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From Carlos Barroto: made 'level' in Picard's CalculateHsMetrics Scala Queue extension an argument.

This commit is contained in:
Eric Banks 2014-06-19 10:04:04 -04:00
parent 2df2a153e6
commit 9212edba41
1 changed files with 3 additions and 3 deletions
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6
public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala
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@ -55,7 +55,8 @@ class CalculateHsMetrics extends org.broadinstitute.gatk.queue.function.JavaComm
@Argument(doc="Reference file", shortName = "reference", fullName = "reference", required = true)
var reference: File = _
val level = MetricAccumulationLevel.SAMPLE
@Argument(doc="The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times.", shortName = "level", fullName = "metric_accumulation_level", required = false)
var level: Seq[picard.analysis.MetricAccumulationLevel] = Seq(MetricAccumulationLevel.SAMPLE)
override def inputBams = input
override def outputFile = output
@ -63,6 +64,5 @@ class CalculateHsMetrics extends org.broadinstitute.gatk.queue.function.JavaComm
required("BAIT_INTERVALS=" + baits) +
required("TARGET_INTERVALS=" + targets) +
required("REFERENCE_SEQUENCE=" + reference) +
optional("METRIC_ACCUMULATION_LEVEL="+level)
repeat("METRIC_ACCUMULATION_LEVEL=", level, spaceSeparated=false, escape=true, format="%s")
}