X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=prcseqscommand.cpp;h=f2ca9db29d7a94ce0d22606d4ad114e11001fd4f;hb=9bbd9b071066b7b11c1ab95aa01942abc933e0fb;hp=5fa71bef6b3474cc516491044c41729a318d449f;hpb=7f1aca4ed9e6db70de82e80ca4771f7680b21d26;p=mothur.git

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 5fa71be..f2ca9db 100644
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -696,10 +696,10 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
 #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"); 	}
 		
         badFile.close();
 		goodFile.close();
@@ -804,7 +804,7 @@ bool PcrSeqsCommand::readOligos(){
 					// get rest of line in case there is a primer name
 					while (!inOligos.eof())	{	
                         char c = inOligos.get(); 
-                        if (c == 10 || c == 13){	break;	} 
+                        if (c == 10 || c == 13 || c == -1){	break;	}
                         else if (c == 32 || c == 9){;} //space or tab
 					} 
 					primers[oligo] = primerCount; primerCount++;
@@ -1088,7 +1088,7 @@ int PcrSeqsCommand::readCount(set<string> badSeqNames){
         //check for groups that have been eliminated
         CountTable ct;
         if (ct.testGroups(goodCountFile)) {
-            ct.readTable(goodCountFile);
+            ct.readTable(goodCountFile, true);
             ct.printTable(goodCountFile);
         }