From 36cea83f926066127bf856e7eae1a70ce7e796d0 Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Tue, 27 Mar 2012 13:29:29 -0400
Subject: [PATCH] initialized numLinkers and numSpacers in trim.seqs and
 trim.flows

---
 trimflowscommand.cpp | 2 ++
 trimseqscommand.cpp  | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index f2d592a..346902c 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -207,6 +207,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
 			numFPrimers = 0;
 			numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
 		}
 		
 	}
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 5d4eb39..f00743c 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -329,6 +329,8 @@ int TrimSeqsCommand::execute(){
 		
 		numFPrimers = 0;  //this needs to be initialized
 		numRPrimers = 0;
+        numSpacers = 0;
+        numLinkers = 0;
 		createGroup = false;
 		vector<vector<string> > fastaFileNames;
 		vector<vector<string> > qualFileNames;
-- 
2.39.2