Enabled banded indel computation by default. Reversed logic in input UG argument so that we can still disable it if required. Minor changes to integration tests due to minor differences in GL's and in annotations

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

@@ -81,7 +81,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
     protected IndelGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
         pairModel = new PairHMMIndelErrorModel(UAC.INDEL_GAP_OPEN_PENALTY,UAC.INDEL_GAP_CONTINUATION_PENALTY,
-                UAC.OUTPUT_DEBUG_INDEL_INFO, UAC.BANDED_INDEL_COMPUTATION);
+                UAC.OUTPUT_DEBUG_INDEL_INFO, !UAC.DONT_DO_BANDED_INDEL_COMPUTATION);
         alleleList = new ArrayList<Allele>();
         getAlleleListFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
         minIndelCountForGenotyping = UAC.MIN_INDEL_COUNT_FOR_GENOTYPING;

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

@@ -146,8 +146,8 @@ public class UnifiedArgumentCollection {
     public int INDEL_HAPLOTYPE_SIZE = 80;
 
     @Hidden
-    @Argument(fullName = "bandedIndel", shortName = "bandedIndel", doc = "Banded Indel likelihood computation", required = false)
+    @Argument(fullName = "noBandedIndel", shortName = "noBandedIndel", doc = "Don't do Banded Indel likelihood computation", required = false)
-    public boolean BANDED_INDEL_COMPUTATION = false;
+    public boolean DONT_DO_BANDED_INDEL_COMPUTATION = false;
 
     @Hidden
     @Argument(fullName = "indelDebug", shortName = "indelDebug", doc = "Output indel debug info", required = false)
@@ -184,7 +184,7 @@ public class UnifiedArgumentCollection {
 
         // todo- arguments to remove
         uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;
-        uac.BANDED_INDEL_COMPUTATION = BANDED_INDEL_COMPUTATION;
+        uac.DONT_DO_BANDED_INDEL_COMPUTATION = DONT_DO_BANDED_INDEL_COMPUTATION;
         uac.MULTI_ALLELIC = MULTI_ALLELIC;
         return uac;
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -265,7 +265,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("fa4f3ee67d98b64102a8a3ec81a3bc81"));
+                Arrays.asList("c60a44ba94a80a0cb1fba8b6f90a13cd"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
     }
 
@@ -275,7 +275,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("df90890e43d735573a3b3e4f289ca46b"));
+                Arrays.asList("36ce53ae4319718ad9c8ae391deebc8c"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
     }
 
@@ -285,7 +285,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2.20101123.indels.sites.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,080,000", 1,
-                Arrays.asList("cff6dd0f4eb1ef0b6fc476da6ffead19"));
+                Arrays.asList("d356cbaf240d7025d1aecdabaff3a3e0"));
         executeTest("test MultiSample Pilot2 indels with complicated records", spec3);
     }
 
@@ -294,7 +294,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
                         "phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
-                Arrays.asList("1e2a4aab26e9ab0dae709d33a669e036"));
+                Arrays.asList("947c12ef2a8c29ae787cd11be8c565c8"));
         executeTest("test MultiSample Phase1 indels with complicated records", spec4);
     }