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

autostyle fixes

parent 134d77a4
......@@ -20,11 +20,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
private var _summaryFile: File = _
private var _statisticsFile: File = _
private var _intervalSummaryFile: File = _
private var _intervalSummaryFile: File = _
private var _intervalStatisticsFile: File = _
private var _geneSummaryFile: File = _
private var _geneStatisticsFile: File = _
private var _cumulativeCoverageCountsFile: File = _
private var _cumulativeCoverageCountsFile: File = _
private var _cumulativeCoverageProportionsFile: File = _
@Output
......@@ -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 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() = {
super.beforeGraph()
......@@ -93,11 +93,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
}
_summaryFile = new File(out + ".sample_summary")
_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")
_geneSummaryFile = new File(out + ".sample_gene_summary")
_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")
}
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.xhmm
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.
......
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.utils.ToolCommand
......
......@@ -30,7 +30,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
"n_bins" -> 200,
"include_ref_n_sites" -> true,
"count_type" -> "COUNT_FRAGMENTS"
)
)
)
}
......
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