X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.h;h=552f4a08bee284bf914e6a50cd51176864b8b1d8;hp=3926e25f3c2ebb484b357464d1514dfc957c4000;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 3926e25..552f4a0 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
 	string getDescription()		{ return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
 	
@@ -113,9 +114,10 @@ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		pDataArray->count = pDataArray->end;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 			
+            pDataArray->count++;
+            
 			if (pDataArray->m->control_pressed) { in.close(); outSummary.close(); pDataArray->count = 1; return 1; }
 			
 			Sequence current(in); pDataArray->m->gobble(in);