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 #include "groupmap.h"
  18
  19 class TrimSeqsCommand : public Command {
  20 public:
  21         TrimSeqsCommand(string);
  22         TrimSeqsCommand();
  23         ~TrimSeqsCommand();
  24         vector<string> getRequiredParameters();
  25         vector<string> getValidParameters();
  26         vector<string> getRequiredFiles();
  27         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  28         int execute();
  29         void help();
  30
  31 private:
  32
  33         GroupMap* groupMap;
  34
  35         struct linePair {
  36                 unsigned long int start;
  37                 unsigned long int end;
  38                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  39         };
  40
  41         void getOligos(vector<string>&, vector<string>&);
  42         int stripBarcode(Sequence&, QualityScores&, int&);
  43         int stripForward(Sequence&, QualityScores&, int&);
  44         bool stripReverse(Sequence&, QualityScores&);
  45         bool keepFirstTrim(Sequence&, QualityScores&);
  46         bool removeLastTrim(Sequence&, QualityScores&);
  47
  48         bool cullLength(Sequence&);
  49         bool cullHomoP(Sequence&);
  50         bool cullAmbigs(Sequence&);
  51         bool compareDNASeq(string, string);
  52         int countDiffs(string, string);
  53         map<string, vector<string> > outputTypes;
  54
  55         bool abort;
  56         string fastaFile, oligoFile, qFileName, groupfile, outputDir;
  57
  58         bool flip, allFiles, qtrim;
  59         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
  60         int qWindowSize, qWindowStep, keepFirst, removeLast;
  61         double qRollAverage, qThreshold, qWindowAverage, qAverage;
  62         vector<string> revPrimer, outputNames;
  63         set<string> filesToRemove;
  64         map<string, int> barcodes;
  65         vector<string> groupVector;
  66         map<string, int> primers;
  67         map<string, int> combos;
  68         map<string, int> groupToIndex;
  69
  70         vector<int> processIDS;   //processid
  71         vector<linePair*> lines;
  72         vector<linePair*> qLines;
  73
  74         int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
  75         int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
  76         int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
  77
  78 };
  79
  80 #endif