rechecking in

diff --git a/bayesian.cpp b/bayesian.cpp
index b46f7703a971b8b5141d42faf14e26d45037cba0..17264776740a0e2f7e1ad2a797118bdb389be817 100644 (file)
--- 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 9dfc8bdeadc83c9784a42c10d66b26efcd52e8d4..b3bfd42369297c2caf5441ce56f65594cfa7c68e 100644 (file)
--- 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 71cf7143c55392208523c390cfb3924304eeede9..5e0a6471010f6d66dafa82037adac1fdb5ab518a 100644 (file)
--- 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;