X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=2c9399bda1dd363d04c1fed89ff9b12ea8c3aace;hb=37b23ba7d98eca13d02cde8d3b1ad08ac92fefb9;hp=e82d1f6600e0b83f79154634ddfbda43d7542d91;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index e82d1f6..2c9399b 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -184,9 +184,6 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			string temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
 			all = m->isTrue(temp);
 			
-			temp = validParameter.validFile(parameters, "distance", false);					if (temp == "not found") { temp = "false"; }
-			createPhylip = m->isTrue(temp);
-			
             temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
 			m->mothurConvert(temp, iters); 
             
@@ -204,6 +201,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             
             if (subsample == false) { iters = 0; }
             
+            temp = validParameter.validFile(parameters, "distance", false);					if (temp == "not found") { temp = "false"; }
+			createPhylip = m->isTrue(temp);
+            if (subsample) { createPhylip = true; }
+            
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
 			m->mothurConvert(temp, processors); 
@@ -703,7 +704,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 vector<summarySharedData*> pDataArray; 
                 DWORD   dwThreadIdArray[processors-1];
-                HANDLE  hThreadArray[processors-1]; 
+                HANDLE  hThreadArray[processors-1];
                 
                 //Create processor worker threads.
                 for( int i=1; i<processors; i++ ){
@@ -716,6 +717,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                         temp->setGroup(thisLookup[k]->getGroup());
                         newLookup.push_back(temp);
                     }
+                
                     
                     //for each bin
                     for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {