review

src/main/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilder.java

@@ -93,7 +93,7 @@ public ArgumentsBuilder addFileArgument(String argumentName, File file){
     }
 
     /**
-     * add an argument with a file as its parameter
+     * add an argument with a boolean as its parameter
      */
     public ArgumentsBuilder addBooleanArgument(String argumentName, boolean yes){
         Utils.nonNull(argumentName);

src/test/java/org/broadinstitute/hellbender/tools/validation/CompareBaseQualitiesIntegrationTest.java

@@ -25,7 +25,7 @@ public void identicalBamTest() throws Exception {
         args.add(secondBam.getCanonicalPath());
         args.add("--throwOnDiff true");
         args.add("--VALIDATION_STRINGENCY SILENT");
-        final Object result = this.runCommandLine(args.getArgsArray());
+        final Object result = this.runCommandLine(args);
         Assert.assertEquals(result, 0);
     }
 
@@ -63,7 +63,7 @@ public void singleReadDiffTest(File firstBam, File secondBam, File referenceFile
             args.add(referenceFile.getAbsolutePath());
         }
 
-        final Object result = this.runCommandLine(args.getArgsArray());
+        final Object result = this.runCommandLine(args);
         if (Objects.equals(firstBam, secondBam)) {
             Assert.assertEquals(result, 0);
         } else {

src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BQSRIntegrationTest.java → src/test/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BothStepsOfBQSRIntegrationTest.java

@@ -12,18 +12,19 @@
 import java.io.File;
 
 //Note: has to be in this package to have access to Main.instanceMain
-public final class BQSRIntegrationTest extends CommandLineProgramTest {
+public final class BothStepsOfBQSRIntegrationTest extends CommandLineProgramTest {
 
     @Test //Tests that BQSR with and without indel recalibration produces the same bam file
     public void testIndelRemoval() throws Exception {
         //Note; using a small 27M file for speed
-        final File bamIn = new File(getToolTestDataDir() + "CEUTrio.HiSeq.WGS.b37.NA12878.20.bam");
+        final File bamIn = new File(NA12878_20_21_WGS_bam);
+        final String interval = "20";
 
-        final File recalOutWithIndels = baseRecalibrator(bamIn, false);
-        final File bamOutWithIndels = applyBQSR(bamIn, recalOutWithIndels, false);
+        final File recalOutWithIndels = baseRecalibrator(bamIn, interval, false);
+        final File bamOutWithIndels = applyBQSR(bamIn, interval, recalOutWithIndels, false);
 
-        final File recalOutWithoutIndels = baseRecalibrator(bamIn, true);
-        final File bamOutWithoutIndels = applyBQSR(bamIn, recalOutWithoutIndels, true);
+        final File recalOutWithoutIndels = baseRecalibrator(bamIn, interval, true);
+        final File bamOutWithoutIndels = applyBQSR(bamIn, interval, recalOutWithoutIndels, true);
 
         final ArgumentsBuilder args1 = new ArgumentsBuilder();
         args1.addArgument("VALIDATION_STRINGENCY", ValidationStringency.SILENT.name());
@@ -33,22 +34,24 @@ public void testIndelRemoval() throws Exception {
         Assert.assertEquals(result, 0);
     }
 
-    private File applyBQSR(final File bamIn, final File recalOut, final boolean skipIndels) {
+    private File applyBQSR(final File bamIn, final String interval, final File recalOut, final boolean skipIndels) {
         final File bamOut = BaseTest.createTempFile("applyBQSR." + skipIndels, ".bam");
         final ArgumentsBuilder args1 = new ArgumentsBuilder();
         args1.addInput(bamIn);
         args1.addFileArgument("bqsr", recalOut);
+        args1.addArgument("L", interval);
         args1.addOutput(bamOut);
         new Main().instanceMain(makeCommandLineArgs(args1.getArgsList(), ApplyBQSR.class.getSimpleName()));
         return bamOut;
     }
 
