X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=458e89d075f0f6044158cfcc6b1b9daee24fc2f7;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=b00cedfba5b4edf8463343618ebdd80acae209be;hpb=2e28b53eb15d5dc11653247ee12aed2c7e5aac43;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b00cedf..458e89d 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();
 	}
@@ -43,8 +46,9 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
 	}
 }
 //***************************************************************************************************************
+//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) : 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; templateSeqs = readSeqs(fastafile);
 		templateFileName = temp; 
@@ -65,11 +69,14 @@ 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++) {  
@@ -213,7 +220,7 @@ 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 +261,11 @@ 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 +334,7 @@ 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; }
 
@@ -370,7 +382,7 @@ Sequence ChimeraSlayer::print(ostream& out, ostream& outAcc) {
 			
 			if (chimeraFlag == "yes") {	
 				if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
-					m->mothurOut(querySeq.getName() + "\tyes"); m->mothurOutEndLine();
+					m->mothurOut(toString(threadID) +"\t"+ querySeq.getName() + "\tyes"); m->mothurOutEndLine();
 					outAcc << querySeq.getName() << endl;
 					
 					if (templateFileName == "self") {  chimericSeqs.insert(querySeq.getName()); }
@@ -747,7 +759,6 @@ 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 +1126,8 @@ 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 +1140,6 @@ vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence q, vector<Sequence*>& db,
 		delete queryRight;
 		delete queryLeft;
 		
-		if (refResults.size() == 0) { m->mothurOut("[WARNING]: megablast found 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) {