1 #ifndef PARSESFFCOMMAND_H
2 #define PARSESFFCOMMAND_H
8 * Created by Pat Schloss on 2/6/10.
9 * Copyright 2010 Patrick D. Schloss. All rights reserved.
14 #include "command.hpp"
16 class ParseSFFCommand : public Command {
18 ParseSFFCommand(string);
21 vector<string> getRequiredParameters();
22 vector<string> getValidParameters();
23 vector<string> getRequiredFiles();
24 map<string, vector<string> > getOutputFiles() { return outputTypes; }
30 int parseHeaderLineToInt(ifstream&);
31 vector<float> parseHeaderLineToFloatVector(ifstream&, int);
32 vector<int> parseHeaderLineToIntVector(ifstream&, int);
33 string parseHeaderLineToString(ifstream&);
34 void screenFlow(vector<float>, int&);
35 string flow2seq(vector<float>, int);
36 bool screenSeq(string&, int&);
37 bool compareDNASeq(string, string);
38 void getOligos(vector<ofstream*>&);
45 int numFPrimers, numRPrimers, numBarcodes;
46 vector<string> forPrimer, revPrimer;
47 map<string, int> barcodes;
48 vector<string> groupVector;
49 vector<string> outputNames;
50 map<string, vector<string> > outputTypes;
52 // string stripSeqQual(string, int, int);
53 // string stripQualQual(string, int, int);