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Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-09-29 22:46:39 +00:00
parent 732aa32758
commit e80742e72f
2 changed files with 6 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -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<Integer, Integer> {
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)

2
java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
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@ -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);
}