Created "variantcalling" test group and split them off from the rest of the integration tests for runtime purposes

.travis.yml

@@ -12,6 +12,7 @@ env:
   - TEST_TYPE=cloud UPLOAD=true
   - TEST_TYPE=integration TEST_DOCKER=true TEST_VERBOSITY=minimal
   - TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
+  - TEST_TYPE=variantcalling TEST_DOCKER=true TEST_VERBOSITY=minimal
   - TEST_TYPE=python TEST_DOCKER=true TEST_VERBOSITY=minimal
   - RUN_CNV_GERMLINE_WDL=true
   - RUN_CNV_SOMATIC_WDL=true

build.gradle

@@ -408,19 +408,22 @@ test {
             includeGroups 'cloud', 'bucket'
         } else if (TEST_TYPE == "integration"){
             include "**/*IntegrationTest.class"
-            excludeGroups "cloud", "bucket", "python", "funcotatorValidation"
+            excludeGroups "cloud", "bucket", "python", "funcotatorValidation", "variantcalling"
         } else if (TEST_TYPE == "unit") {
             exclude "**/*IntegrationTest.class"
+            excludeGroups "cloud", "bucket", "python", "funcotatorValidation", "variantcalling"
+        } else if (TEST_TYPE == "variantcalling") {
+            includeGroups "variantcalling"
             excludeGroups "cloud", "bucket", "python", "funcotatorValidation"
         } else if (TEST_TYPE == "spark") {
             includeGroups "spark"
-            excludeGroups "cloud", "bucket", "python", "funcotatorValidation"
+            excludeGroups "cloud", "bucket", "python", "funcotatorValidation", "variantcalling"
         } else if (TEST_TYPE == "python") {
             includeGroups "python"
         } else if (TEST_TYPE == "all"){
             //include everything
         } else {
-            excludeGroups "cloud", "bucket", "python", "funcotatorValidation"
+            excludeGroups "cloud", "bucket", "python", "funcotatorValidation", "variantcalling"
         }
     }
 

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

@@ -24,6 +24,7 @@
 
 import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerIntegrationTest;
 
+@Test(groups = {"variantcalling"})
 public class HaplotypeCallerSparkIntegrationTest extends CommandLineProgramTest {
 
     private  static final String TEST_FILES_DIR = toolsTestDir + "haplotypecaller/";

src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -44,6 +44,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.StreamSupport;
 
+@Test(groups = {"variantcalling"})
 public class HaplotypeCallerIntegrationTest extends CommandLineProgramTest {
 
     public static final String TEST_FILES_DIR = toolsTestDir + "haplotypecaller/";
@@ -398,7 +399,7 @@ public void testBamoutOnGcs() {
         innerTestBamoutProducesReasonablySizedOutput(bamOutput);
     }
 
-    public void innerTestBamoutProducesReasonablySizedOutput(Path bamOutput) {
+    private void innerTestBamoutProducesReasonablySizedOutput(Path bamOutput) {
         Utils.resetRandomGenerator();
 
         // We will test that when running with -bamout over the testInterval, we produce
@@ -767,7 +768,50 @@ public void testMnps() throws Exception {
                     "-" + HaplotypeCallerArgumentCollection.MAX_MNP_DISTANCE_SHORT_NAME, Integer.toString(maxMnpDistance));
             runCommandLine(args);
 
