org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection Maven / Gradle / Ivy

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package org.broadinstitute.hellbender.cmdline.GATKPlugin;

import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;

import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

/**
 * Arguments for requesting VariantContext annotations to be processed by {@link org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine}
 * for tools that process variants objects.
 */
public class DefaultGATKVariantAnnotationArgumentCollection extends GATKAnnotationArgumentCollection {
    private static final long serialVersionUID = 1L;

    /**
     * Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.
     */
    @Argument(fullName = StandardArgumentDefinitions.ANNOTATION_LONG_NAME, shortName = StandardArgumentDefinitions.ANNOTATION_SHORT_NAME, doc = "One or more specific annotations to add to variant calls", optional = true)
    private List annotationsToUse = new ArrayList<>();

    /**
     * Which annotations to exclude from output in the variant calls.  Note that this argument has higher priority than the
     * -A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other
     * options.
     */
    @Argument(fullName = StandardArgumentDefinitions.ANNOTATIONS_TO_EXCLUDE_LONG_NAME, shortName = StandardArgumentDefinitions.ANNOTATIONS_TO_EXCLUDE_SHORT_NAME, doc = "One or more specific annotations to exclude from variant calls", optional = true)
    private List annotationsToExclude = new ArrayList<>();

    /**
     * Which groups of annotations to add to the output variant calls.
     * Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
     */
    @Argument(fullName = StandardArgumentDefinitions.ANNOTATION_GROUP_LONG_NAME, shortName = StandardArgumentDefinitions.ANNOTATION_GROUP_SHORT_NAME, doc = "One or more groups of annotations to apply to variant calls", optional = true)
    private List annotationGroupsToUse = new ArrayList<>();

    /**
     * Hook allowing for the user to remove default annotations from the tool
     */
    @Advanced
    @Argument(fullName = StandardArgumentDefinitions.DISABLE_TOOL_DEFAULT_ANNOTATIONS, shortName = StandardArgumentDefinitions.DISABLE_TOOL_DEFAULT_ANNOTATIONS, doc = "Disable all tool default annotations", optional = true)
    private boolean disableToolDefaultAnnotations = false;

    /**
     * You can use the -AX argument in combination with this one to exclude specific annotations. Note that some
     * annotations may not be actually applied if they are not applicable to the data provided or if they are
     * unavailable to the tool (e.g. there are several annotations that are currently not hooked up to
     * HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be
     * skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although
     * this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have
     * additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation
     * for individual annotations' requirements).
     */
    @Advanced
    @Argument(fullName=StandardArgumentDefinitions.ENABLE_ALL_ANNOTATIONS, doc="Use all possible annotations (not for the faint of heart)", optional=true)
    private boolean enableAllAnnotations = false;

    @Override
    public List getUserEnabledAnnotationNames() {
        return Collections.unmodifiableList(annotationsToUse);
    }

    @Override
    public List getUserEnabledAnnotationGroups() {
        return Collections.unmodifiableList(annotationGroupsToUse);
    }

    @Override
    public List getUserDisabledAnnotationNames() {
        return Collections.unmodifiableList(annotationsToExclude);
    }

    @Override
    public boolean getDisableToolDefaultAnnotations() {
        return disableToolDefaultAnnotations;
    }

    @Override
    public boolean getEnableAllAnnotations() {
        return enableAllAnnotations;
    }
}