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Continuing the renaming nightmare... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3694 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-06-30 20:24:27 +00:00
parent aa20c52b88
commit 9d7d5f1747
3 changed files with 6 additions and 6 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.vcf;
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broad.tribble.vcf.VCFHeader;
import org.broad.tribble.vcf.VCFHeaderLine;
@ -48,7 +48,7 @@ import java.util.*;
* priority list (if provided), emits a single record instance at every position represented in the rods.
*/
@Requires(value={})
public class VCFCombine extends RodWalker<Integer, Integer> {
public class CombineVariants extends RodWalker<Integer, Integer> {
// the types of combinations we currently allow
public enum ComboType { UNION, MERGE }
@Argument(fullName="combination_type", shortName="type", doc="combination type; MERGE are supported", required=true)

4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVCF.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.vcf;
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -39,7 +39,7 @@ import java.util.List;
* Filters a lifted-over VCF file for ref bases that have been changed.
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
private VCFWriter writer;

4
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVCF.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.vcf;
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
@ -46,7 +46,7 @@ import net.sf.samtools.SAMFileReader;
* Lifts a VCF file over from one build to another. Note that the resulting VCF could be mis-sorted.
*/
@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFRecord.class))
public class LiftoverVCF extends RodWalker<Integer, Integer> {
public class LiftoverVariants extends RodWalker<Integer, Integer> {
@Argument(fullName="chain", shortName="chain", doc="Chain file", required=true)
protected File CHAIN = null;