diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 4f83c8dd7..097421734 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -29,7 +29,9 @@ import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.VCFConstants; +import org.broad.tribble.vcf.VCFWriter; import org.broadinstitute.sting.commandline.Argument; +import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; @@ -52,8 +54,9 @@ public class ProduceBeagleInputWalker extends RodWalker { public static final String ROD_NAME = "variant"; - @Argument(fullName = "beagle_file", shortName = "beagle", doc = "File to print BEAGLE-specific data for use with imputation", required = true) - public PrintStream beagleWriter = null; + @Output(doc="File to which BEAGLE input should be written",required=true) + protected PrintStream beagleWriter = null; + @Argument(fullName = "genotypes_file", shortName = "genotypes", doc = "File to print reference genotypes for error analysis", required = false) public PrintStream beagleGenotypesWriter = null; @Argument(fullName = "inserted_nocall_rate", shortName = "nc_rate", doc = "Rate (0-1) at which genotype no-calls will be randomly inserted, for testing", required = false) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java index 0238d8dd5..563da06d6 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java @@ -50,7 +50,7 @@ public class BeagleIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T ProduceBeagleInput -R " + hg19Reference + " " + "-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " + - "-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e")); + "-o %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e")); executeTest("test BeagleInput", spec); }