Commit 27db07f0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added auto detect on large indexes for bowtie

parent 3b86133f
......@@ -58,16 +58,21 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
var strata: Boolean = config("strata", default = false)
var maqerr: Option[Int] = config("maqerr")
var maxins: Option[Int] = config("maxins")
var largeIndex: Boolean = config("large-index", default = false)
override def beforeGraph() {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
val basename = reference.getName.stripSuffix(".fasta").stripSuffix(".fa")
if (reference.getParentFile.list().toList.filter(_.startsWith(basename)).exists(_.endsWith(".ebwtl")))
largeIndex = config("large-index", default = true)
}
/** return commandline to execute */
def cmdLine = required(executable) +
optional("--threads", threads) +
conditional(sam, "--sam") +
conditional(largeIndex, "--large-index") +
conditional(best, "--best") +
conditional(strata, "--strata") +
optional("--sam-RG", sam_RG) +
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment