working on sra and get.mimarkspackage commands. added file parameter to cluster...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index c3bd3933836c3f67149a96b9dba1661978b31bc4..2f6f5bbb4f99fbdf712cf5830e7e80e066d977d7 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -308,7 +308,6 @@ int ParseFastaQCommand::execute(){
                 }
                 //report progress
                 if((count+1) % 10000 == 0){    m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
-                if(count > 100000){    break;  }
                 count++;
                        }
                }
@@ -503,6 +502,26 @@ int ParseFastaQCommand::findGroup(fastqRead2 thisRead, int& barcode, int& primer
             if(!success)                               {       trashCode += 'r';       }
         }
         
+        if (trashCode.length() == 0) { //is this sequence in the ignore group
+            string thisGroup = "";
+            
+            if(barcodes.size() != 0){
+                thisGroup = barcodeNameVector[barcode];
+                if (numPrimers != 0) {
+                    if (primerNameVector[primer] != "") {
+                        if(thisGroup != "") {
+                            thisGroup += "." + primerNameVector[primer];
+                        }else {
+                            thisGroup = primerNameVector[primer];
+                        }
+                    }
+                }
+            }
+            
+            int pos = thisGroup.find("ignore");
+            if (pos != string::npos) {  trashCode += "i"; }
+        }
+
         
         return trashCode.length();
     }