Fixes bug with shortcut files and windows parallelization

source/chimera/chimeracheckrdp.cpp

@@ -20,7 +20,7 @@ ChimeraCheckRDP::ChimeraCheckRDP(string filename, string temp, string n, bool s,
 		kmerSize = k;
 		outputDir = o; 
 		
-		templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
+		templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand(), true);
 		m->mothurOutEndLine();
 		
 		kmer = new Kmer(kmerSize);

source/commands/aligncommand.cpp

@@ -295,7 +295,7 @@ int AlignCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
-		templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
+		templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand(), true);
 		
 		for (int s = 0; s < candidateFileNames.size(); s++) {
 			if (m->control_pressed) { outputTypes.clear(); return 0; }

source/commands/aligncommand.h

@@ -135,7 +135,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
 			inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
 		}
 		
-		AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+		AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID, false);
 		
 		//moved this into driver to avoid deep copies in windows paralellized version
 		Alignment* alignment;

source/commands/classifyseqscommand.cpp

@@ -908,7 +908,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 			string extension = "";
 			if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 			
-			classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip, writeShortcuts);
+			classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip, false);
 			pDataArray.push_back(tempclass);
 			
 			//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.

source/commands/renamefilecommand.cpp

@@ -463,13 +463,14 @@ RenameFileCommand::RenameFileCommand(string option)  {
             temp = validParameter.validFile(parameters, "deleteold", false);		if (temp == "not found") { temp = "T"; }
             deleteOld = m->isTrue(temp);
             
-            prefix = validParameter.validFile(parameters, "prefix", false);		if (prefix == "not found") { temp = ""; }
+            prefix = validParameter.validFile(parameters, "prefix", false);		if (prefix == "not found") { prefix = ""; }
             
             outputfile = validParameter.validFile(parameters, "new", false);
             if (outputfile == "not found") {
                 if (!mothurGenerated) { m->mothurOut("[ERROR]: you must enter an output file name"); m->mothurOutEndLine();  abort=true; }
                 outputfile = "";
-            }else if (outputDir != "") { outputfile = outputDir + m->getSimpleName(outputfile);  }
+            }else { mothurGenerated=false; }
+            if (outputDir != "") { outputfile = outputDir + m->getSimpleName(outputfile);  }
             
             if ((!mothurGenerated) && (numFiles > 1)) {
                 m->mothurOut("[ERROR]: You cannot use more than one file parameter unless mothur is generating the output filenames for you.\n"); abort= true;
@@ -632,6 +633,7 @@ int RenameFileCommand::execute(){
 string RenameFileCommand::getNewName(string name, string type){
     try {
         string newName = outputfile;
+        name = m->getFullPathName(name);
         
         if (mothurGenerated) {
             string extension = m->getExtension(name);
@@ -644,12 +646,15 @@ string RenameFileCommand::getNewName(string name, string type){
             }else { basicName = prefix; }
             
             if ((type == "shared") || (type == "list") || (type == "relabund") || (type == "rabund") || (type == "sabund")) {
-                vector<string> tags; tags.push_back(".an."); tags.push_back(".tx.");  tags.push_back(".agc."); tags.push_back(".dgc."); tags.push_back(".nn."); tags.push_back(".fn."); tags.push_back(".wn."); tags.push_back(".opti.");
-                vector<string> newTags; newTags.push_back("an"); newTags.push_back("tx");  newTags.push_back("agc"); newTags.push_back("dgc"); newTags.push_back("nn"); newTags.push_back("fn"); newTags.push_back("wn"); tags.push_back(".opti.");
+                vector<string> tags; tags.push_back(".an."); tags.push_back(".tx.");  tags.push_back(".agc."); tags.push_back(".dgc."); tags.push_back(".nn."); tags.push_back(".fn."); tags.push_back(".wn."); tags.push_back(".opti_");
                 
                 for (int i = 0; i < tags.size(); i++) {
-                    int pos2 = name.find_first_of(tags[i]);
-                    if (pos2 != string::npos) { tag = newTags[i]; break; }
+                    int pos2 = name.find(tags[i]);
+                    if (pos2 != string::npos) {
+                        int pos3 = name.substr(pos2+1).find_first_of('.');
+                        tag = name.substr(pos2+1, pos3);
+                        break;
+                    }
                 }
             }else if (type == "constaxonomy") {
                 extension = ".cons.taxonomy";

source/datastructures/alignmentdb.cpp

@@ -13,7 +13,7 @@
 #include "blastdb.hpp"
 
 /**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){		//	This assumes that the template database is in fasta format, may 
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid, bool writeShortcut){		//	This assumes that the template database is in fasta format, may
 	try {											//	need to alter this in the future?
 		m = MothurOut::getInstance();
 		longest = 0;
@@ -104,8 +104,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 				
 				if (m->control_pressed) {  templateSequences.clear();  }
 				
-				search->generateDB();
-				
+                if ((method != "kmer") || ((method == "kmer") && (writeShortcut))) { search->generateDB(); }
+                
 			}else if ((method == "kmer") && (!needToGenerate)) {
 				ifstream kmerFileTest(kmerDBName.c_str());
 				search->readKmerDB(kmerFileTest);	

source/datastructures/alignmentdb.h

@@ -20,7 +20,7 @@ class AlignmentDB {
 
 public:
 
-	AlignmentDB(string, string, int, float, float, float, float, int);  //reads fastafile passed in and stores sequences
+	AlignmentDB(string, string, int, float, float, float, float, int, bool);  //reads fastafile passed in and stores sequences
 	AlignmentDB(string);
 	~AlignmentDB();
 	

source/datastructures/kmerdb.cpp

@@ -123,7 +123,7 @@ vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
 }
 
 /**************************************************************************************************/
-
+//print shortcut file
 void KmerDB::generateDB(){
 	try {