Moved extensions to new module

public/bam2wig/pom.xml

@@ -40,6 +40,11 @@
             <artifactId>BiopetCore</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetExtensions</artifactId>
+            <version>${project.version}</version>
+        </dependency>
     </dependencies>
 
 </project>
\ No newline at end of file

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

@@ -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.extensions
+package nl.lumc.sasc.biopet.core.extensions
 
 import java.io.File
 

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
 import java.io.File
 
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.Md5sum
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
 
 import scala.collection.mutable
 

public/biopet-extentsions/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>Biopet</artifactId>
+        <groupId>nl.lumc.sasc</groupId>
+        <version>0.5.0-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>BiopetExtensions</artifactId>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetCore</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/biopet-extentsions/src/test/resources/log4j.properties

+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala → public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala

@@ -31,7 +31,7 @@ class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
 
   @Test
   def summaryData(): Unit = {
-    val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
+    val file = new File(Paths.get(getClass.getResource("picard.alignmentMetrics").toURI).toString)
     val job = new CollectAlignmentSummaryMetrics(null)
     job.output = file
 

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala → public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala

@@ -31,7 +31,7 @@ class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
 
   @Test
   def summaryData(): Unit = {
-    val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
+    val file = new File(Paths.get(getClass.getResource("picard.insertsizemetrics").toURI).toString)
     val job = new CollectInsertSizeMetrics(null)
     job.output = file