pat's changes to seq.error command

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index b92e8c8d355f6d105c141857bd96c19538ba194b..3497579167210514496ac904f6c9f19d17140b16 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; }