New upstream version 1.40.3 (99042c86) · Commits · Debian Med / mothur

Makefile

+1 −1

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ LOGFILE_NAME ?= yes
		BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
		BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
		MOTHUR_FILES="\"Enter_your_default_path_here\""
		VERSION = "\"1.40.2\""
		VERSION = "\"1.40.3\""

		ifeq ($(strip $(64BIT_VERSION)),yes)
		CXXFLAGS += -DBIT_VERSION

Mothur.xcodeproj/project.pbxproj

+8 −8

Original line number	Diff line number	Diff line
		@@ -3685,10 +3685,10 @@
		GCC_C_LANGUAGE_STANDARD = "compiler-default";
		GCC_DYNAMIC_NO_PIC = NO;
		GCC_MODEL_TUNING = G5;
		GCC_OPTIMIZATION_LEVEL = 0;
		GCC_OPTIMIZATION_LEVEL = 3;
		GCC_PREPROCESSOR_DEFINITIONS = (
		"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
		"VERSION=\"\\\"1.40.0\\\"\"",
		"VERSION=\"\\\"1.40.3\\\"\"",
		"LOGFILE_NAME=\"\\\"silent\\\"\"",
		);
		GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
		@@ -3718,10 +3718,10 @@
		DSTROOT = TARGET_BUILD_DIR;
		GCC_C_LANGUAGE_STANDARD = "compiler-default";
		GCC_MODEL_TUNING = G5;
		GCC_OPTIMIZATION_LEVEL = 0;
		GCC_OPTIMIZATION_LEVEL = 3;
		GCC_PREPROCESSOR_DEFINITIONS = (
		"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
		"VERSION=\"\\\"1.40.0\\\"\"",
		"VERSION=\"\\\"1.40.3\\\"\"",
		"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
		);
		GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
		@@ -3761,10 +3761,10 @@
		GCC_ENABLE_SSE41_EXTENSIONS = NO;
		GCC_ENABLE_SSE42_EXTENSIONS = NO;
		GCC_NO_COMMON_BLOCKS = YES;
		GCC_OPTIMIZATION_LEVEL = 0;
		GCC_OPTIMIZATION_LEVEL = 3;
		GCC_PREPROCESSOR_DEFINITIONS = (
		"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
		"VERSION=\"\\\"1.39.5\\\"\"",
		"VERSION=\"\\\"1.40.3\\\"\"",
		"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
		);
		GCC_VERSION = "";
		@@ -3828,9 +3828,9 @@
		GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
		GCC_MODEL_TUNING = "";
		GCC_NO_COMMON_BLOCKS = YES;
		GCC_OPTIMIZATION_LEVEL = 0;
		GCC_OPTIMIZATION_LEVEL = 3;
		GCC_PREPROCESSOR_DEFINITIONS = (
		"VERSION=\"\\\"1.39.5\\\"\"",
		"VERSION=\"\\\"1.40.3\\\"\"",
		"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
		"LOGFILE_NAME=\"\\\"./mothur.logfile\\\"\"",
		);

makefile-internal

+1 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		USEREADLINE ?= no
		USEBOOST ?= no
		LOGFILE_NAME ?= yes
		VERSION = "\"1.39.5\""
		VERSION = "\"1.40.3\""

		# Optimize to level 3:
		CXXFLAGS += -O3 -std=c++11

source/averagelinkage.cpp

100644 → 100755

+0 −0

File mode changed from 100644 to 100755.

View file

source/calcsparcc.cpp

100644 → 100755

+43 −47

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ CalcSparcc::CalcSparcc(vector<vector<float> > sharedVector, int maxIterations, i
		// unsigned long long cycTimeStart = time(NULL);

		for(int i=0;i<numSamplings;i++){

		if (m->getControl_pressed()) { break; }
		vector<float> logFractions = getLogFractions(sharedVector, method);
		getT_Matrix(logFractions); //this step is slow...
		@@ -61,7 +62,6 @@ CalcSparcc::CalcSparcc(vector<vector<float> > sharedVector, int maxIterations, i
		median = allCorrelations[0];
		}
		}
		// cout << median[0][3] << '\t' << median[0][6] << endl;
		}
		catch(exception& e) {
		m->errorOut(e, "CalcSparcc", "CalcSparcc");
		@@ -84,9 +84,7 @@ void CalcSparcc::addPseudoCount(vector<vector<float> >& sharedVector){
		m->errorOut(e, "CalcSparcc", "addPseudoCount");
		exit(1);
		}

		}

		/**************************************************************************************************/

		vector<float> CalcSparcc::getLogFractions(vector<vector<float> > sharedVector, string method){ //dirichlet by default
		@@ -97,7 +95,7 @@ vector<float> CalcSparcc::getLogFractions(vector<vector<float> > sharedVector, s
		vector<float> alphas(numGroups);
		for(int i=0;i<numGroups;i++){ //iterate across the groups
		if (m->getControl_pressed()) { return logSharedFractions; }
		alphas = RNG.randomDirichlet(sharedVector[i]);
		alphas = util.randomDirichlet(sharedVector[i]);

		for(int j=0;j<numOTUs;j++){
		logSharedFractions[i * numOTUs + j] = alphas[j];
		@@ -137,7 +135,6 @@ void CalcSparcc::getT_Matrix(vector<float> sharedFractions){
		tMatrix.resize(numOTUs * numOTUs, 0);

		vector<float> diff(numGroups);

		for(int j1=0;j1<numOTUs;j1++){
		for(int j2=0;j2<j1;j2++){
		if (m->getControl_pressed()) { return; }
		@@ -146,8 +143,8 @@ void CalcSparcc::getT_Matrix(vector<float> sharedFractions){
		diff[i] = sharedFractions[i * numOTUs + j1] - sharedFractions[i * numOTUs + j2];
		mean += diff[i];
		}
		mean /= float(numGroups);

		mean /= float(numGroups);
		float variance = 0.0;
		for(int i=0;i<numGroups;i++){
		variance += (diff[i] - mean) * (diff[i] - mean);
		@@ -247,7 +244,6 @@ vector<vector<float> > CalcSparcc::getBasisCorrelations(vector<float> basisVaria
		else if(rho[i][j] < -1.0) { rho[i][j] = -1.0; }

		rho[j][i] = rho[i][j];

		}
		}