Commit 9c71efa3 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

style changes, bamMetrics changed in bammetrics

parent cfdfd0b9
...@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.extensions.picard ...@@ -3,12 +3,12 @@ package nl.lumc.sasc.biopet.extensions.picard
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output} import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/** /**
* Created by sajvanderzeeuw on 6-10-15. * Created by sajvanderzeeuw on 6-10-15.
*/ */
class BuildBamIndex (val root: Configurable) extends Picard { class BuildBamIndex(val root: Configurable) extends Picard {
javaMainClass = new picard.sam.BuildBamIndex().getClass.getName javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
......
...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.samtools ...@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output} import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/** /**
* Created by pjvanthof on 22/09/15. * Created by pjvanthof on 22/09/15.
......
...@@ -127,7 +127,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with ...@@ -127,7 +127,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId)) val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
addAll(bamMetricsFilter.functions) addAll(bamMetricsFilter.functions)
bamMetricsFilter.summaryName = "bamMetrics-filter" bamMetricsFilter.summaryName = "bammetrics-filter"
addSummaryQScript(bamMetricsFilter) addSummaryQScript(bamMetricsFilter)
addAll(Bam2Wig(qscript, bamFile).functions) addAll(Bam2Wig(qscript, bamFile).functions)
......
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