From: Pat Schloss <pschloss@umich.edu>
Date: Wed, 4 Apr 2012 19:20:08 +0000 (-0400)
Subject: Pat's testing
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=5d4c0969086285e4aaec2bac1078be0113d0614e

Pat's testing
---

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5378211..1ad0b27 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -386,6 +386,8 @@ int ShhherCommand::execute(){
 				
 				if (m->control_pressed) { break; }
 				
+                
+                
 				getOTUData(listFileName);
 
 				m->mothurRemove(distFileName);
@@ -398,6 +400,7 @@ int ShhherCommand::execute(){
 
 				if (m->control_pressed) { break; }
 				
+            
 				for(int i=1;i<ncpus;i++){
 					MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 					MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
@@ -1111,7 +1114,8 @@ void ShhherCommand::getUniques(){
 		}
 		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]);		}
 	}
@@ -1368,7 +1372,7 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
 		NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
 		clusterNameMap->readMap();
 		read->read(clusterNameMap);
-		
+        
 		ListVector* list = read->getListVector();
 		SparseMatrix* matrix = read->getMatrix();
 		
diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 77dacfe..6a26fac 100644
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -198,6 +198,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
 			numFPrimers = 0;
 			numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
 		}
 		
 	}
@@ -382,7 +384,6 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
 		
 		while(moreSeqs) {
 			//cout << "driver " << count << endl;
-			
 	
 			if (m->control_pressed) { break; }