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[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
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+#ifndef SFFINFOCOMMAND_H
+#define SFFINFOCOMMAND_H
+
+/*
+ *  sffinfocommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 7/7/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+
+/**********************************************************/
+struct CommonHeader {
+       unsigned int magicNumber;
+       string version;
+       unsigned long long indexOffset;
+       unsigned int indexLength;
+       unsigned int numReads;
+       unsigned short headerLength;
+       unsigned short keyLength;
+       unsigned short numFlowsPerRead;
+       int flogramFormatCode;
+       string flowChars; //length depends on number flow reads
+       string keySequence; //length depends on key length
+       
+       CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; } 
+       ~CommonHeader() { }
+};
+/**********************************************************/
+struct Header {
+       unsigned short headerLength;
+       unsigned short nameLength;
+       unsigned int numBases;
+       unsigned short clipQualLeft;
+       unsigned short clipQualRight;
+       unsigned short clipAdapterLeft;
+       unsigned short clipAdapterRight;
+       string name; //length depends on nameLength
+       string timestamp;
+       string region;
+       string xy;
+       
+       Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+       ~Header() { } 
+};
+/**********************************************************/
+struct seqRead {
+       vector<unsigned short> flowgram;
+       vector<unsigned int> flowIndex;
+       string bases;
+       vector<unsigned int> qualScores;
+       
+       seqRead() { } 
+       ~seqRead() { } 
+};
+/**********************************************************/
+
+class SffInfoCommand : public Command {
+       
+public:
+       SffInfoCommand(string);
+       SffInfoCommand();
+       ~SffInfoCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "sffinfo";                                     }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+       string getDescription()         { return "extract sequences reads from a .sff file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       string sffFilename, sfftxtFilename, outputDir, accnosName;
+       vector<string> filenames, outputNames, accnosFileNames;
+       bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
+       int mycount;
+       set<string> seqNames;
+    
+       //extract sff file functions
+       int extractSffInfo(string, string);
+       int readCommonHeader(ifstream&, CommonHeader&);
+       int readHeader(ifstream&, Header&);
+       int readSeqData(ifstream&, seqRead&, int, int);
+       int decodeName(string&, string&, string&, string);
+       
+       int printCommonHeader(ofstream&, CommonHeader&); 
+       int printHeader(ofstream&, Header&);
+       int printSffTxtSeqData(ofstream&, seqRead&, Header&);
+       int printFlowSeqData(ofstream&, seqRead&, Header&);
+       int printFastaSeqData(ofstream&, seqRead&, Header&);
+       int printQualSeqData(ofstream&, seqRead&, Header&);
+       int readAccnosFile(string);
+       int parseSffTxt();
+       bool sanityCheck(Header&, seqRead&);
+    
+       //parsesfftxt file functions
+       int parseHeaderLineToInt(ifstream&);
+       vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+       vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+       string parseHeaderLineToString(ifstream&);
+};
+
+/**********************************************************/
+ 
+#endif
+
+