All output files are written in a directory provided with option -o.

MANUAL_PAGE.txt

@@ -9,6 +9,9 @@ DESCRIPTION:
        -help
               Displays this help page.
 
+       -version
+              Displays Ray version and compilation options.
+
   K-mer length
 
        -k kmerLength
@@ -32,16 +35,16 @@ DESCRIPTION:
 
   Outputs
 
-       -o outputPrefix
-              Specifies the prefix for outputted files.
+       -o outputDirectory
+              Specifies the directory for outputted files. Default is RayOutput
 
        -amos
-              Writes the AMOS file called PREFIX.AMOS.afg
+              Writes the AMOS file called RayOutput/AMOS.afg
               An AMOS file contains read positions on contigs.
               Can be opened with software with graphical user interface.
 
        -write-kmers
-              Writes k-mer graph to PREFIX.kmers.txt
+              Writes k-mer graph to RayOutput/kmers.txt
               The resulting file is not utilised by Ray.
               The resulting file is very large.
 
@@ -144,80 +147,80 @@ FILES
 
   Scaffolds
 
-     PREFIX.Scaffolds.fasta
+     RayOutput/Scaffolds.fasta
      	The scaffold sequences in FASTA format
-     PREFIX.ScaffoldComponents.txt
+     RayOutput/ScaffoldComponents.txt
      	The components of each scaffold
-     PREFIX.ScaffoldLengths.txt
+     RayOutput/ScaffoldLengths.txt
      	The length of each scaffold
-     PREFIX.ScaffoldLinks.txt
+     RayOutput/ScaffoldLinks.txt
      	Scaffold links
 
   Contigs
 
-     PREFIX.Contigs.fasta
+     RayOutput/Contigs.fasta
      	Contiguous sequences in FASTA format
-     PREFIX.ContigLengths.txt
+     RayOutput/ContigLengths.txt
      	The lengths of contiguous sequences
 
   Summary
 
-     PREFIX.OutputNumbers.txt
+     RayOutput/OutputNumbers.txt
      	Overall numbers for the assembly
 
   de Bruijn graph
 
-     PREFIX.CoverageDistribution.txt
+     RayOutput/CoverageDistribution.txt
      	The distribution of coverage values
-     PREFIX.CoverageDistributionAnalysis.txt
+     RayOutput/CoverageDistributionAnalysis.txt
      	Analysis of the coverage distribution
-     PREFIX.degreeDistribution.txt
+     RayOutput/degreeDistribution.txt
      	Distribution of ingoing and outgoing degrees
-     PREFIX.kmers.txt
+     RayOutput/kmers.txt
      	k-mer graph, required option: -write-kmers
          The resulting file is not utilised by Ray.
          The resulting file is very large.
 
   Assembly steps
 
-     PREFIX.SeedLengthDistribution.txt
+     RayOutput/SeedLengthDistribution.txt
          Distribution of seed length
-     PREFIX.<rank>.RaySeeds.fasta
+     RayOutput/<rank>.RaySeeds.fasta
          Seed DNA sequences, required option: -write-seeds
-     PREFIX.<rank>.RayExtensions.fasta
+     RayOutput/<rank>.RayExtensions.fasta
          Extension DNA sequences, required option: -write-extensions
 
   Paired reads
 
-     PREFIX.LibraryStatistics.txt
+     RayOutput/LibraryStatistics.txt
      	Estimation of outer distances for paired reads
-     PREFIX.Library<LibraryNumber>.txt
+     RayOutput/Library<LibraryNumber>.txt
          Frequencies for observed outer distances (insert size + read lengths)
 
   Partition
 
-     PREFIX.NumberOfSequences.txt
+     RayOutput/NumberOfSequences.txt
          Number of reads in each file
-     PREFIX.SequencePartition.txt
+     RayOutput/SequencePartition.txt
      	Sequence partition
 
   Ray software
 
-     PREFIX.RayVersion.txt
+     RayOutput/RayVersion.txt
      	The version of Ray
-     PREFIX.RayCommand.txt
+     RayOutput/RayCommand.txt
      	The exact same command provided 
 
   AMOS
 
-     PREFIX.AMOS.afg
+     RayOutput/AMOS.afg
      	Assembly representation in AMOS format, required option: -amos
 
