added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index b0fa7a0a2e2f1dbe733207686ec5ed8647ba888e..5d4eb39d16f3bdc575a3ee41125705c90da9824f 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1243,9 +1243,10 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        primerNameVector.push_back(group);
                                }
                                else if(type == "REVERSE"){
-                                       Sequence oligoRC("reverse", oligo);
-                                       oligoRC.reverseComplement();
-                                       revPrimer.push_back(oligoRC.getUnaligned());
+                                       //Sequence oligoRC("reverse", oligo);
+                                       //oligoRC.reverseComplement();
+                    string oligoRC = reverseOligo(oligo);
+                                       revPrimer.push_back(oligoRC);
                                }
                                else if(type == "BARCODE"){
                                        inOligos >> group;
@@ -1468,6 +1469,46 @@ bool TrimSeqsCommand::cullHomoP(Sequence& seq){
        }
        
 }
+//********************************************************************/
+string TrimSeqsCommand::reverseOligo(string oligo){
+       try {
+        string reverse = "";
+        
+        for(int i=oligo.length()-1;i>=0;i--){
+            
+            if(oligo[i] == 'A')                {       reverse += 'T'; }
+            else if(oligo[i] == 'T'){  reverse += 'A'; }
+            else if(oligo[i] == 'U'){  reverse += 'A'; }
+            
+            else if(oligo[i] == 'G'){  reverse += 'C'; }
+            else if(oligo[i] == 'C'){  reverse += 'G'; }
+            
+            else if(oligo[i] == 'R'){  reverse += 'Y'; }
+            else if(oligo[i] == 'Y'){  reverse += 'R'; }
+            
+            else if(oligo[i] == 'M'){  reverse += 'K'; }
+            else if(oligo[i] == 'K'){  reverse += 'M'; }
+            
+            else if(oligo[i] == 'W'){  reverse += 'W'; }
+            else if(oligo[i] == 'S'){  reverse += 'S'; }
+            
+            else if(oligo[i] == 'B'){  reverse += 'V'; }
+            else if(oligo[i] == 'V'){  reverse += 'B'; }
+            
+            else if(oligo[i] == 'D'){  reverse += 'H'; }
+            else if(oligo[i] == 'H'){  reverse += 'D'; }
+            
+            else                                               {       reverse += 'N'; }
+        }
+        
+        
+        return reverse;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
+               exit(1);
+       }
+}
 
 //***************************************************************************************************************