X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.h;h=cc904ec7f246aed91970b41cf52e39b7d32b896b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=e467df11c99d735a482328c7dbe64aa623192a95;hpb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;p=mothur.git

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index e467df1..cc904ec 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
+#include "referencedb.h"
 
 struct Compare {
 	int AA, AT, AG, AC,	TA, TT, TG, TC,	GA, GT, GG, GC,	CA, CT, CG, CC,	NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
@@ -58,11 +59,12 @@ public:
 	
 private:
 	bool abort;
+	ReferenceDB* rdb;
 	
 	struct linePair {
-		unsigned long int start;
-		unsigned long int end;
-		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
 	};
 	
 	vector<int> processIDS;   //processid
@@ -80,13 +82,13 @@ private:
 	void printErrorQuality(map<char, vector<int> >);
 	void printQualityFR(vector<vector<int> >, vector<vector<int> >);
 	
-	int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+	int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
 	int driver(string, string, string, string, string, string, linePair, linePair, linePair);
 	int createProcesses(string, string, string, string, string, string);
 
 	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
 	double threshold;
-	bool ignoreChimeras;
+	bool ignoreChimeras, save;
 	int numRefs, processors;
 	int maxLength, totalBases, totalMatches;
 	//ofstream errorSummaryFile, errorSeqFile;