pat's changes to seq.error command

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index ff13590cd3a91cb8960e26af803ca7fa63918035..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++) {
@@ -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;   }
                        }