Fixing behavior of the --regenotype argument in SelectVariants to properly run in GenotypeGivenAlleles mode. Added integration tests to cover recent SV changes.

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

@@ -646,15 +646,17 @@ public class UnifiedGenotyperEngine {
 
         // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
-            final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
+            final VariantContext vcInput = getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
-            if ( vcInput == null )
+            if ( vcInput == null ) {
+                models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
                 return models;
+            }
 
             if ( vcInput.isSNP() )  {
                 // ignore SNPs if the user chose INDEL mode only
                 if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") )
                     models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
-             }
+            }
             else if ( vcInput.isIndel() || vcInput.isMixed() ) {
                 // ignore INDELs if the user chose SNP mode only
                 if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") )
@@ -759,7 +761,7 @@ public class UnifiedGenotyperEngine {
 
     public static VariantContext getVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, GenomeLoc loc, boolean requireSNP, Logger logger, final RodBinding<VariantContext> allelesBinding) {
         if ( tracker == null || ref == null || logger == null )
-            throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
+            return null;
         VariantContext vc = null;
 
         // search for usable record

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -470,6 +470,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
             UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
             UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
+            UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
             UAC.NO_SLOD = true;
             UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
             headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
@@ -567,7 +568,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             VariantContext sub = subsetRecord(vc, EXCLUDE_NON_VARIANTS);
 
             if ( REGENOTYPE && sub.isPolymorphicInSamples() && hasPLs(sub) ) {
-                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(tracker, ref, context, sub)).filters(sub.getFiltersMaybeNull());
+                final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(null, ref, context, sub)).filters(sub.getFiltersMaybeNull());
                 addAnnotations(builder, sub);
                 sub = builder.make();
             }

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -34,7 +34,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString(" -sn A -sn B -sn C --variant " + testfile),
                 1,
-                Arrays.asList("3d98a024bf3aecbd282843e0af89d0e6")
+                Arrays.asList("125d1c9fa111cd38dfa2ff3900f16b57")
         );
 
         executeTest("testRepeatedLineSelection--" + testfile, spec);
@@ -49,7 +49,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                         + b37hapmapGenotypes + " -disc " + testFile
                         + " -o %s --no_cmdline_in_header -U LENIENT_VCF_PROCESSING",
                 1,
-                Arrays.asList("54289033d35d32b8ebbb38c51fbb614c")
+                Arrays.asList("c0b937edb6a8b6392d477511d4f1ebcf")
         );
         spec.disableShadowBCF();
 
@@ -135,7 +135,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant:dbsnp " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("d12ae1617deb38f5ed712dc326935b9a")
+                Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
         );
 
         executeTest("testUsingDbsnpName--" + testFile, spec);
@@ -148,7 +148,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("c22ad8864d9951403672a24c20d6c3c2")
+                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb452cb2f150559ca1457e9df7ec153dbb4")
         );
 
         executeTest("testRegenotype--" + testFile, spec);
@@ -161,10 +161,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("")
+                Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
         );
 
-        executeTest("testRegenotype--" + testFile, spec);
+        executeTest("testRemoveMLE--" + testFile, spec);
     }
 
     @Test
@@ -174,10 +174,10 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
                 1,
-                Arrays.asList("")
+                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
         );
 
-        executeTest("testRegenotype--" + testFile, spec);
+        executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);
     }
 
     @Test