diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java similarity index 98% rename from protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java index c702b3548..07072c4c2 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFs.java @@ -79,7 +79,7 @@ import java.util.*; * Combines gVCF records that were produced by the Haplotype Caller from single sample sources. * *
- * 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 * step and merges the records together in a sophisticated manner. * @@ -101,7 +101,7 @@ import java.util.*; *
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
- * -T CombineReferenceCalculationVariants \
+ * -T GenotypeGVCFs \
* --variant input1.vcf \
* --variant input2.vcf \
* -o output.vcf
@@ -110,7 +110,7 @@ import java.util.*;
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARMANIP, extraDocs = {CommandLineGATK.class} )
@Reference(window=@Window(start=-10,stop=10))
-public class CombineReferenceCalculationVariants extends RodWalker implements AnnotatorCompatible, TreeReducible {
+public class GenotypeGVCFs extends RodWalker implements AnnotatorCompatible, TreeReducible {
/**
* The VCF files to merge together
diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
similarity index 97%
rename from protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java
rename to protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 4a34793ee..f3a56355e 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -51,10 +51,10 @@ import org.testng.annotations.Test;
import java.util.Arrays;
-public class CombineReferenceCalculationVariantsIntegrationTest extends WalkerTest {
+public class GenotypeGVCFsIntegrationTest extends WalkerTest {
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)