X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.cpp;h=102db7478223d0027e676304288552a2148966fb;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=b637000fe688920ac89097358cc50e9ac5ca2fc8;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b637000..102db74 100644
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -46,6 +46,56 @@ 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, string blas, int tid, bool bg) : Chimera()  {  	
+	try {
+		byGroup = bg;
+		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++) {  
+				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()  {  	
@@ -73,10 +123,11 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
 		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++) {  
@@ -523,12 +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;
 		
@@ -577,6 +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) {