New upstream version 1.6.3+dfsg (0f7483af) · Commits · Debian Med / iqtree

CMakeLists.txt

+4 −2

Original line number	Diff line number	Diff line
		@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE)
		# The version number.
		set (iqtree_VERSION_MAJOR 1)
		set (iqtree_VERSION_MINOR 6)
		set (iqtree_VERSION_PATCH "1")
		set (iqtree_VERSION_PATCH "3")

		set(BUILD_SHARED_LIBS OFF)

		@@ -277,7 +277,7 @@ if (NOT IQTREE_FLAGS MATCHES "single")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
		elseif (CLANG)
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp=libomp")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp=libomp -pthread")
		endif()
		else()
		message("OpenMP : NONE")
		@@ -435,6 +435,8 @@ check_function_exists (gettimeofday HAVE_GETTIMEOFDAY)
		check_function_exists (getrusage HAVE_GETRUSAGE)
		check_function_exists (GlobalMemoryStatusEx HAVE_GLOBALMEMORYSTATUSEX)
		check_function_exists (strndup HAVE_STRNDUP)
		check_function_exists (strtok_r HAVE_STRTOK_R)

		find_package(Backtrace)

		# configure a header file to pass some of the CMake settings

alignment/alignment.cpp

+31 −4

Original line number	Diff line number	Diff line
		@@ -3006,15 +3006,29 @@ void Alignment::createBootstrapAlignment(Alignment aln, IntVector pattern_freq
		outError("Unsupported bootstrap feature, pls contact the developers");
		}

		if (Params::getInstance().jackknife_prop > 0.0 && spec) {
		outError((string)"Unsupported jackknife with sampling " + spec);
		}

		IntVector site_vec;
		if (!spec) {
		// standard bootstrap
		int added_sites = 0;
		for (site = 0; site < nsite; site++) {
		int site_id = random_int(nsite);
		int site_id;
		if (Params::getInstance().jackknife_prop == 0.0) {
		// bootstrap sampling with replacement
		site_id = random_int(nsite);
		} else {
		// jacknife without replacement
		if (random_double() < Params::getInstance().jackknife_prop)
		continue;
		site_id = site;
		}
		int ptn_id = aln->getPatternID(site_id);
		Pattern pat = aln->at(ptn_id);
		int nptn = getNPattern();
		addPattern(pat, site);
		addPattern(pat, added_sites);
		if (!aln->site_state_freq.empty() && getNPattern() > nptn) {
		// a new pattern is added, copy state frequency vector
		double *state_freq = new double[num_states];
		@@ -3022,7 +3036,10 @@ void Alignment::createBootstrapAlignment(Alignment aln, IntVector pattern_freq
		site_state_freq.push_back(state_freq);
		}
		if (pattern_freq) ((*pattern_freq)[ptn_id])++;
		added_sites++;
		}
		if (added_sites < nsite)
		site_pattern.resize(added_sites);
		} else if (strncmp(spec, "GENESITE,", 9) == 0) {
		// resampling genes, then resampling sites within resampled genes
		convert_int_vec(spec+9, site_vec);
		@@ -3115,6 +3132,9 @@ void Alignment::createBootstrapAlignment(int pattern_freq, const char spec, in
		int site, nsite = getNSite();
		memset(pattern_freq, 0, getNPattern()*sizeof(int));
		IntVector site_vec;
		if (Params::getInstance().jackknife_prop > 0.0 && spec)
		outError((string)"Unsupported jackknife with " + spec);

		if (!spec \|\| strncmp(spec, "SCALE=", 6) == 0) {

		if (spec) {
		@@ -3123,10 +3143,17 @@ void Alignment::createBootstrapAlignment(int pattern_freq, const char spec, in
		}
		int nptn = getNPattern();

		if (nsite/8 < nptn) {
		if (nsite/8 < nptn \|\| Params::getInstance().jackknife_prop > 0.0) {
		int orig_nsite = getNSite();
		for (site = 0; site < nsite; site++) {
		int site_id = random_int(orig_nsite, rstream);
		int site_id;
		if (Params::getInstance().jackknife_prop == 0.0)
		site_id = random_int(orig_nsite, rstream);
		else {
		if (random_double() < Params::getInstance().jackknife_prop)
		continue;
		site_id = site;
		}
		int ptn_id = getPatternID(site_id);
		pattern_freq[ptn_id]++;
		}

alignment/superalignment.cpp

+48 −4

Original line number	Diff line number	Diff line
		@@ -679,10 +679,54 @@ Alignment *SuperAlignment::concatenateAlignments(set<int> &ids) {
		}

		Alignment *SuperAlignment::concatenateAlignments() {
		set<int> ids;
		for (int i = 0; i < partitions.size(); i++)
		ids.insert(i);
		return concatenateAlignments(ids);
		vector<SeqType> seq_types;
		vector<set<int> > ids;
		for (int i = 0; i < partitions.size(); i++) {
		bool found = false;
		for (int j = 0; j < seq_types.size(); j++)
		if (partitions[i]->seq_type == seq_types[j]) {
		ids[j].insert(i);
		found = true;
		break;
		}
		if (found)
		continue;
		// create a new partition
		seq_types.push_back(partitions[i]->seq_type);
		ids.push_back(set<int>());
		ids.back().insert(i);
		}
		if (seq_types.size() == 1)
		return concatenateAlignments(ids[0]);

		// mixed data with >= 2 partitions
		SuperAlignment *saln = new SuperAlignment();
		saln->max_num_states = 0;
		// first build taxa_index and partitions
		int site, seq, nsite = ids.size();

		// BUG FIX 2016-11-29: when merging partitions with -m TESTMERGE, sequence order is changed
		// get the taxa names from existing tree

		saln->seq_names = seq_names;
		saln->taxa_index.resize(saln->seq_names.size());
		for (auto it = saln->taxa_index.begin(); it != saln->taxa_index.end(); it++)
		it->resize(nsite, -1);

		for (site = 0; site != nsite; site++) {
		Alignment *part_aln = concatenateAlignments(ids[site]);
		saln->partitions.push_back(part_aln);
		int nseq = part_aln->getNSeq();
		//cout << "nseq = " << nseq << endl;
		for (seq = 0; seq < nseq; seq++) {
		int id = saln->getSeqID(part_aln->getSeqName(seq));
		ASSERT(id >= 0);
		saln->taxa_index[id][site] = seq;
		}
		}
		// now the patterns of sequence-genes presence/absence
		saln->buildPattern();
		return saln;
		}

		void SuperAlignment::countConstSite() {

iqtree_config.h.in

+2 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,8 @@
		/#cmakedefine HAVE_PCLOSE/
		/* does the platform provide GlobalMemoryStatusEx functions? */
		#cmakedefine HAVE_GLOBALMEMORYSTATUSEX
		#cmakedefine HAVE_STRNDUP
		#cmakedefine HAVE_STRTOK_R

		/* does the platform provide backtrace functions? */
		#cmakedefine Backtrace_FOUND

lbfgsb/lbfgsb_new.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -1031,7 +1031,7 @@ void mainlb(int n, int m, double *x,
		--ifun;
		--iback;
		}
		strcpy(task, "ERROR: ABNORMAL_TERMINATION_IN_LNSRCH");
		strcpy(task, "WARNING: ABNORMAL_TERMINATION_IN_LNSRCH");
		++iter;
		goto L999;
		} else {