fixes while testing

diff --git a/classify.cpp b/classify.cpp
index 22728eb7a3ee52a57926e5457a33d73c9a1d7d07..2eb3ec1f800654ddd7e28cd8c72b2c5e996774d3 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -138,7 +138,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                }else if ((method == "kmer") && (!needToGenerate)) {    
                        ifstream kmerFileTest(kmerDBName.c_str());
                        database->readKmerDB(kmerFileTest);     
-                       
+               
                        ifstream fastaFile;
                        openInputFile(tempFile, fastaFile);
                        
@@ -150,7 +150,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        }
                        fastaFile.close();
                }
-#endif         
+#endif 
+       
                database->setNumSeqs(names.size());
                
                //sanity check

diff --git a/phylotree.cpp b/phylotree.cpp
index 1c2deba8a303edd692470dd1deb8c4e60062ac15..53492cafe6f17fbc2b167c8393dda6c24c72ea55 100644 (file)
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -598,7 +598,7 @@ bool PhyloTree::ErrorCheck(vector<string> templateFileNames){
                for (int i = 0; i < templateFileNames.size(); i++) {
                        itFind = taxonomyFileNames.find(templateFileNames[i]);
                        
-                       if (itFind != name2Taxonomy.end()) { //found it so erase it
+                       if (itFind != taxonomyFileNames.end()) { //found it so erase it
                                taxonomyFileNames.erase(itFind);
                        }else {
                                m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index f86891bde47d6817a3d65651b989f24c7533ea30..df085b4d05954517e904d4bbf1993bc2b687a026 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -20,7 +20,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"name","group","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //"list",
+                       string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);