   Communication
 
-     PREFIX.MessagePassingInterface.txt
+     RayOutput/MessagePassingInterface.txt
 	    	Number of messages sent
-     PREFIX.NetworkTest.txt
+     RayOutput/NetworkTest.txt
 	    	Latencies in microseconds
 
 DOCUMENTATION

README.md

@@ -99,7 +99,7 @@ Tested C++ compilers:
 	mpirun -np 512 Ray-Large-k-mers/Ray -k 63 -p lib1_1.fastq lib1_2.fastq \
 	-p lib2_1.fastq lib2_2.fastq -o DeadlyBug,Assembler=Ray,K=63
 	# wait
-	ls DeadlyBug,Assembler=Ray,K=63.Scaffolds.fasta
+	ls DeadlyBug,Assembler=Ray,K=63/Scaffolds.fasta
 
 ## Compilation options
 
@@ -116,14 +116,14 @@ see the Makefile for more.
 
 To run Ray on paired reads:
 
-	mpirun -np 25 Ray -p lib1.left.fasta lib1.right.fasta -p lib2.left.fasta lib2.right.fasta -o prefix
-	ls prefix.Contigs.fasta
-	ls prefix.Scaffolds.fasta
-	ls prefix.*
+	mpirun -np 25 Ray -p lib1.left.fasta lib1.right.fasta -p lib2.left.fasta lib2.right.fasta -o RayOutput
+	ls RayOutput/Contigs.fasta
+	ls RayOutput/Scaffolds.fasta
+	ls RayOutput/
 
 # Outputted files
 
-PREFIX.Contigs.fasta and PREFIX.Scaffolds.fasta
+RayOutput/Contigs.fasta and RayOutput/Scaffolds.fasta
 
 type Ray -help for a full list
 

code/assembler/Partitioner.cpp

@@ -83,7 +83,7 @@ void Partitioner::masterMethod(){
 			/* write the number of sequences */
 			ostringstream fileName;
 			fileName<<m_parameters->getPrefix();
-			fileName<<".NumberOfSequences.txt";
+			fileName<<"NumberOfSequences.txt";
 			ofstream f2(fileName.str().c_str());
 
 			f2<<"Files: "<<m_parameters->getNumberOfFiles()<<endl;
@@ -116,7 +116,7 @@ void Partitioner::masterMethod(){
 			/* write the partition */
 			ostringstream fileName2;
 			fileName2<<m_parameters->getPrefix();
-			fileName2<<".SequencePartition.txt";
+			fileName2<<"SequencePartition.txt";
 			ofstream f3(fileName2.str().c_str());
 			uint64_t perRank=totalSequences/m_parameters->getSize();
 			f3<<"#Rank	FirstSequence	LastSequence	NumberOfSequences"<<endl;

code/assembler/SeedExtender.cpp

@@ -105,7 +105,7 @@ int minimumCoverage,OpenAssemblerChooser*oa,bool*edgesReceived,int*m_mode){
 		/** write extensions for debugging purposes */
 		if(m_parameters->hasOption("-write-extensions")){
 			ostringstream fileName;
-			fileName<<m_parameters->getPrefix()<<"."<<m_parameters->getRank()<<".RayExtensions.fasta";
+			fileName<<m_parameters->getPrefix()<<"."<<m_parameters->getRank()<<"RayExtensions.fasta";
 			ofstream f(fileName.str().c_str());
 			for(int i=0;i<(int)ed->m_EXTENSION_identifiers.size();i++){
 				uint64_t id=ed->m_EXTENSION_identifiers[i];

code/assembler/SeedingData.cpp

@@ -322,7 +322,7 @@ void SeedingData::sendSeedLengths(){
 void SeedingData::writeSeedStatistics(){
 	ostringstream file;
 	file<<m_parameters->getPrefix();
-	file<<".SeedLengthDistribution.txt";
+	file<<"SeedLengthDistribution.txt";
 	ofstream f(file.str().c_str());
 	for(map<int,int>::iterator i=m_masterSeedLengths.begin();i!=m_masterSeedLengths.end();i++){
 		int length=i->first;

