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
  25         vector<string> setParameters();
  26         string getCommandName()                 { return "trim.seqs";   }
  27         string getCommandCategory()             { return "Sequence Processing";         }
  28         string getHelpString();
  29         string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
  30         string getDescription()         { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
  31
  32         int execute();
  33         void help() { m->mothurOut(getHelpString()); }
  34
  35 private:
  36
  37         GroupMap* groupMap;
  38
  39         struct linePair {
  40                 unsigned long int start;
  41                 unsigned long int end;
  42                 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
  43         };
  44
  45         bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
  46         int stripBarcode(Sequence&, QualityScores&, int&);
  47         int stripForward(Sequence&, QualityScores&, int&);
  48         bool stripReverse(Sequence&, QualityScores&);
  49
  50         bool keepFirstTrim(Sequence&, QualityScores&);
  51         bool removeLastTrim(Sequence&, QualityScores&);
  52
  53         bool cullLength(Sequence&);
  54         bool cullHomoP(Sequence&);
  55         bool cullAmbigs(Sequence&);
  56         bool compareDNASeq(string, string);
  57         int countDiffs(string, string);
  58
  59         bool abort, createGroup;
  60         string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
  61
  62         bool flip, allFiles, qtrim;
  63         int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
  64         int qWindowSize, qWindowStep, keepFirst, removeLast;
  65         double qRollAverage, qThreshold, qWindowAverage, qAverage;
  66         vector<string> revPrimer, outputNames;
  67         set<string> filesToRemove;
  68         map<string, int> barcodes;
  69         vector<string> groupVector;
  70         map<string, int> primers;
  71         map<string, int> combos;
  72         map<string, int> groupToIndex;
  73         vector<string> primerNameVector;        //needed here?
  74         vector<string> barcodeNameVector;       //needed here?
  75         map<string, int> groupCounts;
  76         map<string, string> nameMap;
  77
  78         vector<int> processIDS;   //processid
  79         vector<linePair*> lines;
  80         vector<linePair*> qLines;
  81
  82         int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);
  83         int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
  84         int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
  85 };
  86
  87 #endif