Commit d2e68c89 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix bug when bowtie2 is not able to find reference files ending with .bt2l...

Fix bug when bowtie2 is not able to find reference files ending with .bt2l (new large file definition)
parent ede07209
......@@ -135,7 +135,12 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
val indexDir = new File(bowtieIndex).getParentFile
val basename = bowtieIndex.stripPrefix(indexDir.getPath + File.separator)
if (indexDir.exists()) {
if (!indexDir.list().toList.filter(_.startsWith(basename)).exists(_.endsWith(".bt2")))
if (!indexDir.list()
.toList
.filter(_.startsWith(basename))
.exists({ p =>
p.endsWith(".bt2") || p.endsWith(".bt2l")
}))
Logging.addError(s"No index files found for bowtie2 in: $indexDir with basename: $basename")
}
}
......
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