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"
18 class TrimSeqsCommand : public Command {
20 TrimSeqsCommand(string);
23 vector<string> getRequiredParameters();
24 vector<string> getValidParameters();
25 vector<string> getRequiredFiles();
26 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 unsigned long int start;
34 unsigned long int end;
35 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
38 void getOligos(vector<string>&, vector<string>&);
39 int stripBarcode(Sequence&, QualityScores&, int&);
40 int stripForward(Sequence&, QualityScores&, int&);
41 bool stripReverse(Sequence&, QualityScores&);
42 bool cullLength(Sequence&);
43 bool cullHomoP(Sequence&);
44 bool cullAmbigs(Sequence&);
45 bool compareDNASeq(string, string);
46 int countDiffs(string, string);
47 map<string, vector<string> > outputTypes;
50 string fastaFile, oligoFile, qFileName, outputDir;
52 bool flip, allFiles, qtrim;
53 int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
54 int qWindowSize, qWindowStep;
55 double qRollAverage, qThreshold, qWindowAverage, qAverage;
56 vector<string> revPrimer, outputNames;
57 set<string> filesToRemove;
58 map<string, int> barcodes;
59 vector<string> groupVector;
60 map<string, int> primers;
61 map<string, int> combos;
63 vector<int> processIDS; //processid
64 vector<linePair*> lines;
65 vector<linePair*> qLines;
67 int driverCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>, linePair*, linePair*);
68 int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>);
69 int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);