X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=1909e2d43e6d83b3d48ef06922b2d369a0e104d5;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=abfaa4b8a088713278a9384c08909f9eaaad70d2;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index abfaa4b..1909e2d 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -11,13 +11,13 @@
  */
 
 #include "command.hpp"
-
+#include "groupmap.h"
 
 /**********************************************************/
 struct CommonHeader {
 	unsigned int magicNumber;
 	string version;
-	unsigned long int indexOffset;
+	unsigned long long indexOffset;
 	unsigned int indexLength;
 	unsigned int numReads;
 	unsigned short headerLength;
@@ -69,25 +69,37 @@ public:
 	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()); }	
 	
 private:
-	string sffFilename, sfftxtFilename, outputDir, accnosName;
-	vector<string> filenames, outputNames, accnosFileNames;
-	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
-	int mycount;
+	string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile, groupfile;
+	vector<string> filenames, outputNames, accnosFileNames, oligosFileNames, groupFileNames;
+	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos, hasGroup;
+	int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, numNoMatch;
 	set<string> seqNames;
-	
+    map<string, int> barcodes;
+    map<string, int> primers;
+    GroupMap* groupMap;
+    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+    vector<vector<int> > numSplitReads;
+    vector<vector<string> > filehandles;
+    vector<vector<string> > filehandlesHeaders;
+    
 	//extract sff file functions
-	int extractSffInfo(string, string);
+	int extractSffInfo(string, string, string);
 	int readCommonHeader(ifstream&, CommonHeader&);
 	int readHeader(ifstream&, Header&);
-	int readSeqData(ifstream&, seqRead&, int, int);
+	bool readSeqData(ifstream&, seqRead&, int, Header&);
 	int decodeName(string&, string&, string&, string);
+    bool readOligos(string oligosFile);
+    bool readGroup(string oligosFile);
 	
 	int printCommonHeader(ofstream&, CommonHeader&); 
 	int printHeader(ofstream&, Header&);
@@ -97,7 +109,12 @@ private:
 	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);
+    int findGroup(Header header, seqRead read, int& barcode, int& primer, string);
+    string reverseOligo(string oligo);
+    
 	//parsesfftxt file functions
 	int parseHeaderLineToInt(ifstream&);
 	vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);