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Commit eceac8c1 authored by Peter van 't Hof's avatar Peter van 't Hof
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Move scripts to bammetrics

parent d0f1cdd7
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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @ eceac8c1
......@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import nl.lumc.sasc.biopet.scripts.CoverageStats
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import org.broadinstitute.gatk.queue.QScript
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala → public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala
View file @ eceac8c1
......@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.scripts
package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
import java.io.File
......
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @ eceac8c1
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import nl.lumc.sasc.biopet.scripts.CoverageStats
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.apache.commons.io.FileUtils
......
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