X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraslayer.cpp;h=102db7478223d0027e676304288552a2148966fb;hp=97b331b65b556baafbd721cc6d0186097bdfa09e;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=75962c819c16814e5c2340d99af1aa62e564dc20

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 97b331b..102db74 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -14,7 +14,7 @@
 
 //***************************************************************************************************************
 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, string mode, int k, int ms, int mms, int win, float div, 
-int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {  	
+int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera()  {  	
 	try {
 		fastafile = file;
 		templateFileName = temp; templateSeqs = readSeqs(temp);
@@ -34,6 +34,9 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 		numWanted = numw;
 		realign = r; 
 		trimChimera = trim;
+		numNoParents = 0;
+		blastlocation = blas;
+		threadID = tid;
 	
 		doPrep();
 	}
@@ -43,9 +46,11 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 	}
 }
 //***************************************************************************************************************
+//template=self, byGroup parameter used for mpienabled version to read the template as MPI_COMM_SELF instead of MPI_COMM_WORLD
 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div, 
-							 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {  	
+							 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid, bool bg) : Chimera()  {  	
 	try {
+		byGroup = bg;
 		fastafile = file; templateSeqs = readSeqs(fastafile);
 		templateFileName = temp; 
 		searchMethod = mode;
@@ -65,11 +70,64 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
 		realign = r; 
 		trimChimera = trim;
 		priority = prior;
+		numNoParents = 0;
+		blastlocation = blas;
+		threadID = tid;
+		
 		
 		createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
 		
 		if (searchMethod == "distance") { 
-			createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+			//createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+			
+			//run filter on template copying templateSeqs into filteredTemplateSeqs
+			for (int i = 0; i < templateSeqs.size(); i++) {  
+				if (m->control_pressed) {  break; }
+				
+				Sequence* newSeq = new Sequence(templateSeqs[i]->getName(), templateSeqs[i]->getAligned());
+				runFilter(newSeq);  
+				filteredTemplateSeqs.push_back(newSeq);
+			}
+		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraSlayer", "ChimeraSlayer");
+		exit(1);
+	}
+}
+//***************************************************************************************************************
+//template=self
+ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div, 
+							 int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r, string blas, int tid) : Chimera()  {  	
+	try {
+		fastafile = file; templateSeqs = readSeqs(fastafile);
+		templateFileName = temp; 
+		searchMethod = mode;
+		kmerSize = k;
+		match = ms;
+		misMatch = mms;
+		window = win;
+		divR = div;
+		minSim = minsim;
+		minCov = mincov;
+		minBS = minbs;
+		minSNP = minsnp;
+		parents = par;
+		iters = it;
+		increment = inc;
+		numWanted = numw;
+		realign = r; 
+		trimChimera = trim;
+		priority = prior;
+		numNoParents = 0;
+		blastlocation = blas;
+		threadID = tid;
+		
+		
+		createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
+		
+		if (searchMethod == "distance") { 
+			//createFilter(templateSeqs, 0.0); //just removed columns where all seqs have a gap
 			
 			//run filter on template copying templateSeqs into filteredTemplateSeqs
 			for (int i = 0; i < templateSeqs.size(); i++) {  
@@ -213,7 +271,7 @@ int ChimeraSlayer::doPrep() {
 		}else if (searchMethod == "blast") {
 		
 			//generate blastdb
-			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
+			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation, threadID);
 			
 			if (m->control_pressed) { return 0; }
 
@@ -254,6 +312,11 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence q, vector<Sequence*>& user
 			}
 		}
 		
+		//avoids nuisance error from formatdb for making blank blast database
+		if (userTemplate.size() == 0) {
+			return userTemplate;
+		}
+		
 		string 	kmerDBNameLeft;
 		string 	kmerDBNameRight;
 		
@@ -322,7 +385,7 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence q, vector<Sequence*>& user
 		}else if (searchMethod == "blast") {
 			
 			//generate blastdb
-			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+			databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation, threadID);
 			
 			if (m->control_pressed) { return userTemplate; }
 
@@ -511,12 +574,13 @@ Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPi
 
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) {
+Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece, bool& chimFlag) {
 	try {
 		MPI_Status status;
 		bool results = false;
 		string outAccString = "";
 		string outputString = "";
+        chimFlag = false;
 		
 		Sequence trim;
 		
@@ -565,6 +629,7 @@ Sequence ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results left
 					memcpy(buf2, outAccString.c_str(), length);
 				
 					MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
+                    chimFlag = true;
 					delete buf2;
 					
 					if (trimChimera) {  
@@ -747,7 +812,6 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
 		else {  thisTemplate = getTemplate(*query, thisFilteredTemplate);  } //fills this template and creates the databases
 		
 		if (m->control_pressed) {  return 0;  }
-		
 		if (thisTemplate.size() == 0) {  return 0; } //not chimeric
 		
 		//moved this out of maligner - 4/29/11
@@ -1115,6 +1179,8 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
 		//string qname = q->getName().substr(0, q->getName().find_last_of('_'));	
 		//cout << qname << endl;	
 		
+		if (mergedResults.size() == 0) { numNoParents++; }
+		
 		for (int i = 0; i < mergedResults.size(); i++) {
 			//cout << q->getName() << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl;	
 			if (db[mergedResults[i]]->getName() != q.getName()) { 
@@ -1127,8 +1193,6 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
 		delete queryRight;
 		delete queryLeft;
 		
-		if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast returned 0 potential parents, so we are not able to check " + q.getName() + ". This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
-		
 		return refResults;
 	}
 	catch(exception& e) {