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Adding PER_TARGET_COVERAGE option 

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This commit is contained in:
meganshand 2015-09-16 16:02:53 -04:00
parent aadf6645f6
commit cdfe0d7b7c
1 changed files with 5 additions and 1 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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@ -58,11 +58,15 @@ class CalculateHsMetrics extends org.broadinstitute.gatk.queue.function.JavaComm
@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) @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) var level: Seq[picard.analysis.MetricAccumulationLevel] = Seq(MetricAccumulationLevel.SAMPLE)
@Argument(doc="Optional file to output per-target coverage", shortName = "coverage", fullName = "per_target_coverage", required = false)
var perTargetCoverage: File = _
override def inputBams = input override def inputBams = input
override def outputFile = output override def outputFile = output
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("BAIT_INTERVALS=" + baits) + required("BAIT_INTERVALS=" + baits) +
required("TARGET_INTERVALS=" + targets) + required("TARGET_INTERVALS=" + targets) +
required("REFERENCE_SEQUENCE=" + reference) + required("REFERENCE_SEQUENCE=" + reference) +
repeat("METRIC_ACCUMULATION_LEVEL=", level, spaceSeparated=false, escape=true, format="%s") repeat("METRIC_ACCUMULATION_LEVEL=", level, spaceSeparated=false, escape=true, format="%s") +
optional("PER_TARGET_COVERAGE=", perTargetCoverage, spaceSeparated = false)
} }