Merged bug fix from Stable into Unstable

ivy.xml

@@ -46,7 +46,7 @@
     <!-- Lucene core utilities -->
     <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/>
 
-    <!-- Dependencies for LSF library -->
+    <!-- Dependencies for LSF, DRMAA, and other C libraries -->
     <dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
 
     <!-- Dependencies for amazon.com S3 support -->
@@ -75,6 +75,9 @@
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
 
+    <!-- snpEff annotator for pipelines -->
+    <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.2" />
+
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
     <exclude org="javax.servlet" />
     <exclude org="javax.jms" />

public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -35,8 +35,10 @@ import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.ConfigurationBuilder;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.Method;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.*;
@@ -57,8 +59,25 @@ public class PluginManager<PluginType> {
         Logger logger = (ch.qos.logback.classic.Logger) LoggerFactory.getLogger(Reflections.class);
         logger.setLevel(Level.OFF);
 
+        Set<URL> classPathUrls = new LinkedHashSet<URL>();
+
+        URL cwd;
+        try {
+            cwd = new File(".").getAbsoluteFile().toURI().toURL();
+        } catch (MalformedURLException e) {
+            throw new RuntimeException(e);
+        }
+
+        // NOTE: Reflections also scans directories for classes.
+        // Meanwhile some of the jar MANIFEST.MF Bundle-ClassPath properties contain "."
+        // Do NOT let reflections scan the CWD where it often picks up test classes when
+        // they weren't explicitly in the classpath, for example the UninstantiableWalker
+        for (URL url: JVMUtils.getClasspathURLs())
+            if (!url.equals(cwd))
+                classPathUrls.add(url);
+
         defaultReflections = new Reflections( new ConfigurationBuilder()
-            .setUrls(JVMUtils.getClasspathURLs())
+            .setUrls(classPathUrls)
             .setScanners(new SubTypesScanner()));
     }
 

public/packages/Queue.xml

@@ -59,7 +59,12 @@
             <dir name="com/sun/jna" />
 
             <!-- Contracts for Java -->
-            <package name="class com.google.java.contract.**" />
+            <package name="com.google.java.contract.**" />
+
+            <!-- snpEff -->
+            <package name="ca.mcgill.mcb.pcingola.**" />
+            <file path="snpEff_genes.ftl" />
+            <file path="snpEff_summary.ftl" />
         </dependencies>
         <modules>
             <module file="GATKEngine.xml"/>

public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala

@@ -0,0 +1,60 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.queue.extensions.snpeff
+
+import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
+import java.io.File
+import org.broadinstitute.sting.commandline.{Argument, Output, Input}
+
+/**
+ * Basic snpEff support.
+ * See: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Genomic_Annotations_Using_SnpEff_and_VariantAnnotator
+ */
+class SnpEff extends JavaCommandLineFunction {
+  javaMainClass = "ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff"
+
+  @Input(doc="snp vcf4 file")
+  var inVcf: File = _
+
+  @Input(doc="config file with path to data dir", required=false)
+  var config: File = _
+
+  @Argument(doc="genome version")
+  var genomeVersion: String = _
+
+  @Argument(doc="verbose", required=false)
+  var verbose = true
+
+  @Output(doc="snp eff output")
+  var outVcf: File = _
+
+  override def commandLine = Array(
+    super.commandLine,
+    " eff",
+    if (verbose) " -v" else "",
+    optional(" -c ", config),
+    " -i vcf -o vcf %s %s > %s".format(genomeVersion, inVcf, outVcf)
+  ).mkString
+}

settings/repository/net.sf.snpeff/snpeff-2.0.2.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.2" status="release" />
+</ivy-module>