X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.cpp;h=34caf654124886f9cd23638a149b2b3487ca53e2;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=7505ae66e453fff787d807117ed2e026f658e6a0;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 7505ae6..34caf65 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -201,7 +201,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			else { distfile = fastafile;  splitmethod = "fasta";  m->setFastaFile(fastafile); }
 			
 			taxFile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxFile == "not open") { abort = true; }	
+			if (taxFile == "not open") { taxFile = ""; abort = true; }	
 			else if (taxFile == "not found") { taxFile = ""; }
 			else {  m->setTaxonomyFile(taxFile); }
 			
@@ -264,7 +264,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
@@ -274,7 +274,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "splitmethod", false);	
 			if (splitmethod != "fasta") {
@@ -283,11 +283,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			}
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { temp = "0.25"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "taxlevel", false);		if (temp == "not found")  { temp = "3"; }
-			convert(temp, taxLevelCutoff); 
+			m->mothurConvert(temp, taxLevelCutoff); 
 			
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found") { method = "average"; }