ReadLikelihoods class introduction final changes before merging

Stories:

        https://www.pivotaltracker.com/story/show/70222086
        https://www.pivotaltracker.com/story/show/67961652

Changes:

  Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM.
  Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set.
  Updated some integration test md5s.

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java

@@ -447,8 +447,8 @@ public class PairHMMIndelErrorModel {
                     final List<Haplotype> distinctHaplotypesList = Arrays.asList(distinctHaplotypesSet.toArray(new Haplotype[distinctHaplotypesSet.size()]));
                     // Get the likelihoods for our clipped read against each of our trimmed haplotypes.
                     final ReadLikelihoods<Haplotype> rl = new ReadLikelihoods<>(
-
                             Collections.singletonList("DUMMY_SAMPLE"),distinctHaplotypesList,Collections.singletonMap("DUMMY_SAMPLE",Collections.singletonList(processedRead)));
+
                     final ReadLikelihoods.Matrix<Haplotype> dummySampleLikelihoods = rl.sampleMatrix(0);
                     pairHMM.computeLikelihoods(rl.sampleMatrix(0), Collections.singletonList(processedRead), readGCPArrayMap);
 
@@ -458,7 +458,7 @@ public class PairHMMIndelErrorModel {
                         final int hIndex = rl.alleleIndex(h);
                         final double readLikelihood = dummySampleLikelihoods.get(hIndex,0);
                         readLikelihoods[readIdx][j++] = readLikelihood;
-                        perReadAlleleLikelihoodMap.add(read,a,readLikelihood);
+                        perReadAlleleLikelihoodMap.add(p,a,readLikelihood);
                     }
                 }
             }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java

@@ -79,6 +79,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "a9730f883a2e01e93d56b11321c9fd52");
+        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "ae90d6be28c19e455083a47bc95c3b1b");
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java

@@ -58,7 +58,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","93cf7ed2645599d0ddd319c6989eadcc");
+        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9fc4f04105bde31bafc93548745cb67e");
     }
 
     @Test(enabled = true)

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java

@@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("24d5f65860507ec7f8d9441bfee8653a"));
+                Arrays.asList("8a4de9e1f59cffe80a4372cf02fe809e"));
         executeTest(String.format("test indel caller in SLX"), spec);
     }
 
@@ -100,7 +100,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("188dc4d70dc5f4de09f645270cc3f4e1"));
+                Arrays.asList("2b92df91a9337b9d9f03db5699bb41f2"));
 
         executeTest(String.format("test indel calling, multiple technologies"), spec);
     }
@@ -110,7 +110,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("31aaad9adbf12bb7fb12d53080e5c2f5"));
+                Arrays.asList("591c9a7bd7d64974b4a2dd932fdef138"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
     }
 
@@ -120,7 +120,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("fecb8ae4e8f5ea2b2bf3826d674298f7"));
+                Arrays.asList("e784b6d1b3725f72a2c42b19e8d24cb1"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
@@ -135,7 +135,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
-                Arrays.asList("0662ec6fe6d6e9807f758b1c82adf056"));
+                Arrays.asList("d101beb3d1f71a14a31438cce9786881"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("3d5140ffc02a125ee26c63ec55449192"));
+                Arrays.asList("96c2ab043f523c7676e4bc36dd3c9d0b"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("7c62eb9142d9124e49c123dcc052ce57"));
+                Arrays.asList("53ce3aa9ee16302ab2ec21f742b5e157"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java

@@ -65,7 +65,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("c6462121e5a419546f50d53646274fd3"));
+                Arrays.asList("058b54cff14527485c7b1ab035ebb6c4"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -97,7 +97,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("85e8ba3cfeef5e3b72418bcfaec11668"));
+                Arrays.asList("120270ddf48dfd461f756c89ea1ab074"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
@@ -113,7 +113,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("bd867fb341e75a9f1fc78d25bda93f63"));
+                Arrays.asList("bc5a143868e3ad3acc9bb7c09798cdf2"));
         executeTest("test reverse trim", spec);
     }
 
@@ -121,7 +121,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("e87419cd42fb9684ee3674ee54abe567"));
+                Arrays.asList("02fd6357bd1082115822c8a931cbb6a3"));
         executeTest("test mismatched PLs", spec);
     }
 }