Reduce intervals of integration tests in HaplotypeCallerIntegrationTest class

Story:

   https://www.pivotaltracker.com/story/show/74858854

Changes:

    Intervals have been shrunk so that the test run in 15s or less.

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -75,6 +75,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     final static String NA12878_PCRFREE250_ADAPTER_TRIMMED = privateTestDir + "PCRFree.2x250.b37_decoy.NA12878.adapter_trimmed-10000000-11000000.bam";
     final static String CEUTRIO_MT_TEST_BAM = privateTestDir + "CEUTrio.HiSeq.b37.MT.1_50.bam";
     final static String INTERVALS_FILE = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals";
+    final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
 
     private void HCTest(String bam, String args, String md5) {
         final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
@@ -114,8 +115,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
+        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
-                "4047ea70f37b59b782402f678ea2dfee");
+                " -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
+                "669aac2aa9c22881eda86ee53b13351a");
     }
 
     @Test
@@ -226,25 +228,25 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("3d1fcf8b4a1d8d328c0a0aae5f4558eb"));
+                Arrays.asList("89b83443b0092530bdad595b14f67f2d"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
     @Test
     public void HCTestDBSNPAnnotationWEx() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
-                Arrays.asList("e64e06ae90a8eab52cabe3687992da73"));
+                Arrays.asList("76277d8ea79e2901364a26740d2f50ae"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
     }
 
     @Test
     public void HCTestDBSNPAnnotationWGSGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1,
+                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
-                Arrays.asList("7748a90ffd7daa15a8d518fc528bfcc5"));
+                Arrays.asList("9aa0a5946de59884c46cde74f817e77d"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
 
@@ -260,7 +262,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestGraphBasedPCRFreePositiveLogLkFix() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,000,000-11,000,000 "
+                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
                         , 1,
                 Arrays.asList(""));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
@@ -275,16 +277,16 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("a97154c320a04f3e21f23b8c793d4111"));
+                Arrays.asList("9b8a822e5ead66f09227d82c94315e59"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
     @Test
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1,
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("df871f2b5cbb01bdc758614ef1923bf7"));
+                Arrays.asList("1d24772716916eede70f6c157d46e931"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 
@@ -299,12 +301,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         executeTest("testGraphBasedNoSuchEdgeBugFix", spec);
     }
 
+    // This test takes longer than 15 secs ... ~ 25-35 ,
     @Test
     public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
         final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
                 b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list",
                 HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
-        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("f2deea31d32c0cfe3298755a83171c8f"));
+        final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("90ab538102f5faf4f4a07860cb8fa1b1"));
         spec.disableShadowBCF();
         executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
     }