diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java index 91013673f..34831471a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java @@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; +import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory; import java.io.File; import java.io.OutputStream; @@ -48,15 +49,8 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor { public static final String NO_HEADER_ARG_NAME = "no_cmdline_in_header"; public static final String SITES_ONLY_ARG_NAME = "sites_only"; public static final String FORCE_BCF = "bcf"; - public static final HashSet SUPPORTED_ZIPPED_SUFFIXES = new HashSet(); - - // - // static list of zipped suffixes supported by this system. - // - static { - SUPPORTED_ZIPPED_SUFFIXES.add(".gz"); - SUPPORTED_ZIPPED_SUFFIXES.add(".gzip"); - } + public static final HashSet SUPPORTED_ZIPPED_SUFFIXES = + new HashSet<>(Arrays.asList(VariantContextWriterFactory.BLOCK_COMPRESSED_EXTENSIONS)); /** * The engine into which output stubs should be fed.