1 #ifndef SEQERRORCOMMAND
2 #define SEQERRORCOMMAND
8 * Created by Pat Schloss on 7/15/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "sequence.hpp"
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;
21 int weight, matches, mismatches, total;
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;
42 class SeqErrorCommand : public Command {
44 SeqErrorCommand(string);
48 vector<string> setParameters();
49 string getCommandName() { return "seq.error"; }
50 string getCommandCategory() { return "Sequence Processing"; }
51 string getHelpString();
54 void help() { m->mothurOut(getHelpString()); }
60 map<string,int> getWeights();
61 Compare getErrors(Sequence, Sequence);
62 void printErrorHeader();
63 void printErrorData(Compare, int);
64 void printSubMatrix();
65 void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
66 void printErrorQuality(map<char, vector<int> >);
67 void printQualityFR(vector<vector<int> >, vector<vector<int> >);
69 string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
74 ofstream errorSummaryFile, errorSeqFile;
75 vector<string> outputNames;
77 vector<Sequence> referenceSeqs;
78 vector<vector<int> > substitutionMatrix;