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Rename CombineReferenceCalculationVariants to GenotypeGVCFs

This commit is contained in:
Eric Banks 2014-02-05 22:01:12 -05:00
parent b2b44c335f
commit 71b47a6148
2 changed files with 5 additions and 5 deletions
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6
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java
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@ -79,7 +79,7 @@ import java.util.*;
* Combines gVCF records that were produced by the Haplotype Caller from single sample sources. * Combines gVCF records that were produced by the Haplotype Caller from single sample sources.
* *
* <p> * <p>
* CombineReferenceCalculationVariants combines gVCF records that were produced as part of the "single sample discovery" * GenotypeGVCFs combines gVCF records that were produced as part of the "single sample discovery"
* pipeline using the '-ERC GVCF' mode of the Haplotype Caller. This tools performs the multi-sample joint aggregation * pipeline using the '-ERC GVCF' mode of the Haplotype Caller. This tools performs the multi-sample joint aggregation
* step and merges the records together in a sophisticated manner. * step and merges the records together in a sophisticated manner.
* *
@ -101,7 +101,7 @@ import java.util.*;
* <pre> * <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \ * -R ref.fasta \
* -T CombineReferenceCalculationVariants \ * -T GenotypeGVCFs \
* --variant input1.vcf \ * --variant input1.vcf \
* --variant input2.vcf \ * --variant input2.vcf \
* -o output.vcf * -o output.vcf
@ -110,7 +110,7 @@ import java.util.*;
*/ */
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-10,stop=10)) @Reference(window=@Window(start=-10,stop=10))
public class CombineReferenceCalculationVariants extends RodWalker<VariantContext, VariantContextWriter> implements AnnotatorCompatible, TreeReducible<VariantContextWriter> { public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWriter> implements AnnotatorCompatible, TreeReducible<VariantContextWriter> {
/** /**
* The VCF files to merge together * The VCF files to merge together

4
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java → protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -51,10 +51,10 @@ import org.testng.annotations.Test;
import java.util.Arrays; import java.util.Arrays;
public class CombineReferenceCalculationVariantsIntegrationTest extends WalkerTest { public class GenotypeGVCFsIntegrationTest extends WalkerTest {
private static String baseTestString(String args, String ref) { private static String baseTestString(String args, String ref) {
return "-T CombineReferenceCalculationVariants --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + ref + args; return "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1-50,000,000 -o %s -R " + ref + args;
} }
@Test(enabled = true) @Test(enabled = true)