Add ExampleLocusWalkerSpark.java and test

src/main/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerSpark.java

@@ -0,0 +1,82 @@
+package org.broadinstitute.hellbender.tools.examples;
+
+import htsjdk.variant.variantcontext.VariantContext;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.Function;
+import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.programgroups.ExampleProgramGroup;
+import org.broadinstitute.hellbender.engine.AlignmentContext;
+import org.broadinstitute.hellbender.engine.FeatureContext;
+import org.broadinstitute.hellbender.engine.FeatureInput;
+import org.broadinstitute.hellbender.engine.ReferenceContext;
+import org.broadinstitute.hellbender.engine.spark.LocusWalkerContext;
+import org.broadinstitute.hellbender.engine.spark.LocusWalkerSpark;
+import org.broadinstitute.hellbender.utils.pileup.ReadPileup;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Example/toy program that shows how to implement the LocusWalker interface. Prints locus-based coverage from supplied
+ * reads, and reference bases/overlapping variants if provided
+ */
+@CommandLineProgramProperties(
+        summary = "Example tool that prints locus-based coverage from supplied read to the specified output file (stdout if none provided), along with overlapping reference bases/features (if provided)",
+        oneLineSummary = "Example tool that prints locus-based coverage with optional contextual data",
+        programGroup = ExampleProgramGroup.class,
+        omitFromCommandLine = true
+)
+public final class ExampleLocusWalkerSpark extends LocusWalkerSpark {
+    private static final long serialVersionUID = 1L;
+
+    @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "Output file (if not provided, defaults to STDOUT)", common = false, optional = true)
+    private String outputFile = null;
+
+    @Argument(fullName = StandardArgumentDefinitions.VARIANT_LONG_NAME, shortName = StandardArgumentDefinitions.VARIANT_SHORT_NAME, doc = "One or more VCF files", optional = true)
+    private List<FeatureInput<VariantContext>> variants;
+
+    private PrintStream outputStream = null;
+
+
+    @Override
+    protected void processAlignments(JavaRDD<LocusWalkerContext> rdd, JavaSparkContext ctx) {
+        rdd.map(intervalFunction(variants)).saveAsTextFile(outputFile);
+    }
+
+    private static Function<LocusWalkerContext, String> intervalFunction(List<FeatureInput<VariantContext>> variants) {
+        return (Function<LocusWalkerContext, String>) context -> {
+            AlignmentContext alignmentContext = context.getAlignmentContext();
+            ReferenceContext referenceContext = context.getReferenceContext();
+            FeatureContext featureContext = context.getFeatureContext();
+
+            StringBuilder sb = new StringBuilder();
+
+            // Get pileup and counts
+            ReadPileup pileup = alignmentContext.getBasePileup();
+            // print the locus and coverage
+            sb.append(String.format("Current locus %s:%d (coverage=%s)\n", alignmentContext.getContig(),
+                    alignmentContext.getPosition(), pileup.size()));
+            // print the reference context if available
+            if ( referenceContext.hasBackingDataSource() ) {
+                sb.append("\tReference base(s): " + new String(referenceContext.getBases()));
+                sb.append("\n");
+            }
+            // print the overlapping variants if there are some
+            if(featureContext.hasBackingDataSource()) {
+                List<VariantContext> vars = featureContext.getValues(variants);
+                if(!vars.isEmpty()) {
+                    sb.append("\tOverlapping variant(s):\n");
+                    for (VariantContext variant : vars) {
+                        sb.append(String.format("\t\t%s:%d-%d, Ref:%s, Alt(s):%s\n", variant.getContig(), variant.getStart(),
+                                variant.getEnd(), variant.getReference(), variant.getAlternateAlleles()));
+                    }
+                }
+            }
+
+            return sb.toString();
+        };
+    }
+}

src/test/java/org/broadinstitute/hellbender/tools/examples/ExampleLocusWalkerSparkIntegrationTest.java

@@ -0,0 +1,34 @@
+package org.broadinstitute.hellbender.tools.examples;
+
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.IntegrationTestSpec;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+
+public final class ExampleLocusWalkerSparkIntegrationTest extends CommandLineProgramTest {
+    private static final String TEST_DATA_DIRECTORY = publicTestDir + "org/broadinstitute/hellbender/engine/";
+    private static final String TEST_OUTPUT_DIRECTORY = exampleTestDir;
+
+    @Test
+    public void testExampleLocusWalker() throws IOException {
+        final File out = File.createTempFile("out", ".txt");
+        out.delete();
+        out.deleteOnExit();
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.add("-L 1");
+        args.add("--input");
+        args.add(TEST_DATA_DIRECTORY + "reads_data_source_test1.bam");
+        args.add("-V");
+        args.add(TEST_DATA_DIRECTORY + "feature_data_source_test.vcf");
+        args.add("--output");
+        args.add(out.getAbsolutePath());
+        args.add("--reference");
+        args.add(hg19MiniReference);
+        this.runCommandLine(args.getArgsArray());
+        File expected = new File(TEST_OUTPUT_DIRECTORY, "expected_ExampleLocusWalkerIntegrationTest_output.txt");
+        IntegrationTestSpec.assertEqualTextFiles(new File(out, "part-00000"), expected);
+    }
+}