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