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Adding argument to GenotypeGVCFs to keep specified raw annotations (#…
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...stitute/hellbender/cmdline/GATKPlugin/DefaultGATKVariantAnnotationArgumentCollection.java
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...rg/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsAnnotationArgumentCollection.java
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package org.broadinstitute.hellbender.tools.walkers; | ||
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import org.broadinstitute.barclay.argparser.Argument; | ||
import org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection; | ||
import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation; | ||
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import java.util.ArrayList; | ||
import java.util.Collections; | ||
import java.util.List; | ||
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public class GenotypeGVCFsAnnotationArgumentCollection extends DefaultGATKVariantAnnotationArgumentCollection { | ||
private static final long serialVersionUID = 1L; | ||
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public static final String KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME = "keep-specific-combined-raw-annotation"; | ||
public static final String KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_SHORT_NAME = "keep-specific-combined"; | ||
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/** | ||
* Keep only the specific combined raw annotations specified. Cannot be used with --keep-combined-raw-annotations which saves all raw annotations. | ||
* Duplicate values will be ignored. See {@link ReducibleAnnotation} for more information on raw annotations. | ||
*/ | ||
@Argument(fullName= KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME, shortName = KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_SHORT_NAME, optional = true, | ||
mutex = {GenotypeGVCFs.KEEP_COMBINED_LONG_NAME}, | ||
doc="Keep only the specific combined raw annotations specified (removing the other raw annotations). Duplicate values will be ignored.") | ||
protected List<String> keepSpecifiedCombined = new ArrayList<>(); | ||
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public List<String> getKeepSpecifiedCombinedAnnotationNames() {return Collections.unmodifiableList(keepSpecifiedCombined);} | ||
} |
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