Passing all unittests

-- Final merge conflicts resolved
-- BCF2Writer now supports case where a sample is present in the header but the sample isn't in the VC, in which case we create an empty sample and encode that

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

@@ -291,7 +291,10 @@ class BCF2Writer extends IndexingVariantContextWriter {
                 writer.start(encoder, vc);
                 for ( final String name : header.getGenotypeSamples() ) {
                     // todo -- can we optimize this get (string -> genotype) which can be expensive
-                    final Genotype g = vc.getGenotype(name);
+                    Genotype g = vc.getGenotype(name);
+                    if ( g == null )
+                        // we don't have any data about g at all
+                        g = new GenotypeBuilder(name).make();
                     writer.addGenotype(encoder, vc, g);
                 }
                 writer.done(encoder, vc);