Commit 5ef60ac7 authored by Sander Bollen's avatar Sander Bollen

config values for all arguments

parent f70051f1
......@@ -44,68 +44,47 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
@Argument(required = false)
var calculateCoveraOverGenes: Option[File] = None
var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var countType: Option[String] = None
var countType: Option[String] = config("count_type", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var maxBaseQuality: Option[Int] = None
var maxBaseQuality: Option[Int] = config("max_base_quality", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var maxMappingQuality: Option[Int] = None
var maxMappingQuality: Option[Int] = config("max_mapping_quality", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var minBaseQuality: Option[Int] = None
var minBaseQuality: Option[Int] = config("min_base_quality", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var minMappingQuality: Option[Int] = None
var minMappingQuality: Option[Int] = config("min_mapping_quality", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var outputFormat: Option[String] = None
var outputFormat: Option[String] = config("output_format", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var partitionType: Option[String] = None
var partitionType: Option[String] = config("partition_type", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var omitDepthOutputAtEachBase: Boolean = false
var omitDepthOutputAtEachBase: Boolean = config("omit_depth_output_at_each_base", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var omitIntervalStatistics: Boolean = false
var omitIntervalStatistics: Boolean = config("omit_interval_statistics", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var omitLocusTable: Boolean = false
var omitLocusTable: Boolean = config("omit_locus_table", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var omitPerSampleStats: Boolean = false
var omitPerSampleStats: Boolean = config("omit_per_sample_stats", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var printBaseCounts: Boolean = false
var printBaseCounts: Boolean = config("print_base_counts", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var nBins: Option[Int] = None
var nBins: Option[Int] = config("n_bins", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var start: Option[Int] = None
var start: Option[Int] = config("start", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var stop: Option[Int] = None
var stop: Option[Int] = config("stop", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var summaryCoverageThreshold: Option[Int] = None
var summaryCoverageThreshold: Option[Int] = config("summary_coverage_threshold", namespace = "depth_of_coverage", default = None)
@Argument(required = false)
var ignoreDeletionSites: Boolean = false
var ignoreDeletionSites: Boolean = config("ignore_deletion_sites", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var includeDeletions: Boolean = false
var includeDeletions: Boolean = config("include_deletions", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var includeRefNSites: Boolean = false
var includeRefNSites: Boolean = config("include_RefNSites", namespace = "depth_of_coverage", default = false)
@Argument(required = false)
var printBinEndpointsAndExit: Boolean = false
var printBinEndpointsAndExit: Boolean = config("print_bin_endpoint_and_exit", namespace = "depth_of_coverage" , default = false)
override def beforeGraph() = {
super.beforeGraph()
......@@ -124,7 +103,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
override def cmdLine = {
super.cmdLine + required("--out", out) +
optional("--calculateCoverageOverGenes", calculateCoveraOverGenes) +
optional("--calculateCoverageOverGenes", calculateCoverageOverGenes) +
optional("--countType", countType) +
optional("--maxBaseQuality", maxBaseQuality) +
optional("--maxMappingQuality", maxMappingQuality) +
......
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