Potential fix for GSA-484: Incomplete writing of temp BCF when running CombineVariants in parallel

-- Keep reading from BCF2 input stream when read(byte[]) returns < number of needed bytes
-- It's possible (I think) that the failure in GSA-484 is due to multi-threading writing/reading of BCF2 records where the underlying stream is not yet flushed so read(byte[]) returns a partial result.  No loops until we get all of the needed bytes or EOF is encounted

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java

@@ -118,6 +118,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
 
             final int sitesBlockSize = decoder.readBlockSize(inputStream);
             final int genotypeBlockSize = decoder.readBlockSize(inputStream);
+
             decoder.readNextBlock(sitesBlockSize, inputStream);
             decodeSiteLoc(builder);
             final SitesInfoForDecoding info = decodeSitesExtendedInfo(builder);