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

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 { ...@@ -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") @Output(fullName = "out", shortName = "o", doc = "File name base to which coverage metric should be written")
var out: File = _ var out: File = _
@Output
private var _summaryFile: File = _ private var _summaryFile: File = _
@Output
private var _statisticsFile: File = _ private var _statisticsFile: File = _
@Output
private var _intervalSummaryFile: File = _ private var _intervalSummaryFile: File = _
@Output
private var _intervalStatisticsFile: File = _ private var _intervalStatisticsFile: File = _
@Output
private var _geneSummaryFile: File = _ private var _geneSummaryFile: File = _
@Output
private var _geneStatisticsFile: File = _ private var _geneStatisticsFile: File = _
@Output
private var _cumulativeCoverageCountsFile: File = _ private var _cumulativeCoverageCountsFile: File = _
@Output
private var _cumulativeCoverageProportionsFile: File = _ private var _cumulativeCoverageProportionsFile: File = _
@Output def summaryFile = new File(out + ".sample_summary")
var summaryFile = _summaryFile def statisticsFile = new File(out + ".sample_statistics")
@Output def intervalSummaryFile = new File(out + ".sample_interval_summary")
var statisticsFile = _statisticsFile def intervalStatisticsFile = new File(out + ".sample_interval_statistics")
@Output def geneSummaryFile = new File(out + ".sample_gene_summary")
var intervalSummaryFile = _intervalSummaryFile def geneStatisticsFile = new File(out + ".sample_gene_statistics")
@Output def cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
var intervalStatisticsFile = _intervalStatisticsFile def cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
@Output
var geneSummaryFile = _geneSummaryFile
@Output
var geneStatisticsFile = _geneStatisticsFile
@Output
var culumativeCoverageCountsFile = _cumulativeCoverageCountsFile
@Output
var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
@Input(required = false) @Input(required = false)
var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None) 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 { ...@@ -92,14 +92,14 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
if (out == null) { if (out == null) {
throw new IllegalStateException("You must set the <out> variable") throw new IllegalStateException("You must set the <out> variable")
} }
_summaryFile = new File(out + ".sample_summary") _summaryFile = summaryFile
_statisticsFile = new File(out + ".sample_statistics") _statisticsFile = statisticsFile
_intervalSummaryFile = new File(out + ".sample_interval_summary") _intervalSummaryFile = intervalSummaryFile
_intervalStatisticsFile = new File(out + ".sample_interval_statistics") _intervalStatisticsFile = intervalStatisticsFile
_geneSummaryFile = new File(out + ".sample_gene_summary") _geneSummaryFile = geneSummaryFile
_geneStatisticsFile = new File(out + ".sample_gene_statistics") _geneStatisticsFile = geneStatisticsFile
_cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts") _cumulativeCoverageCountsFile = cumulativeCoverageCountsFile
_cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions") _cumulativeCoverageProportionsFile = cumulativeCoverageProportionsFile
} }
override def cmdLine = { override def cmdLine = {
......
...@@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable { ...@@ -22,10 +22,10 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
@Input @Input
var r: File = _ var r: File = _
@Output
private var _outputXcnvAuxFile: File = _ private var _outputXcnvAuxFile: File = _
@Output def outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux")
var outputXcnvAuxFile = _outputXcnvAuxFile
var xhmmAnalysisName: String = _ var xhmmAnalysisName: String = _
...@@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable { ...@@ -34,7 +34,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
if (outputXcnv == null) { if (outputXcnv == null) {
throw new IllegalStateException("Must set output file") throw new IllegalStateException("Must set output file")
} }
_outputXcnvAuxFile = new File(outputXcnv.getAbsolutePath + ".aux") _outputXcnvAuxFile = outputXcnvAuxFile
} }
def cmdLine = { def cmdLine = {
......
...@@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -36,7 +36,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
def biopetScript() = { def biopetScript() = {
val depths = inputBams.map { keyValuePair => 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 }.toList
addAll(depths) addAll(depths)
......
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