Merge remote-tracking branch 'mothur/master'

diff --cc shhhercommand.cpp
index 1ad0b27390421d2bf43049d398c3375786077b93,6ef9532790a5fc63905cb598f1e7bc4baa4c9871..32891c333ab5229aec50ed05ff5f03b6799d1396
--- 1/shhhercommand.cpp
--- 2/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 6a26fac949a335999be1cf7c1355f9c5c4f7d48c,0557c71bda3453068175fe3d405ff87972df80e1..86de668b4f57596bf11efb80807b18f932136551
--- 1/trimflowscommand.cpp
--- 2/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;

diff --cc trimflowscommand.h
Simple merge