pat's edits from 1/26/2010

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index a6950aca22d383fdba9dde8d719d0430e62e32d4..b185da0905321c7980f2237a9d938bd260d9397d 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -301,7 +301,9 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
                                        forPrimer.push_back(oligo);
                                }
                                else if(type == "reverse"){
-                                       revPrimer.push_back(oligo);
+                                       Sequence oligoRC("reverse", oligo);
+                                       oligoRC.reverseComplement();
+                                       revPrimer.push_back(oligoRC.getUnaligned());
                                }
                                else if(type == "barcode"){
                                        inOligos >> group;
@@ -406,7 +408,7 @@ bool TrimSeqsCommand::stripReverse(Sequence& seq){
                        }
                        
                        if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
-                               seq.setUnaligned(rawSequence.substr(rawSequence.length()-oligo.length()));
+                               seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
                                success = 1;
                                break;
                        }