Commit 5f6b1817 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed indexes

parent 217e8ee4
......@@ -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") +
......
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