From 92de7f976371d41441ad41f02ca83af8b43cef5c Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Fri, 8 Apr 2011 17:45:10 +0000
Subject: [PATCH] a few meaningless changes that are commented out

---
 bayesian.cpp             | 2 +-
 chimeraslayercommand.cpp | 2 +-
 decalc.cpp               | 1 -
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/bayesian.cpp b/bayesian.cpp
index df83cde..9ae0777 100644
--- 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 15bf954..2e89798 100644
--- 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 9894adb..0b9f466 100644
--- 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++) {
-- 
2.39.2