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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 "referencedb.h"
#include "counttable.h"
class SeqErrorCommand : public Command {
public:
SeqErrorCommand(string);
SeqErrorCommand();
~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:
bool abort;
ReferenceDB* rdb;
struct linePair {
unsigned long long start;
unsigned long long end;
linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
~linePair(){}
};
struct 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;
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(){};
};
vector<int> processIDS; //processid
vector<linePair> lines;
vector<linePair> qLines;
vector<linePair> rLines;
void getReferences();
map<string,int> getWeights();
int getErrors(Sequence, Sequence, Compare&);
void printErrorHeader(ofstream&);
void printErrorData(Compare, int, ofstream&, ofstream&);
void printSubMatrix();
void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
void printErrorQuality(map<char, vector<int> >);
void printQualityFR(vector<vector<int> >, vector<vector<int> >);
int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
int driver(string, string, string, string, string, string, linePair, linePair, linePair);
int createProcesses(string, string, string, string, string, string);
string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
double threshold;
bool ignoreChimeras, save, aligned;
int numRefs, processors;
int maxLength, totalBases, totalMatches;
//ofstream errorSummaryFile, errorSeqFile;
vector<string> outputNames;
vector<Sequence> referenceSeqs;
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;
map<string, int> weights;
vector<string> megaAlignVector;
};
#endif
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