From: westcott <westcott>
Date: Tue, 6 Jul 2010 13:31:58 +0000 (+0000)
Subject: rechecking in
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=c4eb056b457b3832c42fce61d1843b54ca20aa3c

rechecking in
---

diff --git a/bayesian.cpp b/bayesian.cpp
index b46f770..1726477 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -50,6 +50,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 			//create search database and names vector
 			generateDatabaseAndNames(tfile, tempFile, method, ksize, 0.0, 0.0, 0.0, 0.0);
 			
+			//prevents errors caused by creating shortcut files if you had an error in the sanity check.
+			if (m->control_pressed) {  remove(phyloTreeName.c_str());   }
+			
 			genusNodes = phyloTree->getGenusNodes(); 
 			genusTotals = phyloTree->getGenusTotals();
 			
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 9dfc8bd..b3bfd42 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -522,7 +522,7 @@ string GetOTURepCommand::findRep(vector<string> names) {
 	try{
 		// if only 1 sequence in bin or processing the "unique" label, then 
 		// the first sequence of the OTU is the representative one
-		if ((names.size() == 1) || (list->getLabel() == "unique")) {
+		if ((names.size() == 2) || (names.size() == 1) || (list->getLabel() == "unique")) {
 			return names[0];
 		}else{
 			vector<int> seqIndex(names.size());
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 71cf714..5e0a647 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -378,6 +378,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			
 			Sequence currSeq(inFASTA);
 	cout << i << '\t' << currSeq.getName() << endl;
+
 			string origSeq = currSeq.getUnaligned();
 			if (origSeq != "") {
 				int groupBar, groupPrime;