zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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
View File

@ -79,7 +79,7 @@ import java.util.*;
* Combines gVCF records that were produced by the Haplotype Caller from single sample sources.
*
* <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
* step and merges the records together in a sophisticated manner.
*
@ -101,7 +101,7 @@ import java.util.*;
* <pre>
* 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<VariantContext, VariantContextWriter> implements AnnotatorCompatible, TreeReducible<VariantContextWriter> {
public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWriter> implements AnnotatorCompatible, TreeReducible<VariantContextWriter> {
/**
* 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
View File

@ -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)