Fixed nasty bug with defaulting to diploid no-call genotypes

-- For the pooled caller we were writing diploid no-calls even when other samples were haploid.  Changed maxPloidy function to return a defaultPloidy, rather than 0, in the case where all samples are missing.
-- VCF/BCF Writers now create missing genotypes with the ploidy of other samples, or 2 if none are available at all.
-- Updating integration tests for general ploidy, as previously we wrote ./. even when other calls were 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1, but now we write ./././././././././././././././././././././././. (ugly but correct)

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java

@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
 
 import java.util.Arrays;
-import org.testng.annotations.Test;
 
 /**
  * Created by IntelliJ IDEA.
@@ -52,7 +52,7 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","90af837f372e3d5143af30bf5c8c2b75");
+        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","567ae6b2a7f839b1307d4087c2f59cca");
     }
 
     @Test(enabled = true)
@@ -62,7 +62,7 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","26598044436c8044f22ffa767b06a0f0");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","d2a22e12f1969ae199557947e5039b58");
     }
 
     @Test(enabled = true)

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java

@@ -88,8 +88,8 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
             case UNBOUNDED:     return -1;
             case A:             return vc.getNAlleles() - 1;
             case G:
-                final int ploidy = vc.getMaxPloidy();
+                final int ploidy = vc.getMaxPloidy(2);
-                return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy == 0 ? 2 : ploidy);
+                return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy);
             default:
                 throw new ReviewedStingException("Unknown count type: " + countType);
         }

public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java

@@ -53,6 +53,7 @@ import java.util.*;
  */
 @Invariant({"alleles != null"})
 public final class GenotypeBuilder {
+    private static final List<Allele> HAPLOID_NO_CALL = Arrays.asList(Allele.NO_CALL);
     private static final List<Allele> DIPLOID_NO_CALL = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
 
     private String sampleName = null;
@@ -99,8 +100,14 @@ public final class GenotypeBuilder {
      * @param sampleName the name of this sample
      * @return an initialized Genotype with sampleName that's a diploid ./. no call genotype
      */
-    public static Genotype createMissing(final String sampleName) {
+    public static Genotype createMissing(final String sampleName, final int ploidy) {
-        return new GenotypeBuilder(sampleName).alleles(DIPLOID_NO_CALL).make();
+        final GenotypeBuilder builder = new GenotypeBuilder(sampleName);
+        switch ( ploidy ) {
+            case 1:  builder.alleles(HAPLOID_NO_CALL); break;
+            case 2:  builder.alleles(DIPLOID_NO_CALL); break;
+            default: builder.alleles(Collections.nCopies(ploidy, Allele.NO_CALL)); break;
+        }
+        return builder.make();
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java

@@ -413,18 +413,25 @@ public class GenotypesContext implements List<Genotype> {
     }
 
     /**
-     * What is the max ploidy among all samples?  Returns 0 if no genotypes are present
+     * What is the max ploidy among all samples?  Returns defaultPloidy if no genotypes are present
      *
+     * @param defaultPloidy the default ploidy, if all samples are no-called
      * @return
      */
     @Ensures("result >= 0")
-    public int getMaxPloidy() {
+    public int getMaxPloidy(final int defaultPloidy) {
+        if ( defaultPloidy < 0 ) throw new IllegalArgumentException("defaultPloidy must be greater than or equal to 0");
+
         if ( maxPloidy == -1 ) {
             maxPloidy = 0; // necessary in the case where there are no genotypes
             for ( final Genotype g : getGenotypes() ) {
                 maxPloidy = Math.max(g.getPloidy(), maxPloidy);
             }
+
+            // everything is no called so we return the default ploidy
+            if ( maxPloidy == 0 ) maxPloidy = defaultPloidy;
         }
+
         return maxPloidy;
     }
 

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -642,14 +642,15 @@ public class VariantContext implements Feature { // to enable tribble integratio
     }
 
     /**
-     * Returns the maximum ploidy of all samples in this VC, or -1 if there are no genotypes
+     * Returns the maximum ploidy of all samples in this VC, or default if there are no genotypes
      *
      * This function is caching, so it's only expensive on the first call
      *
-     * @return -1, or the max ploidy
+     * @param defaultPloidy the default ploidy, if all samples are no-called
+     * @return default, or the max ploidy
      */
-    public int getMaxPloidy() {
+    public int getMaxPloidy(final int defaultPloidy) {
-        return genotypes.getMaxPloidy();
+        return genotypes.getMaxPloidy(defaultPloidy);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java

@@ -272,11 +272,7 @@ public abstract class BCF2FieldWriter {
 
             encodingType = BCF2Type.INT8;
             buildAlleleMap(vc);
-            nValuesPerGenotype = vc.getMaxPloidy();
+            nValuesPerGenotype = vc.getMaxPloidy(2);
-
-            // deal with the case where we have no call everywhere, in which case we write out diploid
-            if ( nValuesPerGenotype == 0 )
-                nValuesPerGenotype = 2;
 
             super.start(encoder, vc);
         }

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java

@@ -353,7 +353,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             writer.start(encoder, vc);
             for ( final String name : sampleNames ) {
                 Genotype g = vc.getGenotype(name);
-                if ( g == null ) g = GenotypeBuilder.createMissing(name);
+                if ( g == null ) g = GenotypeBuilder.createMissing(name, writer.nValuesPerGenotype);
                 writer.addGenotype(encoder, vc, g);
             }
             writer.done(encoder, vc);

public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java

@@ -338,11 +338,13 @@ class VCFWriter extends IndexingVariantContextWriter {
      */
     private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys)
     throws IOException {
+        final int ploidy = vc.getMaxPloidy(2);
+
         for ( String sample : mHeader.getGenotypeSamples() ) {
             mWriter.write(VCFConstants.FIELD_SEPARATOR);
 
             Genotype g = vc.getGenotype(sample);
-            if ( g == null ) g = GenotypeBuilder.createMissing(sample);
+            if ( g == null ) g = GenotypeBuilder.createMissing(sample, ploidy);
 
             final List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
             for ( String field : genotypeFormatKeys ) {