X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.cpp;h=2a163516952c27f8a3dc7411536023f69e1f5b08;hp=aebb16b42a6455693b7c491f83b1740c58acd0e0;hb=615301e57c25e241356a9c2380648d117709458d;hpb=ac663461b19ad1436a06aa63f97221d1ff105482

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b..2a16351 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -435,7 +435,11 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 				success = 0;
 				trashCode += 'l';
 			}
-			
+            if(!flowData.hasGoodHomoP()){	//screen to see if sequence meets the maximum homopolymer limit
+				success = 0;
+				trashCode += 'h';
+			}
+
 			int primerIndex = 0;
 			int barcodeIndex = 0;