X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=d2fbe935356a2f0752efa683a893a5892e1b2eb2;hp=033fbcad422abb62cd2470866bd4666db9e907bd;hb=c48d91112209b841444923670dca5454da0e2a4d;hpb=b0997605981902442138b9309e9c43d95c3ba10a

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 033fbca..d2fbe93 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -294,7 +294,8 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
             
             summaryfile = validParameter.validFile(parameters, "summary", true);
 			if (summaryfile == "not open") { summaryfile = ""; abort = true; }
-			else if (summaryfile == "not found") { summaryfile = "";  }	
+			else if (summaryfile == "not found") { summaryfile = "";  }
+            else { m->setSummaryFile(summaryfile); }
             
             if ((namefile != "") && (countfile != "")) {
                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
@@ -2408,10 +2409,10 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
 			#endif
 			
 			//report progress
-			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 		}
 		}
 		//report progress
-		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n"); 	}
 		
 			
 		goodFile.close();
@@ -2503,7 +2504,7 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
 			}
 			
 			//report progress
-			if((i) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();		}
+			if((i) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n"); 		}
 		}
 				
 		return 1;