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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
This commit is contained in:
fromer 2011-05-26 20:24:56 +00:00
parent a561d3adc7
commit b4af28c7df
2 changed files with 8 additions and 4 deletions
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6
scala/qscript/oneoffs/fromer/PhaseSamples.scala
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@ -23,7 +23,7 @@ class PhaseSamples extends QScript {
var prefix: String = "" var prefix: String = ""
@Argument(shortName = "L", doc = "Intervals", required = false) @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) @Input(doc = "level of parallelism for BAM phaser. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
var scatterCount = 0 var scatterCount = 0
@ -35,7 +35,9 @@ class PhaseSamples extends QScript {
var outputPhased: File = _ var outputPhased: File = _
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.intervalsString = List(qscript.intervals) if (qscript.intervals != null) {
this.intervalsString = List(qscript.intervals)
}
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
this.memoryLimit = 3 this.memoryLimit = 3

6
scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala
View File

@ -14,7 +14,7 @@ class ScatteredFullVariantAnnotator extends QScript {
var referenceFile: File = _ var referenceFile: File = _
@Argument(shortName = "L", doc = "Intervals", required = false) @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) @Input(doc = "level of parallelism. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
var scatterCount = 0 var scatterCount = 0
@ -36,7 +36,9 @@ class ScatteredFullVariantAnnotator extends QScript {
} }
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {
this.intervalsString = List(qscript.intervals) if (qscript.intervals != null) {
this.intervalsString = List(qscript.intervals)
}
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
this.input_file = List(qscript.bams) this.input_file = List(qscript.bams)