Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -57,8 +57,6 @@ public class GATKArgumentCollection {
     public GATKArgumentCollection() {
     }
 
-    public Map<String, String> walkerArgs = new HashMap<String, String>();
-
     // parameters and their defaults
     @Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = false)
     public List<String> samFiles = new ArrayList<String>();

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/varianteval/stratifications/AlleleCount.java

@@ -51,6 +51,10 @@ public class AlleleCount extends VariantStratifier {
                     AC = Math.max(AC, eval.getCalledChrCount(allele));
             }
 
+            // make sure that the AC isn't invalid
+            if ( AC > eval.getCalledChrCount() )
+                throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount()));
+
             return Collections.singletonList((Object) AC);
         } else {
             return Collections.emptyList();

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();
             }
@@ -730,7 +731,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         if ( vc.getAlleles().size() != sub.getAlleles().size() )
             newGC = VariantContextUtils.stripPLs(sub.getGenotypes());
 
-        //Remove a fraction of the genotypes if needed
+        // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
+        if ( vc.getNSamples() != sub.getNSamples() ) {
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_COUNT_KEY);
+            builder.rmAttribute(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
+        }
+
+        // Remove a fraction of the genotypes if needed
         if ( fractionGenotypes > 0 ){
             ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
             for ( Genotype genotype : newGC ) {
@@ -767,17 +774,21 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         VariantContextUtils.calculateChromosomeCounts(builder, false);
 
+        boolean sawDP = false;
         int depth = 0;
         for (String sample : originalVC.getSampleNames()) {
             Genotype g = originalVC.getGenotype(sample);
 
             if ( ! g.isFiltered() ) {
-                if ( g.hasDP() )
+                if ( g.hasDP() ) {
                     depth += g.getDP();
+                    sawDP = true;
+                }
             }
         }
 
-        builder.attribute("DP", depth);
+        if ( sawDP )
+            builder.attribute("DP", depth);
     }
 
     private void randomlyAddVariant(int rank, VariantContext vc) {

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -585,6 +585,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTest("testStandardIndelEval", spec);
     }
 
+    @Test
+    public void testBadACValue() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + privateTestDir + "vcfexample.withBadAC.vcf",
+                        "-noST -ST AlleleCount",
+                        "-noEV -EV VariantSummary"
+                ),
+                0,
+                UserException.class);
+        executeTest("testBadACValue", spec);
+    }
+
 
     @Test()
     public void testIncompatibleEvalAndStrat() {

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);
@@ -148,12 +148,38 @@ 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);
     }
 
+    @Test
+    public void testRemoveMLE() {
+        String testFile = privateTestDir + "vcfexample.withMLE.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("a554459c9ccafb9812ff6d8c06c11726")
+        );
+
+        executeTest("testRemoveMLE--" + testFile, spec);
+    }
+
+    @Test
+    public void testRemoveMLEAndRegenotype() {
+        String testFile = privateTestDir + "vcfexample.withMLE.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b36KGReference + " -regenotype -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("52cb2f150559ca1457e9df7ec153dbb4")
+        );
+
+        executeTest("testRemoveMLEAndRegenotype--" + testFile, spec);
+    }
+
     @Test
     public void testMultipleRecordsAtOnePosition() {
         String testFile = privateTestDir + "selectVariants.onePosition.vcf";