//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++) {
bool needToGenerateLeft = true;
if(kmerFileTestLeft){
- bool GoodFile = checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
if (GoodFile) { needToGenerateLeft = false; }
}
bool needToGenerateRight = true;
if(kmerFileTestRight){
- bool GoodFile = checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
if (GoodFile) { needToGenerateRight = false; }
}