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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         
48         vector<string> setParameters();
49         string getCommandName()                 { return "seq.error";                           }
50         string getCommandCategory()             { return "Sequence Processing";         }
51         string getHelpString(); 
52         string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
53         string getDescription()         { return "seq.error"; }
54
55         
56         int execute(); 
57         void help() { m->mothurOut(getHelpString()); }  
58         
59 private:
60         bool abort;
61         
62         struct linePair {
63                 unsigned long int start;
64                 unsigned long int end;
65                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
66         };
67         
68         vector<int> processIDS;   //processid
69         vector<linePair> lines;
70         vector<linePair> qLines;
71         vector<linePair> rLines;
72
73         void getReferences();
74         map<string,int> getWeights();
75         Compare getErrors(Sequence, Sequence);
76         void printErrorHeader(ofstream&);
77         void printErrorData(Compare, int, ofstream&, ofstream&);
78         void printSubMatrix();
79         void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
80         void printErrorQuality(map<char, vector<int> >);
81         void printQualityFR(vector<vector<int> >, vector<vector<int> >);
82         
83         int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
84         int driver(string, string, string, string, string, string, linePair, linePair, linePair);
85         int createProcesses(string, string, string, string, string, string);
86
87         string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
88         double threshold;
89         bool ignoreChimeras;
90         int numRefs, processors;
91         int maxLength, totalBases, totalMatches;
92         //ofstream errorSummaryFile, errorSeqFile;
93         vector<string> outputNames;
94         
95         vector<Sequence> referenceSeqs;
96         vector<vector<int> > substitutionMatrix;
97         vector<vector<int> > qualForwardMap;
98         vector<vector<int> > qualReverseMap;
99         vector<int> misMatchCounts;
100         map<char, vector<int> > qScoreErrorMap;
101         map<char, vector<int> > errorForward;
102         map<char, vector<int> > errorReverse;
103         map<string, int> weights;
104         vector<string> megaAlignVector;
105
106 };
107
108 #endif