code/communication/NetworkTest.cpp

@@ -141,7 +141,7 @@ void NetworkTest::masterWork(){
 	}else if(m_doneWithNetworkTest==m_size){
 		ostringstream file;
 		file<<m_parameters->getPrefix();
-		file<<".NetworkTest.txt";
+		file<<"NetworkTest.txt";
 		ofstream f(file.str().c_str());
 		f<<"# average latency in microseconds (10^-6 seconds) when requesting a reply for a message of "<<MAXIMUM_MESSAGE_SIZE_IN_BYTES<<" bytes"<<endl;
 		f<<"# Message passing interface rank\tName\tLatency in microseconds"<<endl;

code/core/Machine.cpp

@@ -56,15 +56,19 @@ Machine::Machine(int argc,char**argv){
 		string param=argv[1];
 		if(param.find("help")!=string::npos){
 			m_parameters.showUsage();
+			m_messagesHandler.destructor();
 			exit(EXIT_NEEDS_ARGUMENTS);
 		}else if(param.find("usage")!=string::npos){
 			m_parameters.showUsage();
+			m_messagesHandler.destructor();
 			exit(EXIT_NEEDS_ARGUMENTS);
 		}else if(param.find("man")!=string::npos){
 			m_parameters.showUsage();
+			m_messagesHandler.destructor();
 			exit(EXIT_NEEDS_ARGUMENTS);
 		}else if(param.find("-version")!=string::npos){
 			showRayVersionShort();
+			m_messagesHandler.destructor();
 			exit(EXIT_NEEDS_ARGUMENTS);
 		}
 	}
@@ -237,11 +241,32 @@ void Machine::start(){
 	}
 
 	/** only show the version. */
-	if(fullReport)
+	if(fullReport){
+		m_messagesHandler.destructor();
 		return;
+	}
 
 	m_parameters.constructor(m_argc,m_argv,getRank());
 
+
+	/** create the directory for the assembly */
+
+	string directory=m_parameters.getPrefix();
+	if(fileExists(directory.c_str())){
+		if(m_parameters.getRank() == MASTER_RANK)
+			cout<<"Error, "<<directory<<" already exists, change the -o parameter to another value."<<endl;
+
+		m_messagesHandler.destructor();
+		return;
+	}
+
+	m_messagesHandler.barrier();
+
+	if(m_parameters.getRank() == MASTER_RANK)
+		createDirectory(directory.c_str());
+
+
+
 	m_seedExtender.constructor(&m_parameters,&m_directionsAllocator,m_ed,&m_subgraph,&m_inbox);
 	ostringstream prefixFull;
 	prefixFull<<m_parameters.getMemoryPrefix()<<"_Main";
@@ -396,7 +421,7 @@ m_seedingData,
 		cout<<endl;
 		cout<<"Rank "<<getRank()<<" wrote "<<m_parameters.getOutputFile()<<endl;
 		cout<<"Rank "<<getRank()<<" wrote "<<m_parameters.getScaffoldFile()<<endl;
-		cout<<"Check for "<<m_parameters.getPrefix()<<".*"<<endl;
+		cout<<"Check for "<<m_parameters.getPrefix()<<"*"<<endl;
 		cout<<endl;
 		if(m_parameters.useAmos()){
 			cout<<"Rank "<<getRank()<<" wrote "<<m_parameters.getAmosFile()<<" (reads mapped onto contiguous sequences in AMOS format)"<<endl;
@@ -580,6 +605,7 @@ void Machine::call_RAY_SLAVE_MODE_SEND_SEED_LENGTHS(){
 }
 
 void Machine::call_RAY_MASTER_MODE_LOAD_CONFIG(){
+
 	if(m_argc==2 && m_argv[1][0]!='-'){
 		ifstream f(m_argv[1]);
 		if(!f){
@@ -759,7 +785,7 @@ void Machine::call_RAY_MASTER_MODE_SEND_COVERAGE_VALUES(){
 
 	ostringstream g;
 	g<<m_parameters.getPrefix();
-	g<<".CoverageDistributionAnalysis.txt";
+	g<<"CoverageDistributionAnalysis.txt";
 	ofstream outputFile(g.str().c_str());
 	outputFile<<"k-mer length:\t"<<m_parameters.getWordSize()<<endl;
 	outputFile<<"Lowest coverage observed:\t"<<lowestCoverage<<endl;
@@ -883,7 +909,7 @@ void Machine::call_RAY_MASTER_MODE_WRITE_KMERS(){
 	}else if(m_numberOfRanksDone==m_parameters.getSize()){
 		if(m_parameters.writeKmers()){
 			cout<<endl;
-			cout<<"Rank "<<getRank()<<" wrote "<<m_parameters.getPrefix()<<".kmers.txt"<<endl;
+			cout<<"Rank "<<getRank()<<" wrote "<<m_parameters.getPrefix()<<"kmers.txt"<<endl;
 		}
 
