trimseqscommand.h

   1 #ifndef TRIMSEQSCOMMAND_H
   2 #define TRIMSEQSCOMMAND_H
   3
   4 /*
   5  *  trimseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 6/6/09.
   9  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "sequence.hpp"
  16 #include "qualityscores.h"
  17
  18 class TrimSeqsCommand : public Command {
  19 public:
  20         TrimSeqsCommand(string);
  21         TrimSeqsCommand();
  22         ~TrimSeqsCommand();
  23         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31
  32         struct linePair {
  33                 unsigned long int start;
  34                 unsigned long int end;
  35                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  36         };
  37
  38         void getOligos(vector<string>&, vector<string>&);
  39         int stripBarcode(Sequence&, QualityScores&, int&);
  40         int stripForward(Sequence&, QualityScores&, int&);
  41         bool stripReverse(Sequence&, QualityScores&);
  42         bool cullLength(Sequence&);
  43         bool cullHomoP(Sequence&);
  44         bool cullAmbigs(Sequence&);
  45         bool compareDNASeq(string, string);
  46         int countDiffs(string, string);
  47         map<string, vector<string> > outputTypes;
  48
  49         bool abort;
  50         string fastaFile, oligoFile, qFileName, outputDir;
  51
  52         bool flip, allFiles, qtrim;
  53         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
  54         int qWindowSize, qWindowStep;
  55         double qRollAverage, qThreshold, qWindowAverage, qAverage;
  56         vector<string> revPrimer, outputNames;
  57         set<string> filesToRemove;
  58         map<string, int> barcodes;
  59         vector<string> groupVector;
  60         map<string, int> primers;
  61         map<string, int> combos;
  62
  63         vector<int> processIDS;   //processid
  64         vector<linePair*> lines;
  65         vector<linePair*> qLines;
  66
  67         int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
  68         int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
  69         int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
  70
  71 };
  72
  73 #endif