Swapping in logless Pair HMM for default usage with UG:

-- Changed default HMM model.
-- Removed check.
-- Changed md5's: PL's in the high 100s change by a point or two due to new implementation.
-- Resulting performance improvement is about 30 to 50% less runtime when using -glm INDEL.

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -76,7 +76,8 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
     private List<Allele> alleleList = new ArrayList<Allele>();
 
 
-    protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
+    protected IndelGenotypeLikelihoodsCalculationModel(final UnifiedArgumentCollection UAC,
+                                                       final Logger logger) {
         super(UAC, logger);
         pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY, UAC.INDEL_GAP_CONTINUATION_PENALTY,
                 UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.pairHMM);
@@ -85,10 +86,11 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         ignoreSNPAllelesWhenGenotypingIndels = UAC.IGNORE_SNP_ALLELES;
     }
 
-    protected static List<Allele> computeConsensusAlleles(ReferenceContext ref,
-                                                 Map<String, AlignmentContext> contexts,
-                                                 AlignmentContextUtils.ReadOrientation contextType,
-                                                 GenomeLocParser locParser, UnifiedArgumentCollection UAC) {
+    protected static List<Allele> computeConsensusAlleles(final ReferenceContext ref,
+                                                 final Map<String, AlignmentContext> contexts,
+                                                 final AlignmentContextUtils.ReadOrientation contextType,
+                                                 final GenomeLocParser locParser,
+                                                 final UnifiedArgumentCollection UAC) {
         ConsensusAlleleCounter counter = new ConsensusAlleleCounter(locParser, true, UAC.MIN_INDEL_COUNT_FOR_GENOTYPING, UAC.MIN_INDEL_FRACTION_PER_SAMPLE);
         return counter.computeConsensusAlleles(ref, contexts, contextType);
     }

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -85,7 +85,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
      * The PairHMM implementation to use for -glm INDEL genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.
      */
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for -glm INDEL genotype likelihood calculations", required = false)
-    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.ORIGINAL;
+    public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
 
     /**
      * The minimum confidence needed in a given base for it to be used in variant calling.  Note that the base quality of a base

protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -54,6 +54,7 @@ import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pairhmm.Log10PairHMM;
+import org.broadinstitute.sting.utils.pairhmm.LoglessPairHMM;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -116,12 +117,11 @@ public class PairHMMIndelErrorModel {
             case ORIGINAL:
                 pairHMM = new Log10PairHMM(false);
                 break;
-            case LOGLESS_CACHING:                //TODO: still not tested so please do not use yet
-                //pairHMM = new LoglessCachingPairHMM(); //TODO - add it back when the figure out how to use the protected LoglessCachingPairHMM class
-                throw new UserException.BadArgumentValue("pairHMM"," this option (LOGLESS_CACHING in UG) is still under development");
-                //break;
+            case LOGLESS_CACHING:
+                pairHMM = new LoglessPairHMM();
+                break;
             default:
-                throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING (the third option is still under development).");
+                throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the UnifiedGenotyper. Acceptable options are ORIGINAL, EXACT or LOGLESS_CACHING.");
         }
 
         // fill gap penalty table, affine naive model:

protected/java/test/org/broadinstitute/sting/gatk/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", "dd28b14d732852bffbba4f22f7697227");
+        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "98f4d78aad745c6e853b81b2e4e207b4");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/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","369ad0ff28bb9ce7974dc2c7343c8737");
+        executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","25902d7a6a0c00c60c2d5845dfaa1a4c");
     }
 
     @Test(enabled = true)

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java

@@ -136,7 +136,7 @@ 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("587bf6bad368ed81189747a84f913ab2"));
+                Arrays.asList("5596851d19582dd1af3901b7d703ae0a"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java

@@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper --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("70a21812d4dd6b72c44f60c74d508d5b"));
+                Arrays.asList("06c85e8eab08b67244cf38fc785aca22"));
         executeTest("test Multiple SNP alleles", spec);
     }