From b4af28c7df0d23e274c43be87af0260c2811476d Mon Sep 17 00:00:00 2001 From: fromer Date: Thu, 26 May 2011 20:24:56 +0000 Subject: [PATCH] Handle case where -L argument (intervals) not given git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5886 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/oneoffs/fromer/PhaseSamples.scala | 6 ++++-- .../oneoffs/fromer/ScatteredFullVariantAnnotator.scala | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/scala/qscript/oneoffs/fromer/PhaseSamples.scala b/scala/qscript/oneoffs/fromer/PhaseSamples.scala index 0c75b557e..1b55d1dd0 100644 --- a/scala/qscript/oneoffs/fromer/PhaseSamples.scala +++ b/scala/qscript/oneoffs/fromer/PhaseSamples.scala @@ -23,7 +23,7 @@ class PhaseSamples extends QScript { var prefix: String = "" @Argument(shortName = "L", doc = "Intervals", required = false) - var intervals: String = _ + var intervals: String = null @Input(doc = "level of parallelism for BAM phaser. By default is set to 0 [no scattering].", shortName = "scatter", required = false) var scatterCount = 0 @@ -35,7 +35,9 @@ class PhaseSamples extends QScript { var outputPhased: File = _ trait CommandLineGATKArgs extends CommandLineGATK { - this.intervalsString = List(qscript.intervals) + if (qscript.intervals != null) { + this.intervalsString = List(qscript.intervals) + } this.jarFile = qscript.gatkJarFile this.reference_sequence = qscript.referenceFile this.memoryLimit = 3 diff --git a/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala b/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala index 1be4c3cf1..b575e9980 100644 --- a/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala +++ b/scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala @@ -14,7 +14,7 @@ class ScatteredFullVariantAnnotator extends QScript { var referenceFile: File = _ @Argument(shortName = "L", doc = "Intervals", required = false) - var intervals: String = _ + var intervals: String = null @Input(doc = "level of parallelism. By default is set to 0 [no scattering].", shortName = "scatter", required = false) var scatterCount = 0 @@ -36,7 +36,9 @@ class ScatteredFullVariantAnnotator extends QScript { } trait CommandLineGATKArgs extends CommandLineGATK { - this.intervalsString = List(qscript.intervals) + if (qscript.intervals != null) { + this.intervalsString = List(qscript.intervals) + } this.jarFile = qscript.gatkJarFile this.reference_sequence = qscript.referenceFile this.input_file = List(qscript.bams)