upped the optimization code for debugging from -O0 to -O3 and fixed the sigma problem...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 7f5122a66039c4dcd90c338dad078d11ce81e601..b455761ed6fdcf2e8c11a6bcbb52b1704caee464 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -25,7 +25,7 @@
 #include "nast.hpp"
 #include "nastreport.hpp"
 
-
+//test
 class AlignCommand : public Command {
        
 public:
@@ -147,7 +147,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
                
                pDataArray->count = pDataArray->end;
                
-               AlignmentDB* templateDB = new AlignmentDB(templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+               AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
                
                //moved this into driver to avoid deep copies in windows paralellized version
                Alignment* alignment;