Merge remote-tracking branch 'mothur/master'

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 978ff0b00b666fb5ca4397c94ccc17148d9b3f31..2e61594d5719fa20176872c5c35140882901a649 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2297,7 +2297,7 @@
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = Mothur;
                                SDKROOT = macosx10.6;

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 518e78d6386521dcb4ef57700c1ffb903ae02a13..72504196039c9f337f8051ecdf54a4af1eed5c90 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -161,7 +161,8 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
                        
                        string temp     = validParameter.validFile(parameters, "sigma", false);         if(temp == "not found"){        temp = "0.01"; }
                        m->mothurConvert(temp, sigma); 
-                       
+                       sigma = 1/sigma;
+            
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
                        m->mothurConvert(temp, processors);