X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=7ab00a7822f7a7fc7ddd1ef0de00d2d24b8c51de;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=33790fe97632525cbb6c155ab953da531f770078;hpb=2bb20fb79f19b8bda48492d89f8e8b7389431413;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 33790fe..7ab00a7 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -28,7 +28,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
 			
-			ValidParameters validParameter;
+			ValidParameters validParameter("filter.seqs");
 			map<string,string>::iterator it;
 			
 			//check to make sure all parameters are valid for command
@@ -72,11 +72,22 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 						if (path == "") {	fastafileNames[i] = inputDir + fastafileNames[i];		}
 					}
 
-					int ableToOpen;
 					ifstream in;
-					ableToOpen = openInputFile(fastafileNames[i], in);
+					int ableToOpen = openInputFile(fastafileNames[i], in, "noerror");
+				
+					//if you can't open it, try default location
+					if (ableToOpen == 1) {
+						if (m->getDefaultPath() != "") { //default path is set
+							string tryPath = m->getDefaultPath() + getSimpleName(fastafileNames[i]);
+							m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+							ableToOpen = openInputFile(tryPath, in, "noerror");
+							fastafileNames[i] = tryPath;
+						}
+					}
+					in.close();
+					
 					if (ableToOpen == 1) { 
-						m->mothurOut(fastafileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+						m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 						//erase from file list
 						fastafileNames.erase(fastafileNames.begin()+i);
 						i--;
@@ -247,12 +258,12 @@ int FilterSeqsCommand::filterSequences() {
 #ifdef USE_MPI	
 				int pid, start, end, numSeqsPerProcessor, num; 
 				int tag = 2001;
-				vector<long>MPIPos;
+				vector<unsigned long int>MPIPos;
 						
 				MPI_Status status; 
 				MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-				
+	cout << pid << "is in create filter " << endl;			
 				MPI_File outMPI;
 				MPI_File tempMPI;
 				MPI_File inMPI;
@@ -382,7 +393,7 @@ int FilterSeqsCommand::filterSequences() {
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {	
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {	
 	try {
 		string outputString = "";
 		int count = 0;
@@ -558,7 +569,7 @@ string FilterSeqsCommand::createFilter() {
 #ifdef USE_MPI	
 				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
-				vector<long> MPIPos;
+				vector<unsigned long int> MPIPos;
 				
 				MPI_Status status; 
 				MPI_File inMPI; 
@@ -786,7 +797,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<long>& MPIPos) {	
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {	
 	try {
 		
 		MPI_Status status; 
@@ -872,7 +883,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 int FilterSeqsCommand::setLines(string filename) {
 	try {
 		
-		vector<long int> positions;
+		vector<unsigned long int> positions;
 		bufferSizes.clear();
 		
 		ifstream inFASTA;
@@ -883,7 +894,7 @@ int FilterSeqsCommand::setLines(string filename) {
 			input = getline(inFASTA);
 
 			if (input.length() != 0) {
-				if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
+				if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);	}
 			}
 		}
 		inFASTA.close();
@@ -891,7 +902,7 @@ int FilterSeqsCommand::setLines(string filename) {
 		int numFastaSeqs = positions.size();
 	
 		FILE * pFile;
-		long size;
+		unsigned long int size;
 		
 		//get num bytes in file
 		pFile = fopen (filename.c_str(),"rb");
@@ -908,12 +919,12 @@ int FilterSeqsCommand::setLines(string filename) {
 		
 		for (int i = 0; i < processors; i++) {
 
-			long int startPos = positions[ i * numSeqsPerProcessor ];
+			unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 			if(i == processors - 1){
 				numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 				bufferSizes.push_back(size - startPos);
 			}else{  
-				long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+				unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 				bufferSizes.push_back(myEnd-startPos);
 			}
 			lines.push_back(new linePair(startPos, numSeqsPerProcessor));