Fixed indexes

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -24,19 +24,19 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
 
   /** SnpEff file from which to get annotations */
   @Input(fullName = "snpEffFile", shortName = "snpEffFile", doc = "SnpEff file from which to get annotations", required = false, exclusiveOf = "", validation = "")
-  var snpEffFile: Option[File] = None
+  var snpEffFile: Option[File] = config("snpEffFile")
 
   /** dbSNP file */
   @Input(fullName = "dbsnp", shortName = "D", doc = "dbSNP file", required = false, exclusiveOf = "", validation = "")
-  var dbsnp: Option[File] = None
+  var dbsnp: Option[File] = config("dbsnp")
 
   /** Comparison VCF file */
   @Input(fullName = "comp", shortName = "comp", doc = "Comparison VCF file", required = false, exclusiveOf = "", validation = "")
-  var comp: Seq[File] = Nil
+  var comp: List[File] = config("comp", default = Nil)
 
   /** External resource VCF file */
   @Input(fullName = "resource", shortName = "resource", doc = "External resource VCF file", required = false, exclusiveOf = "", validation = "")
-  var resource: Seq[File] = Nil
+  var resource: List[File] = config("resource")
 
   /** File to which variants should be written */
   @Output(fullName = "out", shortName = "o", doc = "File to which variants should be written", required = false, exclusiveOf = "", validation = "")
@@ -45,39 +45,35 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
 
   /** One or more specific annotations to apply to variant calls */
   @Argument(fullName = "annotation", shortName = "A", doc = "One or more specific annotations to apply to variant calls", required = false, exclusiveOf = "", validation = "")
-  var annotation: Seq[String] = Nil
+  var annotation: List[String] = config("annotation", default = Nil, freeVar = false)
 
   /** One or more specific annotations to exclude */
   @Argument(fullName = "excludeAnnotation", shortName = "XA", doc = "One or more specific annotations to exclude", required = false, exclusiveOf = "", validation = "")
-  var excludeAnnotation: Seq[String] = Nil
+  var excludeAnnotation: List[String] = config("excludeAnnotation", default = Nil)
 
   /** One or more classes/groups of annotations to apply to variant calls */
   @Argument(fullName = "group", shortName = "G", doc = "One or more classes/groups of annotations to apply to variant calls", required = false, exclusiveOf = "", validation = "")
-  var group: Seq[String] = Nil
+  var group: List[String] = config("group", default = Nil)
 
   /** One or more specific expressions to apply to variant calls */
   @Argument(fullName = "expression", shortName = "E", doc = "One or more specific expressions to apply to variant calls", required = false, exclusiveOf = "", validation = "")
-  var expression: Seq[String] = Nil
+  var expression: List[String] = config("expression", default = Nil)
 
   /** Check for allele concordances when using an external resource VCF file */
   @Argument(fullName = "resourceAlleleConcordance", shortName = "rac", doc = "Check for allele concordances when using an external resource VCF file", required = false, exclusiveOf = "", validation = "")
-  var resourceAlleleConcordance: Boolean = _
+  var resourceAlleleConcordance: Boolean = config("resourceAlleleConcordance", default = false)
 
   /** Use all possible annotations (not for the faint of heart) */
   @Argument(fullName = "useAllAnnotations", shortName = "all", doc = "Use all possible annotations (not for the faint of heart)", required = false, exclusiveOf = "", validation = "")
-  var useAllAnnotations: Boolean = _
-
-  /** List the available annotations and exit */
-  @Argument(fullName = "list", shortName = "ls", doc = "List the available annotations and exit", required = false, exclusiveOf = "", validation = "")
-  var list: Boolean = _
+  var useAllAnnotations: Boolean = config("useAllAnnotations", default = false)
 
   /** Add dbSNP ID even if one is already present */
   @Argument(fullName = "alwaysAppendDbsnpId", shortName = "alwaysAppendDbsnpId", doc = "Add dbSNP ID even if one is already present", required = false, exclusiveOf = "", validation = "")
-  var alwaysAppendDbsnpId: Boolean = _
+  var alwaysAppendDbsnpId: Boolean = config("alwaysAppendDbsnpId", default = false)
 
   /** GQ threshold for annotating MV ratio */
   @Argument(fullName = "MendelViolationGenotypeQualityThreshold", shortName = "mvq", doc = "GQ threshold for annotating MV ratio", required = false, exclusiveOf = "", validation = "")
-  var MendelViolationGenotypeQualityThreshold: Option[Double] = None
+  var MendelViolationGenotypeQualityThreshold: Option[Double] = config("MendelViolationGenotypeQualityThreshold")
 
   /** Format string for MendelViolationGenotypeQualityThreshold */
   @Argument(fullName = "MendelViolationGenotypeQualityThresholdFormat", shortName = "", doc = "Format string for MendelViolationGenotypeQualityThreshold", required = false, exclusiveOf = "", validation = "")
@@ -85,15 +81,15 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
 
   /** Filter out reads with CIGAR containing the N operator, instead of failing with an error */
   @Argument(fullName = "filter_reads_with_N_cigar", shortName = "filterRNC", doc = "Filter out reads with CIGAR containing the N operator, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_reads_with_N_cigar: Boolean = _
+  var filter_reads_with_N_cigar: Boolean = config("filter_reads_with_N_cigar", default = false)
 
   /** Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error */
   @Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "Filter out reads with mismatching numbers of bases and base qualities, instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_mismatching_base_and_quals: Boolean = _
+  var filter_mismatching_base_and_quals: Boolean = config("filter_mismatching_base_and_quals", default = false)
 
   /** Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error */
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
-  var filter_bases_not_stored: Boolean = _
+  var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
   override def beforeGraph() {
     super.beforeGraph()
@@ -121,7 +117,6 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
     repeat("-E", expression, spaceSeparated = true, escape = true, format = "%s") +
     conditional(resourceAlleleConcordance, "-rac", escape = true, format = "%s") +
     conditional(useAllAnnotations, "-all", escape = true, format = "%s") +
-    conditional(list, "-ls", escape = true, format = "%s") +
     conditional(alwaysAppendDbsnpId, "-alwaysAppendDbsnpId", escape = true, format = "%s") +
     optional("-mvq", MendelViolationGenotypeQualityThreshold, spaceSeparated = true, escape = true, format = MendelViolationGenotypeQualityThresholdFormat) +
     conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +