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fixed bug in seqerrorcommand
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1 #ifndef SEQERRORCOMMAND
2 #define SEQERRORCOMMAND
3
4 /*
5  *  seqerrorcommand.h
6  *  Mothur
7  *
8  *  Created by Pat Schloss on 7/15/10.
9  *  Copyright 2010 Schloss Lab. All rights reserved.
10  *
11  */
12
13 #include "mothur.h"
14 #include "command.hpp"
15 #include "sequence.hpp"
16
17 struct Compare {
18         int AA, AT, AG, AC,     TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, CC, NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
19         string refName, queryName, sequence;
20         double errorRate;
21         int weight, matches, mismatches, total;
22         
23         Compare(){
24                 AA=0; AT=0; AG=0; AC=0;
25                 TA=0; TT=0; TG=0; TC=0;
26                 GA=0; GT=0; GG=0; GC=0;
27                 CA=0; CT=0; CG=0; CC=0;
28                 NA=0; NT=0; NG=0; NC=0;
29                 Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
30                 dA=0; dT=0; dG=0; dC=0;
31                 refName = "";
32                 queryName = "";
33                 weight = 1;
34                 matches = 0;
35                 mismatches = 0;
36                 total = 0;
37                 errorRate = 1.0000;
38                 sequence = "";
39         }
40 };
41
42 class SeqErrorCommand : public Command {
43 public:
44         SeqErrorCommand(string);
45         SeqErrorCommand();
46         ~SeqErrorCommand();
47         vector<string> getRequiredParameters();
48         vector<string> getValidParameters();
49         vector<string> getRequiredFiles();
50         map<string, vector<string> > getOutputFiles() { return outputTypes; }
51         int execute();
52         void help();
53         
54 private:
55         bool abort;
56
57         void getReferences();
58         map<string,int> getWeights();
59         Compare getErrors(Sequence, Sequence);
60         void printErrorHeader();
61         void printErrorData(Compare, int);
62         void printSubMatrix();
63         void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
64         void printErrorQuality(map<char, vector<int> >);
65         void printQualityFR(vector<vector<int> >, vector<vector<int> >);
66
67         string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
68         double threshold;
69         bool ignoreChimeras;
70         int numRefs;
71         int maxLength;
72         ofstream errorSummaryFile, errorSeqFile;
73         vector<string> outputNames;
74         map<string, vector<string> > outputTypes;
75         
76         vector<Sequence> referenceSeqs;
77         vector<vector<int> > substitutionMatrix;
78 };
79
80 #endif