 		m_master_mode=RAY_MASTER_MODE_TRIGGER_INDEXING;
@@ -892,7 +918,7 @@ void Machine::call_RAY_MASTER_MODE_WRITE_KMERS(){
 			return;
 
 		ostringstream edgeFile;
-		edgeFile<<m_parameters.getPrefix()<<".degreeDistribution.txt";
+		edgeFile<<m_parameters.getPrefix()<<"degreeDistribution.txt";
 		ofstream f(edgeFile.str().c_str());
 
 		f<<"# Most of the vertices should have an ingoing degree of 1 and an outgoing degree of 1."<<endl;
@@ -1373,7 +1399,7 @@ void Machine::call_RAY_MASTER_MODE_KILL_RANKS(){
 void Machine::call_RAY_SLAVE_MODE_DIE(){
 	/** write message-passing interface file */
 	ostringstream file;
-	file<<m_parameters.getPrefix()<<".MessagePassingInterface.txt";
+	file<<m_parameters.getPrefix()<<"MessagePassingInterface.txt";
 	const char*outputFile=file.str().c_str();
 	m_messagesHandler.appendStatistics(outputFile);
 
@@ -1416,7 +1442,7 @@ void Machine::call_RAY_MASTER_MODE_KILL_ALL_MPI_RANKS(){
 
 		/** empty the file if it exists */
 		ostringstream file;
-		file<<m_parameters.getPrefix()<<".MessagePassingInterface.txt";
+		file<<m_parameters.getPrefix()<<"MessagePassingInterface.txt";
 
 		FILE*fp=fopen(file.str().c_str(),"w+");
 		fprintf(fp,"# Source\tDestination\tTag\tCount\n");

code/core/OperatingSystem.cpp

@@ -191,15 +191,23 @@ void getMicroSeconds(uint64_t*seconds,uint64_t*microSeconds){
  *
  * \see http://msdn.microsoft.com/en-us/library/aa363855(v=vs.85).aspx
  */
-void createDirectory(char*directory){
+void createDirectory(const char*directory){
 	#ifdef OS_POSIX
 
-	/* read, write for owner */
-	/* read, write for group */
-	mode_t mode=S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP;
+	/* 
+ * S_IRWXU
+    read, write, execute/search by owner 
+ *
+ * S_IRWXG
+ *  read, write, execute/search by group 
+ *     */
+	mode_t mode=S_IRWXU | S_IRWXG;
+
 	int status=mkdir(directory,mode);
 
+	#ifdef ASSERT
 	assert(status==0);
+	#endif
 
 	#elif defined(OS_WIN)
 
@@ -209,6 +217,28 @@ void createDirectory(char*directory){
 	#endif
 }
 
+/** \see http://pubs.opengroup.org/onlinepubs/009695399/functions/stat.html
+ * \see http://blog.kowalczyk.info/article/Check-if-file-exists-on-Windows.html */
+bool fileExists(const char*file){
+	#ifdef OS_POSIX
+	struct stat st;
+	int returnValue=stat(file,&st);
+
+	bool theFileExists=(returnValue == 0);
+	return theFileExists;
+
+	#elif defined(OS_WIN)
+	/* Return TRUE if file 'fileName' exists */
+	DWORD fileAttr = GetFileAttributes(fileName);
+	if(0xFFFFFFFF == fileAttr)
+		return false;
+    	return true;
+
+	#else
+	/* not implemented */
+	#endif
+}
+
 void showRayVersionShort(){
 	cout<<"Ray version "<<RAY_VERSION<<" ";
 

code/core/OperatingSystem.h

@@ -47,7 +47,9 @@ void showMemoryUsage(int rank);
 void getMicroSeconds(uint64_t*seconds,uint64_t*microSeconds);
 
 /** create a directory */
-void createDirectory(char*directory);
+void createDirectory(const char*directory);
+
+bool fileExists(const char*file);
 
 void showRayVersion(MessagesHandler*messagesHandler,bool fullReport);