-    private File baseRecalibrator(final File bamIn, final boolean skipIndels) {
+    private File baseRecalibrator(final File bamIn, final String interval, final boolean skipIndels) {
         final File recalOut = BaseTest.createTempFile("baseRecalibrator." + skipIndels, ".recal");
 
         final ArgumentsBuilder args1 = new ArgumentsBuilder();
         args1.addInput(bamIn);
         args1.addOutput(recalOut);
+        args1.addArgument("L", interval);
         args1.addFileArgument("knownSites", new File(dbsnp_138_b37_20_21_vcf));
         args1.addReference(new File(b37_reference_20_21));
         args1.addBooleanArgument("skipIndelBQSR", skipIndels);

src/test/java/org/broadinstitute/hellbender/utils/test/ArgumentsBuilderTest.java

@@ -13,12 +13,12 @@ public void testArgumentsBuilder() {
         args.add("--value1");
         args.add(1);
         args.add("Input=")
-            .add(new File("/path/to/somewhere"))
+            .add(new File("path/to/somewhere"))
             .add("Value2=2")
             .add(" Value3= 3 Value4=4");
 
         Assert.assertEquals(args.getArgsArray(), new String[]{"--value1", "1",
-                "--Input", "/path/to/somewhere","--Value2","2","--Value3","3","--Value4","4"});
+                "--Input", "path/to/somewhere","--Value2","2","--Value3","3","--Value4","4"});
     }
     @Test
     public void testOneBigString(){
@@ -31,8 +31,8 @@ public void testOneBigString(){
 
     @Test
     public void testFromArray(){
-        ArgumentsBuilder args = new ArgumentsBuilder(new Object[]{"Option=" + new File("/path/to"), "OtherOption=" + -1, new File("/somewhere")});
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--Option","/path/to", "--OtherOption", "-1", "/somewhere"});
+        ArgumentsBuilder args = new ArgumentsBuilder(new Object[]{"Option=" + new File("path/to"), "OtherOption=" + -1, new File("somewhere")});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--Option","path/to", "--OtherOption", "-1", "somewhere"});
     }
 
     @Test
@@ -62,41 +62,41 @@ public void testAddBooleanArgument() throws Exception {
     @Test
     public void testAddFileArgument() throws Exception {
         ArgumentsBuilder args = new ArgumentsBuilder();
-        File file = new File("/path/to/somewhere");
+        File file = new File("path/to/somewhere");
         args.addFileArgument("foo", file);
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--foo", file.toString()});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--foo", file.getAbsolutePath()});
     }
 
     @Test
     public void testInput() throws Exception {
         ArgumentsBuilder args = new ArgumentsBuilder();
-        File file = new File("/path/to/somewhere");
+        File file = new File("path/to/somewhere");
         args.addInput(file);
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.INPUT_LONG_NAME, file.toString()});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.INPUT_LONG_NAME, file.getAbsolutePath()});
     }
 
     @Test
     public void testOutput() throws Exception {
         ArgumentsBuilder args = new ArgumentsBuilder();
-        File file = new File("/path/to/somewhere");
+        File file = new File("path/to/somewhere");
         args.addOutput(file);
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME, file.toString()});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME, file.getAbsolutePath()});
     }
 
     @Test
     public void testReference() throws Exception {
         ArgumentsBuilder args = new ArgumentsBuilder();
-        File file = new File("/path/to/somewhere");
+        File file = new File("path/to/somewhere");
         args.addReference(file);
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.REFERENCE_LONG_NAME, file.toString()});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.REFERENCE_LONG_NAME, file.getAbsolutePath()});
     }
 
     @Test
     public void testVcf() throws Exception {
         ArgumentsBuilder args = new ArgumentsBuilder();
-        File file = new File("/path/to/somewhere");
+        File file = new File("path/to/somewhere");
         args.addVCF(file);
-        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.VARIANT_LONG_NAME, file.toString()});
+        Assert.assertEquals(args.getArgsArray(), new String[]{"--" + StandardArgumentDefinitions.VARIANT_LONG_NAME, file.getAbsolutePath()});
     }
 
 }