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Don't output program tag

This commit is contained in:
Ron Levine 2016-05-10 10:47:43 -04:00
parent acabbba57b
commit 831360fd0b
2 changed files with 8 additions and 2 deletions
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4
public/gatk-queue-extensions-public/src/main/qscripts/org/broadinstitute/gatk/queue/qscripts/examples/ExamplePrintReads.scala
View File

@ -44,6 +44,9 @@ class ExamplePrintReads extends QScript {
@Argument(doc="One or more genomic intervals over which to operate", shortName="L", required=false) @Argument(doc="One or more genomic intervals over which to operate", shortName="L", required=false)
var intervals: Seq[String] = Nil var intervals: Seq[String] = Nil
@Argument(doc = "Don't output a program tag", shortName = "npt", required = false)
var noPGTag: Boolean = _
def script() { def script() {
val printReads = new PrintReads val printReads = new PrintReads
printReads.reference_sequence = referenceFile printReads.reference_sequence = referenceFile
@ -52,6 +55,7 @@ class ExamplePrintReads extends QScript {
printReads.input_file :+= bamFile printReads.input_file :+= bamFile
printReads.out = outFile printReads.out = outFile
printReads.intervalsString = intervals printReads.intervalsString = intervals
printReads.no_pg_tag = noPGTag
add(printReads) add(printReads)
} }
} }

6
public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/extensions/gatk/QueueFeaturesQueueTest.scala
View File

@ -42,7 +42,8 @@ class QueueFeaturesQueueTest {
" -S " + QueueTest.publicQScriptsPackageDir + "examples/ExamplePrintReads.scala", " -S " + QueueTest.publicQScriptsPackageDir + "examples/ExamplePrintReads.scala",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam", " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam",
" -out " + testOut).mkString " -out " + testOut,
" -npt ").mkString
spec.fileMD5s += testOut -> "3134a6c732d7f235373095586bc7d470" spec.fileMD5s += testOut -> "3134a6c732d7f235373095586bc7d470"
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
@ -55,7 +56,8 @@ class QueueFeaturesQueueTest {
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta", " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam", " -I " + BaseTest.publicTestDir + "exampleBAM_with_unmapped.bam",
" -L chr1", " -L chr1",
" -out " + testOut2).mkString " -out " + testOut2,
" -npt ").mkString
spec2.fileMD5s += testOut2 -> "aa33e589879c4baf6a470d22da76d885" spec2.fileMD5s += testOut2 -> "aa33e589879c4baf6a470d22da76d885"
QueueTest.executeTest(spec2) QueueTest.executeTest(spec2)
} }