X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffinfocommand.h;h=1909e2d43e6d83b3d48ef06922b2d369a0e104d5;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=541c8bad0b262af72b7637629806643bf6991b78;hpb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;p=mothur.git

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 541c8ba..1909e2d 100644
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -11,7 +11,7 @@
  */
 
 #include "command.hpp"
-
+#include "groupmap.h"
 
 /**********************************************************/
 struct CommonHeader {
@@ -79,17 +79,18 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
-	vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
-	bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
+	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<map<string, ofstream*> > > filehandles;
-    vector<vector<map<string, ofstream*> > > filehandlesHeaders;
+    vector<vector<string> > filehandles;
+    vector<vector<string> > filehandlesHeaders;
     
 	//extract sff file functions
 	int extractSffInfo(string, string, string);
@@ -98,6 +99,7 @@ private:
 	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&);
@@ -110,6 +112,7 @@ private:
 	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