diff --git a/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java b/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java index 6713293de6e..cbff502c7d1 100644 --- a/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java +++ b/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java @@ -33,6 +33,9 @@ private StandardArgumentDefinitions(){} public static final String ADD_OUTPUT_SAM_PROGRAM_RECORD = "addOutputSAMProgramRecord"; public static final String ADD_OUTPUT_VCF_COMMANDLINE = "addOutputVCFCommandLine"; public static final String SEQUENCE_DICTIONARY_NAME = "sequenceDictionary"; + public static final String ANNOTATION_LONG_NAME = "annotation"; + public static final String ANNOTATION_GROUP_LONG_NAME = "annotationGroup"; + public static final String ANNOTATIONS_TO_EXCLUDE_LONG_NAME = "annotationsToExclude"; public static final String INPUT_SHORT_NAME = "I"; public static final String OUTPUT_SHORT_NAME = "O"; @@ -65,6 +68,9 @@ private StandardArgumentDefinitions(){} public static final String CLOUD_PREFETCH_BUFFER_SHORT_NAME = "CPB"; public static final String CLOUD_INDEX_PREFETCH_BUFFER_SHORT_NAME = "CIPB"; public static final String DISABLE_BAM_INDEX_CACHING_SHORT_NAME = "DBIC"; + public static final String ANNOTATION_SHORT_NAME = "A"; + public static final String ANNOTATION_GROUP_SHORT_NAME = "G"; + public static final String ANNOTATIONS_TO_EXCLUDE_SHORT_NAME = "AX"; public static final String SPARK_PROPERTY_NAME = "conf"; diff --git a/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/VariantAnnotationArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/VariantAnnotationArgumentCollection.java new file mode 100644 index 00000000000..ff279a76d6f --- /dev/null +++ b/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/VariantAnnotationArgumentCollection.java @@ -0,0 +1,57 @@ +package org.broadinstitute.hellbender.cmdline.argumentcollections; + +import org.broadinstitute.barclay.argparser.Advanced; +import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.utils.Utils; + +import java.io.Serializable; +import java.util.ArrayList; +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 VariantAnnotationArgumentCollection implements Serializable { + private static final long serialVersionUID = 1L; + + /** + * Argument collection constructor which defines tool default annotation arguments when they are not overridden by the user + * + * @param defaultGroups List annotation group names to be used by default + * @param defaultAnnotations List of annotation class names to be used by default + * @param defaultAnnotationsToExclude List of annotation class names to exclude by default. These override the default annotations and annotation groups. + */ + public VariantAnnotationArgumentCollection(List defaultGroups, List defaultAnnotations, List defaultAnnotationsToExclude) { + Utils.nonNull(defaultGroups); + Utils.nonNull(defaultAnnotations); + Utils.nonNull(defaultAnnotationsToExclude); + + annotationGroupsToUse = new ArrayList<>(defaultGroups); + annotationsToUse = new ArrayList<>(defaultAnnotations); + annotationsToExclude = new ArrayList<>(defaultAnnotationsToExclude); + } + + /** + * 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) + public 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) + public 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) + public List annotationGroupsToUse = new ArrayList<>(); + +} diff --git a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java index d71f18908bf..3e6dcd90b1f 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java @@ -207,7 +207,7 @@ public static JavaRDD callVariantsWithHaplotypeCaller( final Broadcast referenceBroadcast = ctx.broadcast(reference); final Broadcast hcArgsBroadcast = ctx.broadcast(hcArgs); - final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.annotationGroupsToUse, hcArgs.annotationsToUse, hcArgs.annotationsToExclude, hcArgs.dbsnp.dbsnp, hcArgs.comps); + final VariantAnnotatorEngine variantAnnotatorEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.variantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps); final Broadcast annotatorEngineBroadcast = ctx.broadcast(variantAnnotatorEngine); final List shardBoundaries = getShardBoundaries(header, intervals, shardingArgs.readShardSize, shardingArgs.readShardPadding); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java index 7d7545b0abc..4032cf31ac6 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java @@ -8,6 +8,7 @@ import org.broadinstitute.barclay.help.DocumentedFeature; import org.broadinstitute.hellbender.cmdline.