Commit ca7bf0d9 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding missing options

parent 7a95865b
......@@ -21,7 +21,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** Extension for sambemba markdup */
class SambambaMarkdup(val parent: Configurable) extends Sambamba {
override def defaultThreads = 4
@Input(doc = "Bam File")
var input: File = _
......@@ -32,10 +31,14 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
var removeDuplicates: Boolean = config("remove_duplicates", default = false)
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val compressionLevel: Option[Int] = config("compression_level", default = 6)
val hashTableSize: Option[Int] = config("hash-table-size", default = 262144)
val overflowListSize: Option[Int] = config("overflow-list-size", default = 200000)
val ioBufferSize: Option[Int] = config("io-buffer-size", default = 128)
val compressionLevel: Option[Int] = config("compression_level")
val hashTableSize: Option[Int] = config("hash-table-size")
val overflowListSize: Option[Int] = config("overflow-list-size")
val ioBufferSize: Option[Int] = config("io-buffer-size")
val showProgress: Boolean = config("show-progress", default = true)
override def defaultThreads = 4
override def defaultCoreMemory = 4.0
/** Returns command to execute */
def cmdLine = required(executable) +
......@@ -43,6 +46,7 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
conditional(removeDuplicates, "--remove-duplicates") +
optional("-t", nCoresRequest) +
optional("-l", compressionLevel) +
conditional(showProgress, "--show-progress") +
optional("--hash-table-size=", hashTableSize, spaceSeparated = false) +
optional("--overflow-list-size=", overflowListSize, spaceSeparated = false) +
optional("--io-buffer-size=", ioBufferSize, spaceSeparated = false) +
......
......@@ -30,13 +30,22 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
var output: File = _
// @doc: compression_level 6 is average, 0 = no compression, 9 = best
val compressionLevel: Option[Int] = config("compression_level", default = 6)
val compressionLevel: Option[Int] = config("compression_level")
val header: Boolean = config("header", default = false)
val showProgress: Boolean = config("show-progress", default = true)
val filter: Option[String] = config("filter")
override def defaultThreads = 4
override def defaultCoreMemory = 4.0
/** Returns command to execute */
def cmdLine = required(executable) +
required("merge") +
optional("-t", nCoresRequest) +
optional("-l", compressionLevel) +
optional("-F", filter) +
conditional(header, "--header") +
conditional(showProgress, "--show-progress") +
required(output) +
repeat("", input)
}
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