seqerrorcommand.h

   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 "command.hpp"
  14 #include "sequence.hpp"
  15 #include "referencedb.h"
  16 #include "counttable.h"
  17
  18
  19 class SeqErrorCommand : public Command {
  20 public:
  21         SeqErrorCommand(string);
  22         SeqErrorCommand();
  23         ~SeqErrorCommand(){}
  24
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "seq.error";                           }
  27         string getCommandCategory()             { return "Sequence Processing";         }
  28
  29         string getHelpString();
  30     string getOutputPattern(string);
  31         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"; }
  32         string getDescription()         { return "seq.error"; }
  33
  34
  35         int execute();
  36         void help() { m->mothurOut(getHelpString()); }
  37
  38 private:
  39         bool abort;
  40         ReferenceDB* rdb;
  41
  42         struct linePair {
  43                 unsigned long long start;
  44                 unsigned long long end;
  45                 linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
  46         ~linePair(){}
  47         };
  48
  49     struct Compare {
  50         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;
  51         string refName, queryName, sequence;
  52         double errorRate;
  53         int weight, matches, mismatches, total;
  54
  55         Compare(){
  56             AA=0; AT=0; AG=0; AC=0;
  57             TA=0; TT=0; TG=0; TC=0;
  58             GA=0; GT=0; GG=0; GC=0;
  59             CA=0; CT=0; CG=0; CC=0;
  60             NA=0; NT=0; NG=0; NC=0;
  61             Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
  62             dA=0; dT=0; dG=0; dC=0;
  63             refName = "";
  64             queryName = "";
  65             weight = 1;
  66             matches = 0;
  67             mismatches = 0;
  68             total = 0;
  69             errorRate = 1.0000;
  70             sequence = "";
  71         }
  72         ~Compare(){};
  73     };
  74
  75         vector<int> processIDS;   //processid
  76         vector<linePair> lines;
  77         vector<linePair> qLines;
  78         vector<linePair> rLines;
  79
  80         void getReferences();
  81         map<string,int> getWeights();
  82         int getErrors(Sequence, Sequence, Compare&);
  83         void printErrorHeader(ofstream&);
  84         void printErrorData(Compare, int, ofstream&, ofstream&);
  85         void printSubMatrix();
  86         void printErrorFRFile(map<char, vector<int> >, map<char, vector<int> >);
  87         void printErrorQuality(map<char, vector<int> >);
  88         void printQualityFR(vector<vector<int> >, vector<vector<int> >);
  89
  90         int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
  91         int driver(string, string, string, string, string, string, linePair, linePair, linePair);
  92         int createProcesses(string, string, string, string, string, string);
  93
  94         string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
  95         double threshold;
  96         bool ignoreChimeras, save, aligned;
  97         int numRefs, processors;
  98         int maxLength, totalBases, totalMatches;
  99         //ofstream errorSummaryFile, errorSeqFile;
 100         vector<string> outputNames;
 101
 102         vector<Sequence> referenceSeqs;
 103         vector<vector<int> > substitutionMatrix;
 104         vector<vector<int> > qualForwardMap;
 105         vector<vector<int> > qualReverseMap;
 106         vector<int> misMatchCounts;
 107         map<char, vector<int> > qScoreErrorMap;
 108         map<char, vector<int> > errorForward;
 109         map<char, vector<int> > errorReverse;
 110         map<string, int> weights;
 111         vector<string> megaAlignVector;
 112
 113 };
 114
 115 #endif