changes while testing

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 9da0d3c522526a7fb76720aef8a38c83fab11814..102db7478223d0027e676304288552a2148966fb 100644 (file)
--- 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, string blas) : 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);
@@ -36,6 +36,7 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
                trimChimera = trim;
                numNoParents = 0;
                blastlocation = blas;
+               threadID = tid;
        
                doPrep();
        }
@@ -45,9 +46,59 @@ 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) : 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; 
@@ -70,11 +121,13 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
                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++) {  
@@ -218,7 +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, blastlocation);
+                       databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3, blastlocation, threadID);
                        
                        if (m->control_pressed) { return 0; }
 
@@ -332,7 +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, blastlocation);
+                       databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3, blastlocation, threadID);
                        
                        if (m->control_pressed) { return userTemplate; }
 
@@ -521,12 +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;
                
@@ -575,6 +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) {