CMakeLists.txt

@@ -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 "8")
+set (iqtree_VERSION_PATCH "9")
 
 set(BUILD_SHARED_LIBS OFF)
 

README.md

 IQ-TREE
 =======
 
+[![Build Status](https://travis-ci.org/bqminh/IQ-TREE.svg?branch=master)](https://travis-ci.org/bqminh/IQ-TREE)
+[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
+
 Efficient and versatile phylogenomic software by maximum likelihood <http://www.iqtree.org>
 
 Introduction

alignment/superalignment.cpp

@@ -1008,6 +1008,9 @@ void SuperAlignment::createBootstrapAlignment(int *pattern_freq, const char *spe
 		// resampling sites within genes
 		int offset = 0;
 		for (vector<Alignment*>::iterator it = partitions.begin(); it != partitions.end(); it++) {
+            if (spec && strncmp(spec, "SCALE=", 6) == 0)
+                (*it)->createBootstrapAlignment(pattern_freq + offset, spec, rstream);
+            else
                 (*it)->createBootstrapAlignment(pattern_freq + offset, NULL, rstream);
 			offset += (*it)->getNPattern();
 		}
@@ -1259,11 +1262,12 @@ Alignment *SuperAlignment::concatenateAlignments(set<int> &ids) {
 
 Alignment *SuperAlignment::concatenateAlignments() {
     vector<SeqType> seq_types;
+    vector<char*> genetic_codes;
     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]) {
+            if (partitions[i]->seq_type == seq_types[j] && partitions[i]->genetic_code == genetic_codes[j]) {
                 ids[j].insert(i);
                 found = true;
                 break;
@@ -1272,6 +1276,7 @@ Alignment *SuperAlignment::concatenateAlignments() {
             continue;
         // create a new partition
         seq_types.push_back(partitions[i]->seq_type);
+        genetic_codes.push_back(partitions[i]->genetic_code);
         ids.push_back(set<int>());
         ids.back().insert(i);
     }

debian/changelog

+iqtree (1.6.9+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille@debian.org>  Wed, 02 Jan 2019 14:13:38 +0100
+
 iqtree (1.6.8+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                help2man,
                time,
                chrpath
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/iqtree
 Vcs-Git: https://salsa.debian.org/med-team/iqtree.git
 Homepage: http://www.cibiv.at/software/iqtree/

nclextra/msetsblock.cpp

@@ -267,6 +267,9 @@ void MSetsBlock::Read(NxsToken &token)
 
 		else
 		{
+            errormsg = "Unknown command ";
+            errormsg += token.GetToken();
+            throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
 			SkippingCommand(token.GetToken());
 			do
 			{
@@ -284,6 +287,11 @@ void MSetsBlock::Read(NxsToken &token)
 
 }
 
+void MSetsBlock::SkippingCommand(NxsString commandName) {
+    cout << "WARNING: Skipping unknown command " << commandName << endl;
+}
+
+
 CharSet *MSetsBlock::findCharSet(string name) {
 	for (vector<CharSet*>::iterator it = charsets.begin(); it != charsets.end(); it++)
 		if ((*it)->name == name) return (*it);

nclextra/msetsblock.h

@@ -95,6 +95,12 @@ public:
 	*/
 	virtual void Reset();
 
+    /**
+     called when some commands are skipped
+     @param commandName command name
+     */
+    virtual void SkippingCommand(NxsString commandName);
+
 	/**
 		@return the number of sets
 	*/

tree/iqtree.cpp

@@ -2885,6 +2885,15 @@ void IQTree::refineBootTrees() {
     finish_random();
     randstream = saved_randstream;
 
+    SplitGraph *sg = new SplitGraph;
+    summarizeBootstrap(*sg);
+    sg->removeTrivialSplits();
+    sg->setCheckpoint(checkpoint);
+    boot_splits.push_back(sg);
+
+    saveCheckpoint();
+    checkpoint->dump();
+    
     // restore
     params->gbo_replicates = boot_trees.size();
     params->nni_type = saved_nni_type;
@@ -4051,6 +4060,8 @@ void IQTree::printResultTree(ostream &out) {
 void IQTree::printBestCandidateTree() {
     if (MPIHelper::getInstance().isWorker())
         return;
+    if (params->suppress_output_flags & OUT_TREEFILE)
+        return;
     string tree_file_name = params->out_prefix;
     tree_file_name += ".treefile";
     readTreeString(candidateTrees.getBestTreeStrings(1)[0]);

utils/checkpoint.cpp

@@ -9,6 +9,7 @@
 #include "tools.h"
 #include "timeutil.h"
 #include "gzstream.h"
+#include <cstdio>
 
 const char* CKP_HEADER =     "--- # IQ-TREE Checkpoint ver >= 1.6";
 const char* CKP_HEADER_OLD = "--- # IQ-TREE Checkpoint";
@@ -149,12 +150,18 @@ void Checkpoint::dump(bool force) {
         return;
     }
     prev_dump_time = getRealTime();
+    string filename_tmp = filename + ".tmp";
+    if (fileExists(filename_tmp)) {
+        outWarning("IQ-TREE was killed while writing temporary checkpoint file " + filename_tmp);
+        outWarning("You should increase checkpoint interval from the default 60 seconds");
+        outWarning("via -cptime option to avoid too frequent checkpoint for large datasets");
+    }
     try {
         ostream *out;
         if (compression) 
-            out = new ogzstream(filename.c_str());
+            out = new ogzstream(filename_tmp.c_str());
         else
-            out = new ofstream(filename.c_str()); 
+            out = new ofstream(filename_tmp.c_str());
         out->exceptions(ios::failbit | ios::badbit);
         *out << header << endl;
         // call dump stream
@@ -165,6 +172,12 @@ void Checkpoint::dump(bool force) {
             ((ofstream*)out)->close();
         delete out;
 //        cout << "Checkpoint dumped" << endl;
+        if (fileExists(filename)) {
+            if (std::remove(filename.c_str()) != 0)
+                outError("Cannot remove file ", filename);
+        }
+        if (std::rename(filename_tmp.c_str(), filename.c_str()) != 0)
+            outError("Cannot rename file ", filename_tmp);
     } catch (ios::failure &) {
         outError(ERR_WRITE_OUTPUT, filename.c_str());
     }

utils/tools.cpp

@@ -1707,7 +1707,7 @@ void parseArg(int argc, char *argv[], Params &params) {
             if (strcmp(argv[cnt], "-rclusterf") == 0) {
 				cnt++;
 				if (cnt >= argc)
-					throw "Use -rcluster <percent>";
+					throw "Use -rclusterf <percent>";
                 params.partfinder_rcluster = convert_double(argv[cnt]);
                 if (params.partfinder_rcluster < 0 || params.partfinder_rcluster > 100)
                     throw "rcluster percentage must be between 0 and 100";
@@ -1722,6 +1722,8 @@ void parseArg(int argc, char *argv[], Params &params) {
                 params.partfinder_rcluster_max = convert_int(argv[cnt]);
                 if (params.partfinder_rcluster_max <= 0)
                     throw "rcluster-max must be between > 0";
+                if (params.partfinder_rcluster == 100)
+                    params.partfinder_rcluster = 99.9999;
 				continue;
             }