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#ifndef SEQERRORCOMMAND
#define SEQERRORCOMMAND
/*
* seqerrorcommand.h
* Mothur
*
* Created by Pat Schloss on 7/15/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
#include "counttable.h"
struct Compare {
Compare(){
AA=0; AT=0; AG=0; AC=0;
TA=0; TT=0; TG=0; TC=0;
GA=0; GT=0; GG=0; GC=0;
CA=0; CT=0; CG=0; CC=0;
NA=0; NT=0; NG=0; NC=0;
Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
dA=0; dT=0; dG=0; dC=0;
refName = "";
queryName = "";
weight = 1;
matches = 0;
mismatches = 0;
total = 0;
errorRate = 1.0000;
sequence = "";
}
~Compare(){}
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;
string refName, queryName, sequence;
double errorRate;
int weight, matches, mismatches, total;
};
class SeqErrorCommand : public Command {
public:
SeqErrorCommand(string);
~SeqErrorCommand(){}
vector<string> setParameters();
string getCommandName() { return "seq.error"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
string getDescription() { return "seq.error"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<Sequence> getReferences(string);
void printSubMatrix(vector<vector<int> >& substitutionMatrix);
void printErrorFRFile(map<char, vector<int> >& errorForward, map<char, vector<int> >& errorReverse);
void printErrorQuality(map<char, vector<int> >&);
void printQualityFR(vector<vector<int> >& qualForwardMap, vector<vector<int> >& qualReverseMap);
long long process(string, string, string, string, string, string, vector<Sequence>&);
string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, countfile;
double threshold;
bool ignoreChimeras, aligned, abort;
int maxLength, totalBases, totalMatches, numRefs;
vector<string> outputNames;
vector<vector<int> > substitutionMatrix;
vector<vector<int> > qualForwardMap;
vector<vector<int> > qualReverseMap;
vector<int> misMatchCounts;
map<char, vector<int> > qScoreErrorMap;
map<char, vector<int> > errorForward;
map<char, vector<int> > errorReverse;
vector<string> megaAlignVector;
};
#endif
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