Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/fullCallingPipeline.q

@@ -284,7 +284,7 @@ def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndel
  handFilter.unfilteredVCF = annotated.annotatedVCF
  handFilter.indelMask = indels.indelVCF
  handFilter.filterNames = List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
- handFilter.filterExpressions = List("SB>=0.10","AB>=0.75","QD<5","HRun>=4")
+ handFilter.filterExpressions = List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
  handFilter.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".handfiltered.vcf")
  // 3.i generate gaussian clusters on the masked vcf
  val clusters = new GenerateVariantClusters

scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala

@@ -14,5 +14,13 @@ class CreateTempDirsFunction extends CommandLineFunction {
   @Input(doc="Sleep seconds", required=false)
   var mkdirSleepSeconds: Option[Int] = None
 
+  // TODO: After port of LSF submitter use -cwd <dir> instead of trying to run from the directory
+  // For now, create the directory so that BroadCore can run bsub from it -kshakir July 27, 2010 on chartl's computer
+
+  override def freeze = {
+    super.freeze
+    tempDirectories.foreach(_.mkdirs)
+  }
+
   def commandLine = "mkdir -pv%s%s".format(repeat(" '", tempDirectories, "'"), optional(" && sleep ", mkdirSleepSeconds))
 }