1 #ifndef CHIMERASLAYER_H
2 #define CHIMERASLAYER_H
8 * Created by westcott on 9/25/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
20 //***********************************************************************/
21 //This class was modeled after the chimeraSlayer written by the Broad Institute
22 /***********************************************************************/
24 class ChimeraSlayer : public Chimera {
27 ChimeraSlayer(string, string, bool, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
28 ChimeraSlayer(string, string, bool, map<string, int>&, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
32 int getChimeras(Sequence*);
33 Sequence print(ostream&, ostream&);
34 Sequence print(ostream&, ostream&, data_results, data_results);
35 void printHeader(ostream&);
37 int getNumNoParents() { return numNoParents; }
38 data_results getResults() { return printResults; }
41 Sequence print(MPI_File&, MPI_File&);
42 Sequence print(MPI_File&, MPI_File&, data_results, data_results);
49 Database* databaseRight;
50 Database* databaseLeft;
51 map<string, int> priority; //for template=self, seqname, seqAligned, abundance
52 set<string> chimericSeqs; //for template=self, so we don't add chimeric sequences to the userTemplate set
55 vector<data_struct> chimeraResults;
56 data_results printResults;
57 string chimeraFlags, searchMethod, fastafile;
58 bool realign, trimChimera;
59 int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
62 void printBlock(data_struct, string, ostream&);
63 void printBlock(data_results, data_results, bool, bool, string, ostream&);
64 string getBlock(data_struct, string);
65 string getBlock(data_results, data_results, bool, bool, string);
66 //int readNameFile(string);
67 vector<Sequence*> getTemplate(Sequence, vector<Sequence*>&);
68 vector<Sequence> getRefSeqs(Sequence, vector<Sequence*>&, vector<Sequence*>&);
69 vector<Sequence> getBlastSeqs(Sequence, vector<Sequence*>&, int);
70 vector<Sequence> getKmerSeqs(Sequence, vector<Sequence*>&, int);
74 /************************************************************************/