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Adding argument to GenotypeGVCFs to keep only RAW_GT_COUNT #7996
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9ec8ca4
adding argument to GenotypeGVCFs to keep only RAW_GT_COUNT (not all r…
meganshand 4a8b3cf
making the argument more general
meganshand 522cd29
making arg optional
meganshand 470c858
WIP
meganshand bf9fffc
WIP - adding annotation list as argument
meganshand 263d2d8
Integrate GenotypeGVCFsAnnotationArgumentCollection.
cmnbroad 7462183
trying to fix annotation argument
meganshand aaad296
addressing comments
meganshand 65e4309
fixing ReblockGvcf tests
meganshand 27b3994
addressing argument collection comments
meganshand fdccc7b
Update src/main/java/org/broadinstitute/hellbender/cmdline/GATKPlugin…
meganshand 8d314f6
addressing comments
meganshand f7b8aa9
cleaning up
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1 change: 0 additions & 1 deletion
1
...stitute/hellbender/cmdline/GATKPlugin/DefaultGATKVariantAnnotationArgumentCollection.java
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27 changes: 27 additions & 0 deletions
27
...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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One other minor nit: why introduce this intermediate alias ? To me having the additional alias with a slightly different name just obfuscates whats going on - I'd suggest just allocating and using the
rawAnnotationsToKeep
instance variable directly, since this winds up being assigned there anyway.There was a problem hiding this comment.
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Yup, good catch. I fixed this and removed
variantAnnotationKeys
since it wasn't being used anymore (after moving the error message to GenotypeGVCFs)