-            Mutect2IntegrationTest.checkMnpOutput(maxMnpDistance, outputVcf);
+            checkMnpOutput(maxMnpDistance, outputVcf);
+        }
+    }
+
+    // this is particular to our particular artificial MNP bam -- we extract a method in order to use it for HaplotypeCaller
+    private static void checkMnpOutput(int maxMnpDistance, File outputVcf) {
+        // note that for testing HaplotypeCaller GVCF mode we will always have the symbolic <NON REF> allele
+        final Map<Integer, List<String>> alleles = StreamSupport.stream(new FeatureDataSource<VariantContext>(outputVcf).spliterator(), false)
+                .collect(Collectors.toMap(VariantContext::getStart, vc -> vc.getAlternateAlleles().stream().filter(a -> !a.isSymbolic()).map(Allele::getBaseString).collect(Collectors.toList())));
+
+        // phased, two bases apart
+        if (maxMnpDistance < 2) {
+            Assert.assertEquals(alleles.get(10019968), Arrays.asList("G"));
+            Assert.assertEquals(alleles.get(10019970), Arrays.asList("G"));
+        } else {
+            Assert.assertEquals(alleles.get(10019968), Arrays.asList("GAG"));
+            Assert.assertTrue(!alleles.containsKey(10019970));
+        }
+
+        // adjacent and out of phase
+        Assert.assertEquals(alleles.get(10020229), Arrays.asList("A"));
+        Assert.assertEquals(alleles.get(10020230), Arrays.asList("G"));
+
+        // 4-substitution MNP w/ spacings 2, 3, 4
+        if (maxMnpDistance < 2) {
+            Assert.assertEquals(alleles.get(10020430), Arrays.asList("G"));
+            Assert.assertEquals(alleles.get(10020432), Arrays.asList("G"));
+            Assert.assertEquals(alleles.get(10020435), Arrays.asList("G"));
+            Assert.assertEquals(alleles.get(10020439), Arrays.asList("G"));
+        } else if (maxMnpDistance < 3) {
+            Assert.assertEquals(alleles.get(10020430), Arrays.asList("GAG"));
+            Assert.assertEquals(alleles.get(10020435), Arrays.asList("G"));
+            Assert.assertEquals(alleles.get(10020439), Arrays.asList("G"));
+        } else if (maxMnpDistance < 4) {
+            Assert.assertEquals(alleles.get(10020430), Arrays.asList("GAGTTG"));
+            Assert.assertEquals(alleles.get(10020439), Arrays.asList("G"));
+        } else {
+            Assert.assertEquals(alleles.get(10020430), Arrays.asList("GAGTTGTCTG"));
+        }
+
+        // two out of phase DNPs that overlap and have a base in common
+        if (maxMnpDistance > 0) {
+            Assert.assertEquals(alleles.get(10020680), Arrays.asList("TA"));
+            Assert.assertEquals(alleles.get(10020681), Arrays.asList("AT"));
         }
     }
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CreateSomaticPanelOfNormalsIntegrationTest.java

@@ -20,6 +20,7 @@
 /**
  * Created by David Benjamin on 2/17/17.
  */
+@Test(groups = {"variantcalling"})
 public class CreateSomaticPanelOfNormalsIntegrationTest extends CommandLineProgramTest {
 
     private static final File PON_VCFS_DIR = new File(toolsTestDir, "mutect/createpon/");

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java

@@ -34,6 +34,7 @@
 /**
  * Created by davidben on 9/1/16.
  */
+@Test(groups = {"variantcalling"})
 public class Mutect2IntegrationTest extends CommandLineProgramTest {
     // positions 10,000,000 - 11,000,000 of chr 20 and with most annotations removed
     private static final File GNOMAD = new File(largeFileTestDir, "very-small-gnomad.vcf");
@@ -252,7 +253,7 @@ public void testMnps() throws Exception {
     }
 
     // this is particular to our particular artificial MNP bam -- we extract a method in order to use it for HaplotypeCaller
-    public static void checkMnpOutput(int maxMnpDistance, File outputVcf) {
+    private static void checkMnpOutput(int maxMnpDistance, File outputVcf) {
         // note that for testing HaplotypeCaller GVCF mode we will always have the symbolic <NON REF> allele
         final Map<Integer, List<String>> alleles = StreamSupport.stream(new FeatureDataSource<VariantContext>(outputVcf).spliterator(), false)
                 .collect(Collectors.toMap(VariantContext::getStart, vc -> vc.getAlternateAlleles().stream().filter(a -> !a.isSymbolic()).map(Allele::getBaseString).collect(Collectors.toList())));