From f07bf12e0d04340698aff7a36d2fee7c959ffe59 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Thu, 17 Jun 2010 12:57:40 +0000
Subject: [PATCH] made a small mod to the alignment parameters in trim.seqs

---
 makefile            | 2 +-
 trimseqscommand.cpp | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/makefile b/makefile
index 3e83112..ef5cfe7 100644
--- a/makefile
+++ b/makefile
@@ -463,7 +463,7 @@ mothur : \
 		./logsd.o\
 		./geom.o\
 		./setlogfilecommand.o\
-		-o ../Release/mothur
+		-o mothur
 
 clean : 
 		rm \
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3fd3ad1..580fc22 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -652,7 +652,7 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 						maxLength = it->first.length();
 					}
 				}
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+bdiffs+1));  
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));  
 
 			}else{ alignment = NULL; } 
 			
@@ -686,6 +686,9 @@ int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 				
 				int newStart=0;
 				int numDiff = countDiffs(oligo, temp);
+				
+//				cout << oligo << '\t' << temp << '\t' << numDiff << endl;				
+				
 				if(numDiff < minDiff){
 					minDiff = numDiff;
 					minCount = 1;
@@ -766,7 +769,7 @@ int TrimSeqsCommand::stripForward(Sequence& seq){
 						maxLength = forPrimer[i].length();
 					}
 				}
-				alignment = new NeedlemanOverlap(-2.0, 1.0, -1.0, (maxLength+pdiffs+1));  
+				alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));  
 
 			}else{ alignment = NULL; } 
 			
-- 
2.39.2