X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=5ec6e72239d0772548ce10f584ebccb435230d25;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=2385d588fce9c4b03ac77d28203954cb3c19b028;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 2385d58..5ec6e72 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -12,24 +12,23 @@
 
 #include "command.hpp"
 
-#define SFF_MAGIC   0x2e736666 /* ".sff" */
-#define SFF_VERSION "\0\0\0\1"
 
 /**********************************************************/
 struct CommonHeader {
-	uint32_t magicNumber;
-	char* version;
-	uint64_t indexOffset;
-	uint32_t indexLength;
-	uint32_t numReads;
-	uint16_t headerLength;
-	uint16_t keyLength;
-	uint16_t numFlowsPerRead;
-	uint8_t flogramFormatCode;
-	char* flowChars; //length depends on number flow reads
-	char* keySequence; //length depends on key length
+	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(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; } 
+	~CommonHeader() { }
 };
 /**********************************************************/
 struct Header {
@@ -40,16 +39,23 @@ struct Header {
 	unsigned short clipQualRight;
 	unsigned short clipAdapterLeft;
 	unsigned short clipAdapterRight;
-	char* name; //length depends on nameLength
-
+	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;
-	char* bases;
+	string bases;
 	vector<unsigned int> qualScores;
+	
+	seqRead() { } 
+	~seqRead() { } 
 };
 /**********************************************************/
 
@@ -57,24 +63,59 @@ class SffInfoCommand : public Command {
 	
 public:
 	SffInfoCommand(string);
-	~SffInfoCommand();
-	int execute();
-	void help();
+	SffInfoCommand();
+	~SffInfoCommand(){}
 	
-private:
-	string sffFilename, outputDir;
-	vector<string> filenames, outputNames;
-	bool abort;
+	vector<string> setParameters();
+	string getCommandName()			{ return "sffinfo";					}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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()); }	
 	
-	int extractSffInfo(string, string);
-	CommonHeader* readCommonHeader(ifstream&);
-	Header* readHeader(ifstream&);
-	seqRead* readSeqData(ifstream&, int, int);
+private:
+	string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
+	vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
+	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
+	int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
+	set<string> seqNames;
+    map<string, int> barcodes;
+    map<string, int> primers;
+    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+    vector<vector<int> > numSplitReads;
+    vector<vector<string> > filehandles, filehandlesHeaders;
+    
+	//extract sff file functions
+	int extractSffInfo(string, string, string);
+	int readCommonHeader(ifstream&, CommonHeader&);
+	//int readHeader(ifstream&, Header&);
+	int readSeqData(ifstream&, seqRead&, int, Header&);
+	int decodeName(string&, string&, string&, string);
+    bool readOligos(string oligosFile);
 	
-	int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
-	int printHeader(ofstream&, Header*, bool);
-	int printSeqData(ofstream&, seqRead*, bool);
-		
+	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&);
+    int adjustCommonHeader(CommonHeader);
+    int findGroup(Header header, seqRead read, int& barcode, int& primer);
+    string reverseOligo(string oligo);
+    
+	//parsesfftxt file functions
+	int parseHeaderLineToInt(ifstream&);
+	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+	vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+	string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/