made a small mod to the alignment parameters in trim.seqs

diff --git a/makefile b/makefile
index 3e831124a7cc7a026dcad63df44da4a0674d186b..ef5cfe7ebb9550c5b5fa275e128f1ff013585e33 100644 (file)
--- a/makefile
+++ b/makefile
@@ -463,7 +463,7 @@ mothur : \
                ./logsd.o\\r
                ./geom.o\\r
                ./setlogfilecommand.o\\r
-               -o ../Release/mothur\r
+               -o mothur\r
 \r
 clean : \r
                rm \\r

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 3fd3ad1d8376125c5d2f85b6cf66078f0c083f2f..580fc22c978e0105b464e214593599fe15970f1d 100644 (file)
--- 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; }