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