Commit 992d265a authored by Sander Bollen's avatar Sander Bollen
Browse files

autostyle fixes

parent 134d77a4
...@@ -20,11 +20,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK { ...@@ -20,11 +20,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
private var _summaryFile: File = _ private var _summaryFile: File = _
private var _statisticsFile: File = _ private var _statisticsFile: File = _
private var _intervalSummaryFile: File = _ private var _intervalSummaryFile: File = _
private var _intervalStatisticsFile: File = _ private var _intervalStatisticsFile: File = _
private var _geneSummaryFile: File = _ private var _geneSummaryFile: File = _
private var _geneStatisticsFile: File = _ private var _geneStatisticsFile: File = _
private var _cumulativeCoverageCountsFile: File = _ private var _cumulativeCoverageCountsFile: File = _
private var _cumulativeCoverageProportionsFile: File = _ private var _cumulativeCoverageProportionsFile: File = _
@Output @Output
...@@ -84,7 +84,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK { ...@@ -84,7 +84,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
var includeRefNSites: Boolean = config("include_ref_n_sites", namespace = "depth_of_coverage", default = false) var includeRefNSites: Boolean = config("include_ref_n_sites", namespace = "depth_of_coverage", default = false)
var printBinEndpointsAndExit: Boolean = config("print_bin_endpoint_and_exit", namespace = "depth_of_coverage" , default = false) var printBinEndpointsAndExit: Boolean = config("print_bin_endpoint_and_exit", namespace = "depth_of_coverage", default = false)
override def beforeGraph() = { override def beforeGraph() = {
super.beforeGraph() super.beforeGraph()
...@@ -93,11 +93,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK { ...@@ -93,11 +93,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
} }
_summaryFile = new File(out + ".sample_summary") _summaryFile = new File(out + ".sample_summary")
_statisticsFile = new File(out + ".sample_statistics") _statisticsFile = new File(out + ".sample_statistics")
_intervalSummaryFile = new File(out + ".sample_interval_summary") _intervalSummaryFile = new File(out + ".sample_interval_summary")
_intervalStatisticsFile = new File(out + ".sample_interval_statistics") _intervalStatisticsFile = new File(out + ".sample_interval_statistics")
_geneSummaryFile = new File(out + ".sample_gene_summary") _geneSummaryFile = new File(out + ".sample_gene_summary")
_geneStatisticsFile = new File(out + ".sample_gene_statistics") _geneStatisticsFile = new File(out + ".sample_gene_statistics")
_cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts") _cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
_cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions") _cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
} }
......
...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.xhmm ...@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version} import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
/** /**
* Created by Sander Bollen on 23-11-16. * Created by Sander Bollen on 23-11-16.
......
package nl.lumc.sasc.biopet.tools package nl.lumc.sasc.biopet.tools
import java.io.{BufferedWriter, File, FileWriter, PrintWriter} import java.io.{ BufferedWriter, File, FileWriter, PrintWriter }
import nl.lumc.sasc.biopet.tools.VepNormalizer.Args import nl.lumc.sasc.biopet.tools.VepNormalizer.Args
import nl.lumc.sasc.biopet.utils.ToolCommand import nl.lumc.sasc.biopet.utils.ToolCommand
......
...@@ -30,7 +30,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference { ...@@ -30,7 +30,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
"n_bins" -> 200, "n_bins" -> 200,
"include_ref_n_sites" -> true, "include_ref_n_sites" -> true,
"count_type" -> "COUNT_FRAGMENTS" "count_type" -> "COUNT_FRAGMENTS"
) )
) )
} }
......
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