added get.dists and remove.dists commands. fixed bug in trim.seqs windows paralelliza...

[mothur.git] / pcrseqscommand.h

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index d35850ce74296fa4f4471927817becd21145dbee..c6f7ff9c7f6670073a7080496f80eac1cdfb2a72 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -26,8 +26,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pcr.seqs";    }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
        string getDescription()         { return "pcr.seqs"; }
     
@@ -131,9 +132,9 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                }
         
         set<int> lengths;
-               pDataArray->count = pDataArray->fend;
+               
                for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
-            
+            pDataArray->count++;
                        if (pDataArray->m->control_pressed) {  break; }
                        
                        Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);