Add ReblockGVCF -- a tool to merge reference blocks in single-sample …

…GVCFs for smaller filesize

src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java

@@ -88,6 +88,7 @@ public final class GenotypeGVCFs extends VariantWalker {
     public static final String PHASED_HOM_VAR_STRING = "1|1";
     public static final String ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME = "only-output-calls-starting-in-intervals";
     public static final String ALL_SITES_LONG_NAME = "include-non-variant-sites";
+    public static final String ALL_SITES_SHORT_NAME = "all-sites";
     private static final String GVCF_BLOCK = "GVCFBlock";
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
@@ -271,29 +272,20 @@ private VariantContext calculateGenotypes(VariantContext vc){
     /**
      * Determines whether the provided VariantContext has real alternate alleles.
      *
-     * There is a bit of a hack to handle the <NON-REF> case because it is not defined in htsjdk.Allele
-     * We check for this as a biallelic symbolic allele.
-     *
      * @param vc  the VariantContext to evaluate
      * @return true if it has proper alternate alleles, false otherwise
      */
-    @VisibleForTesting
-    static boolean isProperlyPolymorphic(final VariantContext vc) {
+    public static boolean isProperlyPolymorphic(final VariantContext vc) {
         //obvious cases
         if (vc == null || vc.getAlternateAlleles().isEmpty()) {
             return false;
         } else if (vc.isBiallelic()) {
-            return !(isSpanningDeletion(vc.getAlternateAllele(0)) || vc.isSymbolic());
+            return !(GATKVCFConstants.isSpanningDeletion(vc.getAlternateAllele(0)) || vc.isSymbolic());
         } else {
             return true;
         }
     }
 
-    @VisibleForTesting
-    static boolean isSpanningDeletion(final Allele allele){
-        return allele.equals(Allele.SPAN_DEL) || allele.equals(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_DEPRECATED);
-    }
-
     /**
      * Add genotyping-based annotations to the new VC
      *

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/QualByDepth.java

@@ -67,6 +67,39 @@ public Map<String, Object> annotate(final ReferenceContext ref,
             return Collections.emptyMap();
         }
 
+        final int depth = getDepth(genotypes, likelihoods);
+
+        if ( depth == 0 ) {
+            return Collections.emptyMap();
+        }
+
+        final double qual = -10.0 * vc.getLog10PError();
+        double QD = qual / depth;
+
+        // Hack: see note in the fixTooHighQD method below
+        QD = fixTooHighQD(QD);
+
+        return Collections.singletonMap(getKeyNames().get(0), String.format("%.2f", QD));
+    }
+
+    /**
+     * The haplotype caller generates very high quality scores when multiple events are on the
+     * same haplotype.  This causes some very good variants to have unusually high QD values,
+     * and VQSR will filter these out.  This code looks at the QD value, and if it is above
+     * threshold we map it down to the mean high QD value, with some jittering
+     *
+     * @param QD the raw QD score
+     * @return a QD value
+     */
+    public static double fixTooHighQD(final double QD) {
+        if ( QD < MAX_QD_BEFORE_FIXING ) {
+            return QD;
+        } else {
+            return IDEAL_HIGH_QD + Utils.getRandomGenerator().nextGaussian() * JITTER_SIGMA;
+        }
+    }
+
+    public static int getDepth(final GenotypesContext genotypes, final ReadLikelihoods<Allele> likelihoods) {
         int depth = 0;
         int ADrestrictedDepth = 0;
 
@@ -100,35 +133,7 @@ public Map<String, Object> annotate(final ReferenceContext ref,
         if ( ADrestrictedDepth > 0 ) {
             depth = ADrestrictedDepth;
         }
-
-        if ( depth == 0 ) {
-            return Collections.emptyMap();
-        }
-
-        final double qual = -10.0 * vc.getLog10PError();
-        double QD = qual / depth;
-
-        // Hack: see note in the fixTooHighQD method below
-        QD = fixTooHighQD(QD);
-
-        return Collections.singletonMap(getKeyNames().get(0), String.format("%.2f", QD));
-    }
-
-    /**
-     * The haplotype caller generates very high quality scores when multiple events are on the
-     * same haplotype.  This causes some very good variants to have unusually high QD values,
-     * and VQSR will filter these out.  This code looks at the QD value, and if it is above
-     * threshold we map it down to the mean high QD value, with some jittering
-     *
-     * @param QD the raw QD score
-     * @return a QD value
-     */
-    public static double fixTooHighQD(final double QD) {
-        if ( QD < MAX_QD_BEFORE_FIXING ) {
-            return QD;
-        } else {
-            return IDEAL_HIGH_QD + Utils.getRandomGenerator().nextGaussian() * JITTER_SIGMA;
-        }
+        return depth;
     }
 
     @Override

src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/RMSMappingQuality.java

@@ -53,12 +53,12 @@ public List<String> getKeyNames() {
 
     @Override
     public List<VCFInfoHeaderLine> getDescriptions() {
-        return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)), GATKVCFHeaderLines.getInfoLine(getRawKeyName()));
+        return Arrays.asList(VCFStandardHeaderLines.getInfoLine(getKeyNames().get(0)));
     }
 
     @Override
     public List<VCFInfoHeaderLine> getRawDescriptions() {
-        return getDescriptions();
+        return Arrays.asList(GATKVCFHeaderLines.getInfoLine(getRawKeyName()));
     }
 
     /**

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java

@@ -22,6 +22,8 @@ public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgume
 
     public static final String MAX_MNP_DISTANCE_LONG_NAME = "max-mnp-distance";
     public static final String MAX_MNP_DISTANCE_SHORT_NAME = "mnp-dist";
+    public static final String GQ_BAND_LONG_NAME = "gvcf-gq-bands";
+    public static final String GQ_BAND_SHORT_NAME = "GQB";
 
     /**
      * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This
@@ -73,7 +75,7 @@ public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgume
      * and end at 100 (exclusive).
      */
     @Advanced
-    @Argument(fullName = "gvcf-gq-bands", shortName = "GQB", doc= "Exclusive upper bounds for reference confidence GQ bands " +
+    @Argument(fullName = GQ_BAND_LONG_NAME, shortName = GQ_BAND_SHORT_NAME, doc= "Exclusive upper bounds for reference confidence GQ bands " +
             "(must be in [1, 100] and specified in increasing order)", optional = true)
     public List<Integer> GVCFGQBands = new ArrayList<>(70);
     {

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java

@@ -69,7 +69,7 @@ protected String callSourceString() {
 
     @Override
     protected boolean forceKeepAllele(final Allele allele) {
-        return allele == Allele.NON_REF_ALLELE || referenceConfidenceMode != ReferenceConfidenceMode.NONE
+        return allele.equals(Allele.NON_REF_ALLELE,false) || referenceConfidenceMode != ReferenceConfidenceMode.NONE
                 || configuration.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;
     }