chimera.slayer fix

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index a5a0ec0ed7e35c49440b3ce0ffa0abef91ee951a..9c84429fe3cc00df92fff4e2ae358ae8553692a4 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -947,28 +947,35 @@ map<int, int> DeCalculator::trimSeqs(Sequence* query, vector<Sequence*> topMatch
                
                //save this spot if it is the farthest
                if (pos < rearPos) { rearPos = pos; }
-
-               //check to make sure that is not whole seq
-               if ((rearPos - frontPos - 1) <= 0) {  m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1);  }
-//cout << query->getName() << " front = " << frontPos << " rear = " << rearPos << endl;                
-               //trim query
-               string newAligned = query->getAligned();
-               newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
-               query->setAligned(newAligned);
-               
-               //trim topMatches
-               for (int i = 0; i < topMatches.size(); i++) {
-                       newAligned = topMatches[i]->getAligned();
-                       newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
-                       topMatches[i]->setAligned(newAligned);
-               }
                
                map<int, int> trimmedPos;
-               
-               for (int i = 0; i < newAligned.length(); i++) {
-                       trimmedPos[i] = i+frontPos;
+               //check to make sure that is not whole seq
+               if ((rearPos - frontPos - 1) <= 0) {  
+                       m->mothurOut("[ERROR]: when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine();  
+                       query->setAligned("");
+                       //trim topMatches
+                       for (int i = 0; i < topMatches.size(); i++) {
+                               topMatches[i]->setAligned("");
+                       }
+                       
+               }else {
+
+                       //trim query
+                       string newAligned = query->getAligned();
+                       newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
+                       query->setAligned(newAligned);
+                       
+                       //trim topMatches
+                       for (int i = 0; i < topMatches.size(); i++) {
+                               newAligned = topMatches[i]->getAligned();
+                               newAligned = newAligned.substr(frontPos, (rearPos-frontPos+1));
+                               topMatches[i]->setAligned(newAligned);
+                       }
+                       
+                       for (int i = 0; i < newAligned.length(); i++) {
+                               trimmedPos[i] = i+frontPos;
+                       }
                }
-               
                return trimmedPos;
        }
        catch(exception& e) {