From: Pat Schloss <pschloss@umich.edu>
Date: Tue, 1 May 2012 18:00:53 +0000 (-0400)
Subject: fix rarefaction.single
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=ece154e5d02f83d0ba6bf0438e3e1f085a2920bd

fix rarefaction.single
---

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 2214c5e..e6b00ba 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -152,11 +152,11 @@ ShhherCommand::ShhherCommand(string option) {
                 string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
                 
 				//flow.files = 9 character offset
-				compositeFASTAFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+				compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
 				m->openOutputFile(compositeFASTAFileName, temp);
 				temp.close();
 				
-				compositeNamesFileName = outputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+				compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
 				m->openOutputFile(compositeNamesFileName, temp);
 				temp.close();
 			}
@@ -1769,7 +1769,7 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
         
         
         if(compositeNamesFileName != ""){
-            m->appendFiles(nameFileName, uchimecompositeNamesFileName);
+            m->appendFiles(nameFileName, compositeNamesFileName);
         }		
     }
     catch(exception& e) {
@@ -2400,8 +2400,7 @@ int ShhherCommand::getUniques(int numSeqs, int numFlowCells, vector<short>& uniq
 		}
 		uniqueFlowDataIntI.resize(numFlowCells * numUniques);
 		uniqueLengths.resize(numUniques);	
-		uniqueFlowgrams.resize(numFlowCells * numUniques);
-        
+		
 		flowDataPrI.resize(numSeqs * numFlowCells, 0);
 		for(int i=0;i<flowDataPrI.size();i++)	{	if (m->control_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);		}
         
diff --git a/uchime_src.zip b/uchime_src.zip
deleted file mode 100644
index d8678a7..0000000
Binary files a/uchime_src.zip and /dev/null differ