Added decode method to LazyGenotypesContext

-- AbstractVCFCodec calls this if the samples are not sorted.  Previously called getGenotypes() which didn't actually trigger the decode

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java

@@ -178,8 +178,8 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         // ignore places where we don't have a variant
         if ( beagleR2Feature == null || beagleProbsFeature == null ||  beaglePhasedFeature == null)
         {
-           vcfWriter.add(vc_input);
-           return 1;
+            vcfWriter.add(vc_input);
+            return 1;
         }
 
 
@@ -249,9 +249,9 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             Allele bglAlleleA, bglAlleleB;
 
             if (alleleA.matches(refString))
-               bglAlleleA = Allele.create(alleleA,true);
+                bglAlleleA = Allele.create(alleleA,true);
             else
-               bglAlleleA = Allele.create(alleleA,false);
+                bglAlleleA = Allele.create(alleleA,false);
 
             if (alleleB.matches(refString))
                 bglAlleleB = Allele.create(alleleB,true);
@@ -280,7 +280,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             // deal with numerical errors coming from limited formatting value on Beagle output files
             if (probWrongGenotype > 1 - MIN_PROB_ERROR)
                 probWrongGenotype = 1 - MIN_PROB_ERROR;
-            
+
             if (1-probWrongGenotype < noCallThreshold) {
                 // quality is bad: don't call genotype
                 alleles.clear();

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

@@ -321,6 +321,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
             final LazyGenotypesContext.LazyParser lazyParser = new LazyVCFGenotypesParser(alleles, chr, pos);
             final int nGenotypes = header.getGenotypeSamples().size();
             LazyGenotypesContext lazy = new LazyGenotypesContext(lazyParser, parts[8], nGenotypes);
+
+            // did we resort the sample names?  If so, we need to load the genotype data
+            if ( !header.samplesWereAlreadySorted() )
+                lazy.decode();
+
             builder.genotypesNoValidation(lazy);
         }
 
@@ -332,9 +337,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
             generateException(e.getMessage());
         }
 
-        // did we resort the sample names?  If so, we need to load the genotype data
-        if ( !header.samplesWereAlreadySorted() )
-            vc.getGenotypes();
 
         return vc;
     }

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

@@ -177,4 +177,11 @@ public class LazyGenotypesContext extends GenotypesContext {
     public Object getUnparsedGenotypeData() {
         return unparsedGenotypeData;
     }
+
+    /**
+     * Force us to decode the genotypes
+     */
+    public void decode() {
+        buildCache();
+    }
 }