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Merge pull request #662 from broadinstitute/eb_Carlos_Borroto_commits 

Eb carlos borroto commits
This commit is contained in:
Eric Banks 2014-06-19 12:49:14 -04:00
parent 2df2a153e6 1092dd6e25
commit 41d2a793f0
2 changed files with 4 additions and 4 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")
}

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFile.java
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@ -57,7 +57,7 @@ import java.util.Map;
@Requires({DataSource.READS})
public class SplitSamFile extends ReadWalker<SAMRecord, Map<String, SAMFileWriter>> {
@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;