From e9a9b24f05e69ab94bf89a423f782e6a50462bba Mon Sep 17 00:00:00 2001
From: Pat Schloss <pschloss@umich.edu>
Date: Wed, 17 Jul 2013 14:51:48 -0400
Subject: [PATCH] fixed problem where order=B was not checking for the maximum
 homopolymer length

---
 flowdata.cpp         | 21 +++++++++++++++++++++
 flowdata.h           |  2 ++
 trimflowscommand.cpp |  6 +++++-
 3 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/flowdata.cpp b/flowdata.cpp
index 66261e3..7d61f8c 100644
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -190,6 +190,27 @@ void FlowData::capFlows(int mF){
 
 //**********************************************************************************************************************
 
+bool FlowData::hasGoodHomoP(){
+	
+	try{
+        
+        float maxIntensity = (float) maxHomoP + 0.49;
+
+        for(int i=0;i<endFlow;i++){
+            if(flowData[i] > maxIntensity){
+                return 0;
+            }
+        }
+		return 1;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "FlowData", "hasMinFlows");
+		exit(1);
+	}
+}
+
+//**********************************************************************************************************************
+
 bool FlowData::hasMinFlows(int minFlows){
 	
 	try{
diff --git a/flowdata.h b/flowdata.h
index c7fd08a..cfe349c 100644
--- a/flowdata.h
+++ b/flowdata.h
@@ -24,6 +24,8 @@ public:
 	string getName();
 	void capFlows(int);
 	bool hasMinFlows(int);
+    bool hasGoodHomoP();
+
 	Sequence getSequence();
 
 	void printFlows(ofstream&);
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;
 			
-- 
2.39.2