Source:
<code><START> public static JavaRDD<VariantContext> callVariantsWithHaplotypeCaller( <END> final AuthHolder authHolder, final JavaSparkContext ctx, final JavaRDD<GATKRead> reads, final SAMFileHeader header, final ReferenceMultiSource reference, final List<SimpleInterval> intervals, final HaplotypeCallerArgumentCollection hcArgs, final ShardingArgumentCollection shardingArgs) { Utils.validateArg(hcArgs.dbsnp.dbsnp == null && hcArgs.comps.isEmpty(), "HaplotypeCallerSpark does not yet support dbsnp or comp side inputs." ); if ( !reference.isCompatibleWithSparkBroadcast()){ throw new UserException.Require2BitReferenceForBroadcast(); } final Broadcast<ReferenceMultiSource> referenceBroadcast = ctx.broadcast(reference); final Broadcast<HaplotypeCallerArgumentCollection> hcArgsBroadcast = ctx.broadcast(hcArgs); final OverlapDetector<ReadShard.ShardBoundary> overlaps = getShardBoundaryOverlapDetector(header, intervals, shardingArgs.readShardSize, shardingArgs.readShardPadding); final Broadcast<OverlapDetector<ReadShard.ShardBoundary>> shardBoundariesBroadcast = ctx.broadcast(overlaps); final JavaRDD<ReadShard> readShards = createReadShards(shardBoundariesBroadcast, reads); final JavaRDD<Tuple2<AssemblyRegion, SimpleInterval>> assemblyRegions = readShards .flatMap(shardsToAssemblyRegions(authHolder, referenceBroadcast, hcArgsBroadcast, shardingArgs, header)); return assemblyRegions.flatMap(callVariantsFromAssemblyRegions(authHolder, header, referenceBroadcast, hcArgsBroadcast)); }</code><technical_language>is this method public? is static</technical_language>

Target:
public static JavaRDD<VariantContext> callVariantsWithHaplotypeCaller( final AuthHolder authHolder, final JavaSparkContext ctx, final JavaRDD<GATKRead> reads, final SAMFileHeader header, final ReferenceMultiSource reference, final List<SimpleInterval> intervals, final HaplotypeCallerArgumentCollection hcArgs, final ShardingArgumentCollection shardingArgs) { Utils.validateArg(hcArgs.dbsnp.dbsnp == null, "HaplotypeCallerSpark does not yet support -D or --dbsnp arguments" ); Utils.validateArg(hcArgs.comps.isEmpty(), "HaplotypeCallerSpark does not yet support -comp or --comp arguments" ); Utils.validateArg(hcArgs.bamOutputPath == null, "HaplotypeCallerSpark does not yet support -bamout or --bamOutput"); if ( !reference.isCompatibleWithSparkBroadcast()){ throw new UserException.Require2BitReferenceForBroadcast(); } final Broadcast<ReferenceMultiSource> referenceBroadcast = ctx.broadcast(reference); final Broadcast<HaplotypeCallerArgumentCollection> hcArgsBroadcast = ctx.broadcast(hcArgs); final OverlapDetector<ShardBoundary> overlaps = getShardBoundaryOverlapDetector(header, intervals, shardingArgs.readShardSize, shardingArgs.readShardPadding); final Broadcast<OverlapDetector<ShardBoundary>> shardBoundariesBroadcast = ctx.broadcast(overlaps); final JavaRDD<Shard<GATKRead>> readShards = createReadShards(shardBoundariesBroadcast, reads); final JavaRDD<Tuple2<AssemblyRegion, SimpleInterval>> assemblyRegions = readShards .mapPartitions(shardsToAssemblyRegions(authHolder, referenceBroadcast, hcArgsBroadcast, shardingArgs, header)); return assemblyRegions.mapPartitions(callVariantsFromAssemblyRegions(authHolder, header, referenceBroadcast, hcArgsBroadcast)); }