X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summaryqualcommand.h;h=b9edc5148ca5f7a834433815204b40f9ea317db4;hp=ac65938bc23075fc7db7cb40b9ce6d05d0d5d64e;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index ac65938..b9edc51 100644
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.qual";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
 	string getDescription()		{ return "summarize the quality of a set of sequences"; }
 	
@@ -65,7 +66,7 @@ struct seqSumQualData {
 	string filename; 
 	unsigned long long start;
 	unsigned long long end;
-	int count;
+	int count, numSeqs;
 	MothurOut* m;
     bool hasNameMap;
 	map<string, int> nameMap;
@@ -100,7 +101,8 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		int count = 0;
+		pDataArray->count = 0;
+        pDataArray->numSeqs = 0;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 				
 			if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
@@ -137,11 +139,11 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 					else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
 				}
 				
-				count += num;
+				pDataArray->numSeqs += num;
+                pDataArray->count++;
 			}
 		}
 		
-		pDataArray->count = count;
 		in.close();
 		
 		return 0;