fixed problem where order=B was not checking for the maximum homopolymer length

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index aebb16b42a6455693b7c491f83b1740c58acd0e0..2a163516952c27f8a3dc7411536023f69e1f5b08 100644 (file)
--- 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;