Added bammetrics as artifact

public/bammetrics/.gitignore

+/target/
\ No newline at end of file

public/bammetrics/pom.xml

+<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">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>BamMetrics</artifactId>
+    <version>0.2.0-DEV</version>
+    <packaging>jar</packaging>
+    
+    <inceptionYear>2014</inceptionYear>
+    <name>BamMetrics</name>
+    <url>http://maven.apache.org</url>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <sting.unpack.phase>prepare-package</sting.unpack.phase>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <includes>
+                    <include>**/*</include>
+                </includes>
+            </resource>
+        </resources>
+        <plugins>
+            <plugin>
+                <groupId>org.scala-tools</groupId>
+                <artifactId>maven-scala-plugin</artifactId>
+                <version>2.15.2</version>
+                <executions>
+                    <execution>
+                        <id>scala-compile</id>
+                        <goals>
+                            <goal>compile</goal>
+                            <goal>testCompile</goal>
+                        </goals>
+                        <configuration>
+                            <args>
+                                <arg>-dependencyfile</arg>
+                                <arg>${project.build.directory}/.scala_dependencies</arg>
+                                <arg>-deprecation</arg>
+                                <arg>-feature</arg>
+                            </args>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>2.5</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>2.3.2</version>
+                <configuration>
+                    <showDeprecation>true</showDeprecation>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

+package nl.lumc.sasc.biopet.pipelines.bammetrics
+
+import nl.lumc.sasc.biopet.scripts.CoverageStats
+import org.broadinstitute.gatk.queue.QScript
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import java.io.File
+import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
+
+class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Bam File", shortName = "BAM", required = true)
+  var inputBam: File = _
+
+  @Input(doc = "Bed tracks targets", shortName = "target", required = false)
+  var bedFiles: List[File] = Nil
+
+  @Input(doc = "Bed tracks bait", shortName = "bait", required = false)
+  var baitBedFile: File = _
+
+  @Argument(doc = "", required = false)
+  var wholeGenome = false
+
+  def init() {
+    if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
+    else if (!outputDir.endsWith("/")) outputDir += "/"
+    if (config.contains("target_bed")) {
+      for (file <- config("target_bed").asList) {
+        bedFiles +:= new File(file.toString)
+      }
+    }
+    if (baitBedFile == null && config.contains("target_bait")) baitBedFile = config("target_bait")
+  }
+
+  def biopetScript() {
+    add(SamtoolsFlagstat(this, inputBam, outputDir))
+    add(BiopetFlagstat(this, inputBam, outputDir))
+    add(CollectGcBiasMetrics(this, inputBam, outputDir))
+    add(CollectInsertSizeMetrics(this, inputBam, outputDir))
+    add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
+
+    val baitIntervalFile = if (baitBedFile != null) new File(outputDir, baitBedFile.getName.stripSuffix(".bed") + ".interval") else null
+    if (baitIntervalFile != null)
+      add(BedToInterval(this, baitBedFile, inputBam, outputDir), true)
+
+    for (bedFile <- bedFiles) {
+      val targetDir = outputDir + bedFile.getName.stripSuffix(".bed") + "/"
+      val targetInterval = BedToInterval(this, bedFile, inputBam, targetDir)
+      add(targetInterval, true)
+      add(CalculateHsMetrics(this, inputBam, if (baitIntervalFile != null) baitIntervalFile
+      else targetInterval.output, targetInterval.output, targetDir))
+
+      val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
+      add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
+      add(SamtoolsFlagstat(this, strictOutputBam))
+      add(BiopetFlagstat(this, strictOutputBam, targetDir))
+
+      val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
+      add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
+      add(SamtoolsFlagstat(this, looseOutputBam))
+      add(BiopetFlagstat(this, looseOutputBam, targetDir))
+
+      val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
+      add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
+      add(CoverageStats(this, coverageFile, targetDir))
+    }
+  }
+}
+
+object BamMetrics extends PipelineCommand {
+  def apply(root: Configurable, bamFile: File, outputDir: String): BamMetrics = {
+    val bamMetrics = new BamMetrics(root)
+    bamMetrics.inputBam = bamFile
+    bamMetrics.outputDir = outputDir
+
+    bamMetrics.init
+    bamMetrics.biopetScript
+    return bamMetrics
+  }
+}