sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 3926e25f3c2ebb484b357464d1514dfc957c4000..552f4a08bee284bf914e6a50cd51176864b8b1d8 100644 (file)
--- 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);