From 9212edba41f33a26a6ea1b9d52e4e5f6826f5df1 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 19 Jun 2014 10:04:04 -0400 Subject: [PATCH 1/2] From Carlos Barroto: made 'level' in Picard's CalculateHsMetrics Scala Queue extension an argument. --- .../gatk/queue/extensions/picard/CalculateHsMetrics.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala index 51c3b00a6..68c4ca730 100644 --- a/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala +++ b/public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/CalculateHsMetrics.scala @@ -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") } From 1092dd6e254e601d15df0ffdb1dc122d4e1da8ac Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 19 Jun 2014 10:05:51 -0400 Subject: [PATCH 2/2] From Carlos Barroto: switch outputRoot in SplitSamFile to an empty string instead of null. --- .../gatk/tools/walkers/readutils/SplitSamFile.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java index b19a2d735..157a44f0a 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java @@ -57,7 +57,7 @@ import java.util.Map; @Requires({DataSource.READS}) public class SplitSamFile extends ReadWalker> { @Argument(fullName="outputRoot", doc="output BAM file", required=false) - public String outputRoot = null; + public String outputRoot = ""; @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false) public Integer BAMcompression = 5;