Rebase and update to obtain latest test hooks. This rebase will remov…

…e existing line comments, but I believe they are all addressed.

Still TODO: Merge in other tool functionality also requested in the other PR comments.

src/main/java/org/broadinstitute/hellbender/tools/PrintReadsByReadGroup.java

@@ -3,6 +3,7 @@
 import htsjdk.samtools.*;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.IOUtil;
+import org.apache.commons.io.FilenameUtils;
 import org.broadinstitute.hellbender.cmdline.CommandLineProgram;
 import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
 import org.broadinstitute.hellbender.cmdline.Option;
@@ -29,23 +30,20 @@ public class PrintReadsByReadGroup extends CommandLineProgram {
 
     @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME,
             doc = "The directory to write SAM or BAM or CRAM files by read group.")
-    public Path OUTPUT_DIRECTORY = Paths.get("");
-
-    public static void main(final String[] args) {
-        new PrintReadsByReadGroup().instanceMain(args);
-    }
+    public File OUTPUT_DIRECTORY = new File("");
 
     @Override
-    protected int doWork() {
+    protected Object doWork() {
         printReadsByReadGroup();
-        return 0;
+        return null;
     }
 
     /**
      * This is factored out of doWork only for unit testing.
      */
     protected void printReadsByReadGroup() {
         IOUtil.assertFileIsReadable(INPUT);
+        IOUtil.assertDirectoryIsWritable(OUTPUT_DIRECTORY);
         final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
         Map<String, SAMFileWriter> outs = createWriters(in);
         for (final SAMRecord rec : in) {
@@ -59,20 +57,17 @@ private Map<String, SAMFileWriter> createWriters(final SamReader in) {
         final Map<String, SAMFileWriter> outs = new HashMap<>();
 
         final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
-        samFileWriterFactory.setCreateIndex(true);
-        samFileWriterFactory.setUseAsyncIo(true);
 
         final SAMFileHeader samFileHeaderIn = in.getFileHeader();
-        final String[] tokens = INPUT.getName().split("\\.");
-        final String extension = tokens[tokens.length - 1];
+        final String extension = FilenameUtils.getExtension(INPUT.getName());
 
         samFileHeaderIn.getReadGroups().forEach(samReadGroupRecord -> {
             final SAMFileHeader samFileHeaderOut = samFileHeaderIn.clone();
             samFileHeaderOut.setReadGroups(Collections.singletonList(samReadGroupRecord));
 
             final String sample = samReadGroupRecord.getSample();
             final String readGroupId = samReadGroupRecord.getReadGroupId();
-            final File outFile = OUTPUT_DIRECTORY.resolve(sample + "." + readGroupId + "." + extension).toFile();
+            final File outFile = new File(OUTPUT_DIRECTORY, sample + "." + readGroupId + "." + extension);
 
             outs.put(readGroupId, samFileWriterFactory.makeWriter(samFileHeaderOut, true, outFile, REFERENCE_SEQUENCE));
         });

src/test/java/org/broadinstitute/hellbender/tools/PrintReadsByReadGroupTest.java

@@ -28,6 +28,8 @@
 import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.util.CloserUtil;
 import htsjdk.samtools.util.IOUtil;
+import org.broadinstitute.hellbender.CommandLineProgramTest;
+import org.broadinstitute.hellbender.cmdline.StandardOptionDefinitions;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
@@ -36,13 +38,20 @@
 import java.lang.reflect.Modifier;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.concurrent.Callable;
 import java.util.stream.Stream;
 
-public class PrintReadsByReadGroupTest {
-    private static final String TEST_DATA_PREFIX =
-            "src/test/resources/org/broadinstitute/hellbender/tools/print_reads_by_read_group.";
-    private static final File REFERENCE_SEQUENCE = new File(TEST_DATA_PREFIX + "fasta");
+public class PrintReadsByReadGroupTest extends CommandLineProgramTest {
+
+
+    private static final String TEST_DATA_PREFIX = "print_reads_by_read_group.";
+    private static final String REFERENCE_SEQUENCE = TEST_DATA_PREFIX + "fasta";
+
+    private File getReferenceSequence() {
+        return new File(getTestDataDir(), REFERENCE_SEQUENCE);
+    }
 
     @DataProvider(name = "printReadsByReadGroupData", parallel = true)
     public Object[][] getPrintReadsByReadGroupData() {
@@ -55,19 +64,30 @@ public Object[][] getPrintReadsByReadGroupData() {
     @Test(dataProvider = "printReadsByReadGroupData")
     public void testPrintReadsByReadGroup(final SamReader.Type type, final boolean useReference) throws Exception {
         final String fileExtension = type.fileExtension();
-        final PrintReadsByReadGroup printReadsByReadGroup = new PrintReadsByReadGroup();
-        printReadsByReadGroup.INPUT = new File(TEST_DATA_PREFIX + fileExtension);
-        printReadsByReadGroup.OUTPUT_DIRECTORY = Files.createTempDirectory("printReadsByReadGroupData.");
-        if (useReference)
-            printReadsByReadGroup.REFERENCE_SEQUENCE = REFERENCE_SEQUENCE;
-        printReadsByReadGroup.printReadsByReadGroup();
+        final List<String> args = new ArrayList<>();
+
+        Path outputDir = Files.createTempDirectory("printReadsByReadGroupData.");
+        outputDir.toFile().deleteOnExit();
+
+        args.add(StandardOptionDefinitions.INPUT_SHORT_NAME + "=");
+        args.add(getTestDataDir() + "/" + TEST_DATA_PREFIX + fileExtension);
+
+        args.add(StandardOptionDefinitions.OUTPUT_SHORT_NAME + "=");
+        args.add(outputDir.toString());
+
+        if (useReference) {
+            args.add(StandardOptionDefinitions.REFERENCE_SHORT_NAME + "=");
+            args.add(getTestDataDir()+ "/" + REFERENCE_SEQUENCE);
+        }
+
+        Assert.assertEquals(runCommandLine(args), null);
 
         Assert.assertEquals(
-                getReadCounts(printReadsByReadGroup.OUTPUT_DIRECTORY, "Momma.0", fileExtension),
+                getReadCounts(outputDir, "Momma.0", fileExtension),
                 17,
                 "expected read group 0 count for " + fileExtension);
         Assert.assertEquals(
-                getReadCounts(printReadsByReadGroup.OUTPUT_DIRECTORY, "Poppa.1", fileExtension),
+                getReadCounts(outputDir, "Poppa.1", fileExtension),
                 2,
                 "expected read group 1 count for " + fileExtension);
     }
@@ -76,7 +96,7 @@ private int getReadCounts(final Path tempDirectory, final String readGroupInfo,
         final File path = tempDirectory.resolve(readGroupInfo + "." + fileExtension).toFile();
         int count = 0;
         IOUtil.assertFileIsReadable(path);
-        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(path);
+        final SamReader in = SamReaderFactory.makeDefault().referenceSequence(getReferenceSequence()).open(path);
         for (@SuppressWarnings("unused") final SAMRecord rec : in) {
             count++;
         }