From: Pat Schloss <pschloss@umich.edu>
Date: Fri, 3 Feb 2012 16:16:33 +0000 (-0500)
Subject: upped the optimization code for debugging from -O0 to -O3 and fixed the sigma problem... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=2a1b3d95377f9b52ba1ec019d836e98b4fed323e

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 545f7b3..df21610 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2291,7 +2291,7 @@
 				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 518e78d..7250419 100644
--- 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);