X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=a7d42b331bc3044de372c030175da4663f9e3a9c;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hp=806ca0d69cabd6056de8ce1870c628e40916e080;hpb=26cf6509c41e1f38fe5a178bf9d22c02d9d97580;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 806ca0d..a7d42b3 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -125,7 +125,12 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 			fasta = validParameter.validFile(parameters, "fasta", false);
 			if (fasta == "not found") { 				
 				fasta = m->getFastaFile(); 
-				if (fasta != "") { fastafileNames.push_back(fasta);  m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+				if (fasta != "") { 
+                    fastafileNames.push_back(fasta);  
+                    m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+                    string simpleName = m->getSimpleName(fasta);
+                    filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+                }
 				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else { 
@@ -420,8 +425,21 @@ int FilterSeqsCommand::filterSequences() {
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 				
 #else
-			vector<unsigned long long> positions = savedPositions[s];
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+            
+            vector<unsigned long long> positions;
+            if (savedPositions.size() != 0) { positions = savedPositions[s]; }
+            else {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				positions = m->divideFile(fastafileNames[s], processors);
+#else
+                if(processors != 1){
+                    int numFastaSeqs = 0;
+                    positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
+                }
+#endif
+            }
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			//vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 			
 			for (int i = 0; i < (positions.size()-1); i++) {
@@ -578,7 +596,7 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
 				count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -611,7 +629,7 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, strin
 		int num = 0;
 		processIDS.clear();
         
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		
 		
 		//loop through and create all the processes you want
@@ -799,7 +817,7 @@ string FilterSeqsCommand::createFilter() {
 #else
 				
                 vector<unsigned long long> positions;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				positions = m->divideFile(fastafileNames[s], processors);
 				for (int i = 0; i < (positions.size()-1); i++) {
 					lines.push_back(new linePair(positions[i], positions[(i+1)]));
@@ -820,6 +838,7 @@ string FilterSeqsCommand::createFilter() {
 				}else {
                     int numFastaSeqs = 0;
                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                     
                     //figure out how many sequences you have to process
                     int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -957,7 +976,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 					count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -1033,7 +1052,7 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 		int num = 0;
 		processIDS.clear();
 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				
 		//loop through and create all the processes you want
 		while (process != processors) {