Commit 0b4c76c5 authored by Peter van 't Hof's avatar Peter van 't Hof

Merge branch 'fix-xhmm' into 'develop'

fix biopet-495



See merge request !496
parents 5c13638f e735b32d
......@@ -18,31 +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
private var _summaryFile: File = _
@Output
private var _statisticsFile: File = _
@Output
private var _intervalSummaryFile: File = _
@Output
private var _intervalStatisticsFile: File = _
@Output
private var _geneSummaryFile: File = _
@Output
private var _geneStatisticsFile: File = _
@Output
private var _cumulativeCoverageCountsFile: File = _
@Output
private var _cumulativeCoverageProportionsFile: File = _
@Output
var summaryFile = _summaryFile
@Output
var statisticsFile = _statisticsFile
@Output
var intervalSummaryFile = _intervalSummaryFile
@Output
var intervalStatisticsFile = _intervalStatisticsFile
@Output
var geneSummaryFile = _geneSummaryFile
@Output
var geneStatisticsFile = _geneStatisticsFile
@Output
var culumativeCoverageCountsFile = _cumulativeCoverageCountsFile
@Output
var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
def summaryFile = new File(out + ".sample_summary")
def statisticsFile = new File(out + ".sample_statistics")
def intervalSummaryFile = new File(out + ".sample_interval_summary")
def intervalStatisticsFile = new File(out + ".sample_interval_statistics")
def geneSummaryFile = new File(out + ".sample_gene_summary")
def geneStatisticsFile = new File(out + ".sample_gene_statistics")
def cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
def cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
@Input(required = false)
var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None)
......@@ -92,14 +92,14 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
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")
_summaryFile = summaryFile
_statisticsFile = statisticsFile
_intervalSummaryFile = intervalSummaryFile
_intervalStatisticsFile = intervalStatisticsFile
_geneSummaryFile = geneSummaryFile
_geneStatisticsFile = geneStatisticsFile
_cumulativeCoverageCountsFile = cumulativeCoverageCountsFile
_cumulativeCoverageProportionsFile = cumulativeCoverageProportionsFile
}
override def cmdLine = {
......
......@@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
@Input
var r: File = _
@Output
private var _outputXcnvAuxFile: File = _
@Output
var outputXcnvAuxFile = _outputXcnvAuxFile
def outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
var xhmmAnalysisName: String = _
......@@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
if (outputXcnv == null) {
throw new IllegalStateException("Must set output file")
}
_outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
_outputXcnvAuxFile = outputXcnvAuxFile
}
def cmdLine = {
......
......@@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
def biopetScript() = {
val depths = inputBams.map { keyValuePair =>
DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, ".bam", ".dcov"), List(targets))
DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, keyValuePair._2, ".bam", ".dcov"), List(targets))
}.toList
addAll(depths)
......
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