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