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Minor fixes for my last commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4090 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-23 23:25:29 +00:00
parent ef795825fd
commit 90aef66ec5
3 changed files with 3 additions and 4 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -163,7 +163,6 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
for ( Pair<VariantContext, Byte> record : records ) for ( Pair<VariantContext, Byte> record : records )
vcfwriter.add(record.first, record.second); vcfwriter.add(record.first, record.second);
vcfwriter.close();
} }

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
View File

@ -65,9 +65,9 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null; protected VCFWriter vcfWriter = null;
@Argument(fullName="output_file", shortName="output", doc="Please use --out instead") @Argument(fullName="output_file", shortName="output", doc="Please use --out instead" ,required=false)
@Deprecated @Deprecated
private String oldOutputArg; protected String oldOutputArg;
@Argument(fullName="no" + @Argument(fullName="no" +
"call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false) "call_threshold", shortName="ncthr", doc="Threshold of confidence at which a genotype won't be called", required=false)

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
View File

@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " + "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " + "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " + "-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
"-output %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0")); "-o %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
executeTest("test BeagleOutputToVCF", spec); executeTest("test BeagleOutputToVCF", spec);
} }