Change the behavior of SelectVariants for PL/AD when it encounters a …

…record that has lost one or more alternate alleles.

Previously, we would strip out the PLs and AD values since they were no longer accurate.  However, this is not ideal because
then that information is just lost and 1) users complain on the forum and post it as a bug and 2) it gives us problems in both
the current and future (single sample) calling pipelines because we subset samples/alleles all the time and lose info.

Now the PLs and AD get correctly selected down.

While I was in there I also refactored some related code in subsetDiploidAlleles().  There were no real changes there - I just
broke it out into smaller chunks as per our best practices.

Added unit tests and updated integration tests.
Addressed reviews.

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

@@ -299,7 +299,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(doc="indel size select",required=false,fullName="maxIndelSize")
     private int maxIndelSize = Integer.MAX_VALUE;
 
-    @Argument(doc="Allow a samples other than those in the VCF to be specified on the command line. These samples will be ignored.",required=false,fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")
+    @Argument(doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.",required=false,fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES")
     private boolean ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES = false;
 
 
@@ -657,6 +657,7 @@ public void onTraversalDone(Integer result) {
      * Helper method to subset a VC record, modifying some metadata stored in the INFO field (i.e. AN, AC, AF).
      *
      * @param vc       the VariantContext record to subset
+     * @param excludeNonVariants should we exclude sites that have AC=0 for any alternate alleles?
      * @return the subsetted VariantContext
      */
     private VariantContext subsetRecord(final VariantContext vc, final boolean excludeNonVariants) {
@@ -665,14 +666,10 @@ private VariantContext subsetRecord(final VariantContext vc, final boolean exclu
 
         final VariantContext sub = vc.subContextFromSamples(samples, excludeNonVariants); // strip out the alternate alleles that aren't being used
 
-        VariantContextBuilder builder = new VariantContextBuilder(sub);
+        final VariantContextBuilder builder = new VariantContextBuilder(sub);
 
-        GenotypesContext newGC = sub.getGenotypes();
-
-        // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate)
-        final boolean lostAllelesInSelection = vc.getAlleles().size() != sub.getAlleles().size();
-        if ( lostAllelesInSelection )
-            newGC = GATKVariantContextUtils.stripPLsAndAD(sub.getGenotypes());
+        // if there are fewer alternate alleles now in the selected VC, we need to fix the PL and AD values
+        GenotypesContext newGC = GATKVariantContextUtils.updatePLsAndAD(sub, vc);
 
         // 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() ) {
@@ -682,11 +679,11 @@ private VariantContext subsetRecord(final VariantContext vc, final boolean exclu
 
         // Remove a fraction of the genotypes if needed
         if ( fractionGenotypes > 0 ){
-            ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
+            final ArrayList<Genotype> genotypes = new ArrayList<>();
             for ( Genotype genotype : newGC ) {
                 //Set genotype to no call if it falls in the fraction.
                 if(fractionGenotypes>0 && randomGenotypes.nextDouble()<fractionGenotypes){
-                    List<Allele> alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+                    final List<Allele> alleles = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
                     genotypes.add(new GenotypeBuilder(genotype).alleles(alleles).noGQ().make());
                 }
                 else{
@@ -698,7 +695,7 @@ private VariantContext subsetRecord(final VariantContext vc, final boolean exclu
 
         builder.genotypes(newGC);
 
-        addAnnotations(builder, sub, lostAllelesInSelection);
+        addAnnotations(builder, sub, vc.getAlleles().size() != sub.getAlleles().size());
 
         return builder.make();
     }

public/java/src/org/broadinstitute/sting/utils/MathUtils.java

@@ -976,6 +976,16 @@ public static int countOccurrences(byte element, byte[] array) {
         return count;
     }
 
+    public static int countOccurrences(final boolean element, final boolean[] array) {
+        int count = 0;
+        for (final boolean b : array) {
+            if (element == b)
+                count++;
+        }
+
+        return count;
+    }
+
 
     /**
      * Returns n random indices drawn with replacement from the range 0..(k-1)