Make the default that we only output SNPs (so that when I make another release we don't get flooded with questions about why the UG is all of a sudden so slow)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5729 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -36,7 +36,7 @@ public class UnifiedArgumentCollection {
 
     // control the various models to be used
     @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only", required = false)
-    public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
+    public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP;
 
     @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false)
     public AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT;

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

@@ -16,7 +16,8 @@ import java.util.Map;
 
 public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
-    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER";
+    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH";
+    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL";
 
     // --------------------------------------------------------------------------------------------------------------
     //
@@ -64,8 +65,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -glm SNP -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("2241d97972b72233cb7b4c565739698e"));
+                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
+                Arrays.asList("66e3fc85a6037a24bc2b4896f79ea263"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
@@ -242,10 +243,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testSimpleIndels() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand +
+                baseCommandIndels +
                         " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" +
                         " -o %s" +
-                        " -glm INDEL" +
                         " -L 1:10,000,000-10,500,000",
                 1,
                 Arrays.asList("84bc209f38d60f325f1a8b6292a82c82"));
@@ -257,10 +257,10 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testIndelsWithLowMinAlleleCnt() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand +
+                baseCommandIndels +
                         " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" +
                         " -o %s" +
-                        " -glm INDEL -minIndelCnt 1" +
+                        " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
                 Arrays.asList("f536ca23cb86b14fc20e453859dafc01"));
@@ -271,10 +271,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testMultiTechnologyIndels() {
          WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                 baseCommand +
+                 baseCommandIndels +
                          " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" +
                          " -o %s" +
-                         " -glm INDEL" +
                          " -L 1:10,000,000-10,500,000",
                  1,
                  Arrays.asList("e9b4fef2cdfa4c4657f0df53309131b6"));
@@ -286,15 +285,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //@Test
     public void testWithIndelAllelesPassedIn() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
-                        "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000 -glm INDEL", 1,
+                baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
+                        "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("e95c545b8ae06f0721f260125cfbe1f0"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1);
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
+                baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf "
                         + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
-                        "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000 -glm INDEL", 1,
+                        "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
                 Arrays.asList("6c96d76b9bc3aade0c768d7c657ae210"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec2);
     }

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java

@@ -12,6 +12,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
+                        " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-50,000,000" +
                         " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" +
@@ -26,6 +27,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
+                        " -glm BOTH" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" +
@@ -41,6 +43,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest {
                 "-R " + hg18Reference +
                         " -T UnifiedGenotyper" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
+                        " -glm BOTH" +
                         " -L chr1:1-50,000,000" +
                         " -nt 10" +
                         " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" +