Commit 4e14ca72 authored by bow's avatar bow
Browse files

Rename directories and package identifiers for consistency with Queue

parent fcaccd90
/*
/*
* Copyright (c) 2012 The Broad Institute
* Modifications (c) 2014 Leiden University Medical Center
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
......
package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.InProcessFunction
......
package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
......
package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
package nl.lumc.sasc.biopet.wrappers
package nl.lumc.sasc.biopet.function
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
package nl.lumc.sasc.biopet.wrappers.fastq
package nl.lumc.sasc.biopet.function.fastq
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
package nl.lumc.sasc.biopet.pipelines.flexiprep
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.fastq._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.fastq._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard._
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
//import java.io.FileOutputStream
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.function._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
......@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
import nl.lumc.sasc.biopet.wrappers.Python
import nl.lumc.sasc.biopet.function.Python
import org.broadinstitute.sting.commandline._
import java.io.File
......
package nl.lumc.sasc.biopet.pipelines.gatk
import nl.lumc.sasc.biopet.wrappers._
import nl.lumc.sasc.biopet.wrappers.aligners._
import nl.lumc.sasc.biopet.function._
import nl.lumc.sasc.biopet.function.aligners._
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.pipelines.mapping._
import nl.lumc.sasc.biopet.pipelines.flexiprep._
......
package nl.lumc.sasc.biopet.wrappers.aligners
package nl.lumc.sasc.biopet.function.aligners
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
......
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