added shhh.seqs command

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index ff13590cd3a91cb8960e26af803ca7fa63918035..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++) {
@@ -105,7 +106,7 @@ int ChimeraSlayer::doPrep() {
                        bool needToGenerateLeft = true;
                        
                        if(kmerFileTestLeft){   
-                               bool GoodFile = checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
                                if (GoodFile) {  needToGenerateLeft = false;    }
                        }
                        
@@ -136,7 +137,7 @@ int ChimeraSlayer::doPrep() {
                        bool needToGenerateRight = true;
                        
                        if(kmerFileTestRight){  
-                               bool GoodFile = checkReleaseVersion(kmerFileTestRight, m->getVersion());
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
                                if (GoodFile) {  needToGenerateRight = false;   }
                        }
                        
@@ -296,14 +297,14 @@ 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) {
@@ -380,16 +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;
        }