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         int execute();
  23         void help();
  24
  25 private:
  26
  27         struct linePair {
  28                 unsigned long int start;
  29                 unsigned long int end;
  30                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  31         };
  32
  33         void getOligos(vector<string>&, vector<string>&);
  34         int stripBarcode(Sequence&, QualityScores&, int&);
  35         int stripForward(Sequence&, QualityScores&, int&);
  36         bool stripReverse(Sequence&, QualityScores&);
  37         bool cullLength(Sequence&);
  38         bool cullHomoP(Sequence&);
  39         bool cullAmbigs(Sequence&);
  40         bool compareDNASeq(string, string);
  41         int countDiffs(string, string);
  42
  43         bool abort;
  44         string fastaFile, oligoFile, qFileName, outputDir;
  45
  46         bool flip, allFiles, qtrim;
  47         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
  48         int qWindowSize, qWindowStep;
  49         double qRollAverage, qThreshold, qWindowAverage, qAverage;
  50         vector<string> revPrimer, outputNames;
  51         set<string> filesToRemove;
  52         map<string, int> barcodes;
  53         vector<string> groupVector;
  54         map<string, int> primers;
  55         map<string, int> combos;
  56
  57         vector<int> processIDS;   //processid
  58         vector<linePair*> lines;
  59         vector<linePair*> qLines;
  60
  61         int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
  62         int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
  63         int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
  64
  65 };
  66
  67 #endif