Minor usability improvements to the standard eval script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5551 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/core/StandardVariantEvaluation.scala

@@ -21,6 +21,9 @@ class StandardVariantEvaluation extends QScript {
   @Argument(shortName = "dataDir", doc="Path to the standard evaluation data files", required=false)
   val DATA_DIR = "/humgen/gsa-hpprojects/GATK/data/Comparisons/StandardForEvaluation/b37/"
 
+  @Argument(shortName = "evalStandard1000GCalls", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
+  val EVAL_STANDARD_1000G_CALLS: Boolean = false
+
   val COMPS_DIR = DATA_DIR + "/comps/"
   val EVALS_DIR = DATA_DIR + "/evals/"
 
@@ -77,13 +80,17 @@ class StandardVariantEvaluation extends QScript {
     addComp(new Comp("NA12878.homvar.CG", "indels", "NA12878.CG.b37.indels.vcf", true))
     addComp(new Comp("g1k.pilot1.validation", "indels", "pilot1_indel_validation_2009.b37.vcf"))
     addComp(new Comp("NA12878.hand_curated", "indels", "NA12878.validated.curated.polymorphic.indels.vcf"))
+    addComp(new Comp("NA12878.Mullikin", "indels", "NA12878.DIPline.NQScm.expanded.chr20.b37.minReads_2_or_gt2bp.vcf"))
+
 
     //
     // INDEL call sets
     //
+    if ( EVAL_STANDARD_1000G_CALLS ) {
       addEval(new Eval("dindel", "indels", "20110208.chr20.dindel2.EUR.sites.vcf"))
       addEval(new Eval("si", "indels", "20101123.chr20.si.v2.EUR.sites.vcf"))
       addEval(new Eval("gatk", "indels", "EUR.phase1.chr20.broad.filtered.indels.sites.vcf"))
+    }
 
     //
     // Standard evaluation files for SNPs
@@ -98,10 +105,10 @@ class StandardVariantEvaluation extends QScript {
     //
     // SNP call sets
     //
+    if ( EVAL_STANDARD_1000G_CALLS ) {
       addEval(new Eval("1000G.gatk.eurPlus.phase1", "snps", "EUR+.phase1.chr20.broad.recal.vrcut1p0.sites.vcf"))
       addEval(new Eval("1000G.high_specificity.phase1", "snps", "ALL.phase1.chr20.projectConsensus.highSpecificity.snps.genotypes.sites.vcf"))
-    // todo -- are there other good call sets for evaluation?
+    }
-    // todo -- add hg19 na12878 64x
   }
 
   def script = {
@@ -131,6 +138,8 @@ class StandardVariantEvaluation extends QScript {
       var evalsOfType = EVALS.filter(_.evalType == evalType)
       val compsOfType = COMPS.filter(_.evalType == evalType)
 
+      if ( evalsOfType.size > 0 ) {
+
         // if desired and possible, create a union.X.vcf file
         if ( CREATE_UNION && evalsOfType.size > 1 ) {
           val union: File = new File("union.%s.vcf".format(evalType))
@@ -155,6 +164,7 @@ class StandardVariantEvaluation extends QScript {
         add(VE)
       }
     }
+  }
 
   /**
    * Select homozygous non-reference sites from a single deep data set