a few meaningless changes that are commented out

diff --git a/bayesian.cpp b/bayesian.cpp
index df83cde86fa61b87b5498c0eb35569a92bb9bef4..9ae0777912ba21ad231540eed5658c09298b4ece 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -357,7 +357,7 @@ int Bayesian::getMostProbableTaxonomy(vector<int> queryKmer) {
                                maxProbability = prob;
                        }
                }
-
+//             cout << phyloTree->get(indexofGenus).name << '\t' << maxProbability << endl;
                return indexofGenus;
        }
        catch(exception& e) {

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 15bf954f301b3585cbb595f28832d316842b199e..2e897988a6d5538dbf7ef4e0ebd26564aa174fd8 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -321,7 +321,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
                        trim = m->isTrue(temp); 
                        
-                       temp = validParameter.validFile(parameters, "split", false);                            if (temp == "not found") { temp = "f"; }
+                       temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
                        trimera = m->isTrue(temp); 
                        
                        search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }

diff --git a/decalc.cpp b/decalc.cpp
index 9894adbda2aab2f4ddac2b786c69bffc8778335f..0b9f466a55e3e42175260468713d34702d8d2831 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -952,7 +952,6 @@ map<int, int> DeCalculator::trimSeqs(Sequence* query, vector<Sequence*> topMatch
                map<int, int> trimmedPos;
                //check to make sure that is not whole seq
                if ((rearPos - frontPos - 1) <= 0) {  
-                       //m->mothurOut("[ERROR]: when I trim " + query->getName() + ", the entire sequence is trimmed. Skipping."); m->mothurOutEndLine();  
                        query->setAligned("");
                        //trim topMatches
                        for (int i = 0; i < topMatches.size(); i++) {