1 #ifndef TRIMSEQSCOMMAND_H
2 #define TRIMSEQSCOMMAND_H
8 * Created by Pat Schloss on 6/6/09.
9 * Copyright 2009 Patrick D. Schloss. All rights reserved.
14 #include "command.hpp"
15 #include "sequence.hpp"
16 #include "qualityscores.h"
19 class TrimSeqsCommand : public Command {
21 TrimSeqsCommand(string);
24 vector<string> getRequiredParameters();
25 vector<string> getValidParameters();
26 vector<string> getRequiredFiles();
27 map<string, vector<string> > getOutputFiles() { return outputTypes; }
36 unsigned long int start;
37 unsigned long int end;
38 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
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&);
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;
56 string fastaFile, oligoFile, qFileName, groupfile, outputDir;
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;
70 vector<int> processIDS; //processid
71 vector<linePair*> lines;
72 vector<linePair*> qLines;
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>&);