From: Pat Schloss <pschloss@umich.edu>
Date: Wed, 4 Apr 2012 19:26:37 +0000 (-0400)
Subject: Merge remote-tracking branch 'mothur/master'
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=91a27e0483827c06c21c4fe89558923bbfe86573

Merge remote-tracking branch 'mothur/master'
---

91a27e0483827c06c21c4fe89558923bbfe86573
diff --cc shhhercommand.cpp
index 1ad0b27,6ef9532..32891c3
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@@ -1114,10 -2400,11 +2403,12 @@@ int ShhherCommand::getUniques(int numSe
  		}
  		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]);		}
+         
+         return numUniques;
  	}
  	catch(exception& e) {
  		m->errorOut(e, "ShhherCommand", "getUniques");
diff --cc trimflowscommand.cpp
index 6a26fac,0557c71..86de668
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@@ -380,11 -389,10 +389,11 @@@ int TrimFlowsCommand::driverCreateTrim(
  		int count = 0;
  		bool moreSeqs = 1;
  		
- 		TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
+ 		TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
  		
  		while(moreSeqs) {
 -				
 +			//cout << "driver " << count << endl;
 +	
  			if (m->control_pressed) { break; }
  			
  			int success = 1;