence*>&, int);
70 /************************************************************************/