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;
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;
41 class SeqErrorCommand : public Command {
43 SeqErrorCommand(string);
46 vector<string> getRequiredParameters();
47 vector<string> getValidParameters();
48 vector<string> getRequiredFiles();
49 map<string, vector<string> > getOutputFiles() { return outputTypes; }
57 map<string,int> getWeights();
58 Compare getErrors(Sequence, Sequence);
59 void printErrorHeader();
60 void printErrorData(Compare);
62 string queryFileName, referenceFileName, namesFileName, errorFileName, outputDir;
66 vector<string> outputNames;
67 map<string, vector<string> > outputTypes;
69 vector<Sequence> referenceSeqs;