added shhh.seqs command

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 2c4f7fba4253c2cb4c2693bb3cb18e676c5d938b..1336876966f110dc25e0e18eee8bd13ec4e8d6fd 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -67,10 +67,11 @@ int ChimeraSlayer::doPrep() {
        
                //generate the kmerdb to pass to maligner
                if (searchMethod == "kmer") { 
-                       string rightTemplateFileName = "right." + templateFileName;
+                       string templatePath = m->hasPath(templateFileName);
+                       string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
                        databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
                                
-                       string leftTemplateFileName = "left." + templateFileName;
+                       string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
                        databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);      
                #ifdef USE_MPI
                        for (int i = 0; i < templateSeqs.size(); i++) {
@@ -102,8 +103,14 @@ int ChimeraSlayer::doPrep() {
                        //leftside
                        kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
                        ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
+                       bool needToGenerateLeft = true;
                        
-                       if(!kmerFileTestLeft){  
+                       if(kmerFileTestLeft){   
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+                               if (GoodFile) {  needToGenerateLeft = false;    }
+                       }
+                       
+                       if(needToGenerateLeft){ 
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
                                        
@@ -127,8 +134,14 @@ int ChimeraSlayer::doPrep() {
                        //rightside
                        kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
                        ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+                       bool needToGenerateRight = true;
+                       
+                       if(kmerFileTestRight){  
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+                               if (GoodFile) {  needToGenerateRight = false;   }
+                       }
                        
-                       if(!kmerFileTestRight){ 
+                       if(needToGenerateRight){        
                        
                                for (int i = 0; i < templateSeqs.size(); i++) {
                                        if (m->control_pressed) { return 0; } 
@@ -196,7 +209,7 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                                }
                        }
                        
-                       printBlock(chimeraResults[0], out);
+                       printBlock(chimeraResults[0], chimeraFlag, out);
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
@@ -240,7 +253,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                }
                        }
                        
-                       outputString = getBlock(chimeraResults[0]);
+                       outputString = getBlock(chimeraResults[0], chimeraFlag);
                        outputString += "\n";
        //cout << outputString << endl;         
                        //write to output file
@@ -284,15 +297,15 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                querySeq = query;
                
                //referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
-               maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
-               slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
-               
+               Maligner maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
+               Slayer slayer(window, increment, minSim, divR, iters, minSNP);
+       
                if (m->control_pressed) {  return 0;  }
                
-               string chimeraFlag = maligner->getResults(query, decalc);
+               string chimeraFlag = maligner.getResults(query, decalc);
                if (m->control_pressed) {  return 0;  }
-               vector<results> Results = maligner->getOutput();
-                               
+               vector<results> Results = maligner.getOutput();
+                       
                //found in testing realigning only made things worse
                if (realign) {
                        ChimeraReAligner realigner(templateSeqs, match, misMatch);
@@ -368,16 +381,16 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                        if (m->control_pressed) {  for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }  return 0;  }
                        
                        //send to slayer
-                       chimeraFlags = slayer->getResults(query, seqsForSlayer);
+                       chimeraFlags = slayer.getResults(query, seqsForSlayer);
                        if (m->control_pressed) {  return 0;  }
-                       chimeraResults = slayer->getOutput();
+                       chimeraResults = slayer.getOutput();
                        
                        //free memory
                        for (int k = 0; k < seqs.size(); k++) {  delete seqs[k].seq;   }
                }
                
-               delete maligner;
-               delete slayer;
+               //delete maligner;
+               //delete slayer;
                
                return 0;
        }
@@ -387,7 +400,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
        }
 }
 //***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
        try {
        //out << ":)\n";
                
@@ -399,7 +412,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
                out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
                out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
                
-               out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+               out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
                
                //out << "Similarity of parents: " << data.ab << endl;
                //out << "Similarity of query to parentA: " << data.qa << endl;
@@ -422,7 +435,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
        }
 }
 //***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
        try {
                
                string outputString = "";
@@ -433,7 +446,7 @@ string ChimeraSlayer::getBlock(data_struct data){
                outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
                outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
                
-               outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+               outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
                
                return outputString;
        }