Commit f70051f1 authored by Sander Bollen's avatar Sander Bollen

re-arrange auto-generated files from depth of coverage

parent c5544c76
......@@ -18,45 +18,31 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written")
var out: File = _
@Output
lazy val summaryFile: File = {
new File(out + ".sample_summary")
}
private var _summaryFile: File = _
private var _statisticsFile: File = _
private var _intervalSummaryFile: File = _
private var _intervalStatisticsFile: File = _
private var _geneSummaryFile: File = _
private var _geneStatisticsFile: File = _
private var _cumulativeCoverageCountsFile: File = _
private var _cumulativeCoverageProportionsFile: File = _
@Output
lazy val statisticsFile: File = {
new File(out + ".sample_statistics")
}
var summaryFile = _summaryFile
@Output
lazy val intervalSummaryFile: File = {
new File(out + ".sample_interval_summary")
}
var statisticsFile = _statisticsFile
@Output
lazy val intervalStatisticsFile: File = {
new File(out + ".sample_interval_statistics")
}
var intervalSummaryFile = _intervalSummaryFile
@Output
lazy val geneSummaryFile: File = {
new File(out + ".sample_gene_summary")
}
var intervalStatisticsFile = _intervalStatisticsFile
@Output
lazy val geneStatisticsFile: File = {
new File(out + ".sample_gene_statistics")
}
var geneSummaryFile = _geneSummaryFile
@Output
lazy val cumulativeCoverageCountsFile: File = {
new File(out + ".sample_cumulative_coverage_counts")
}
var geneStatisticsFile = _geneStatisticsFile
@Output
lazy val cumulativeCoverageProportionsFile: File = {
new File(out + ".sample_cumulative_coverage_proportions")
}
var culumativeCoverageCountsFile = _cumulativeCoverageCountsFile
@Output
var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
@Argument(required = false)
var calculateCoveraOverGenes: Option[File] = None
......@@ -121,6 +107,21 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Argument(required = false)
var printBinEndpointsAndExit: Boolean = false
override def beforeGraph() = {
super.beforeGraph()
if (out == null) {
throw new IllegalStateException("You must set the <out> variable")
}
_summaryFile = new File(out + ".sample_summary")
_statisticsFile = new File(out + ".sample_statistics")
_intervalSummaryFile = new File(out + ".sample_interval_summary")
_intervalStatisticsFile = new File(out + ".sample_interval_statistics")
_geneSummaryFile = new File(out + ".sample_gene_summary")
_geneStatisticsFile = new File(out + ".sample_gene_statistics")
_cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
_cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
}
override def cmdLine = {
super.cmdLine + required("--out", out) +
optional("--calculateCoverageOverGenes", calculateCoveraOverGenes) +
......
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