*; import org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection; +import org.broadinstitute.hellbender.cmdline.argumentcollections.VariantAnnotationArgumentCollection; import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup; import org.broadinstitute.hellbender.engine.*; import org.broadinstitute.hellbender.tools.walkers.annotator.*; @@ -94,26 +95,11 @@ public final class GenotypeGVCFs extends VariantWalker { @ArgumentCollection private GenotypeCalculationArgumentCollection genotypeArgs = new GenotypeCalculationArgumentCollection(); - /** - * Which annotations to recompute for the combined output VCF file. - */ - @Advanced - @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to recompute", optional=true) - private List annotationsToUse = new ArrayList<>(); - - - @Advanced - @Argument(fullName="annotationsToExclude", shortName="AX", doc="One or more specific annotations to exclude from recomputation", optional=true) - private List annotationsToExclude = new ArrayList<>(); - - /** - * This argument controls which groups of annotations to add to the output VCF file. Not recommended for normal - * operation of the tool because it obscures the specific requirements of individual annotations. 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. - */ - @Advanced - @Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", optional=true) - private List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName()})); + @ArgumentCollection + private final VariantAnnotationArgumentCollection variantAnnotationArgumentCollection = new VariantAnnotationArgumentCollection( + Arrays.asList(StandardAnnotation.class.getSimpleName()), + Collections.emptyList(), + Collections.emptyList()); /** * This option can only be activated if intervals are specified. @@ -164,7 +150,7 @@ public void onTraversalStart() { genotypingEngine = new MinimalGenotypingEngine(createUAC(), samples, new GeneralPloidyFailOverAFCalculatorProvider(genotypeArgs)); - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude, dbsnp.dbsnp, Collections.emptyList()); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(variantAnnotationArgumentCollection, dbsnp.dbsnp, Collections.emptyList()); merger = new ReferenceConfidenceVariantContextMerger(); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java index 0a252130f95..a3650e40c22 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/BaseQuality.java @@ -1,9 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; -import com.google.common.primitives.Doubles; import com.google.common.primitives.Ints; import htsjdk.variant.variantcontext.VariantContext; -import org.apache.commons.math3.stat.descriptive.rank.Median; import org.broadinstitute.hellbender.utils.GATKProtectedMathUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.read.AlignmentUtils; @@ -11,7 +9,6 @@ import org.broadinstitute.hellbender.utils.read.ReadUtils; import java.util.List; -import java.util.OptionalDouble; import java.util.OptionalInt; /** @@ -19,7 +16,7 @@ * * Created by David Benjamin on 3/20/17. */ -public class BaseQuality extends PerAlleleAnnotation { +public class BaseQuality extends PerAlleleAnnotation implements StandardMutectAnnotation { public static final String KEY = "MBQ"; @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/Coverage.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/Coverage.java index f4390a04c3d..f0d4cb6bac2 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/Coverage.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/Coverage.java @@ -31,7 +31,7 @@ *
  • DepthPerSampleHC calculates depth of coverage after filtering by HaplotypeCaller.
    • * */ -public final class Coverage extends InfoFieldAnnotation implements StandardAnnotation { +public final class Coverage extends InfoFieldAnnotation implements StandardAnnotation, StandardMutectAnnotation { @Override public Map annotate(final ReferenceContext ref, diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java index f9cc6423c0e..4df9614cb91 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/DepthPerAlleleBySample.java @@ -34,7 +34,7 @@ *
  • AlleleBalanceBySample calculates allele balance for each individual sample.
    • * */ -public final class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation { +public final class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation, StandardMutectAnnotation { @Override public void annotate(final ReferenceContext ref, diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FragmentLength.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FragmentLength.java index 5565d075510..0fb59f9a39b 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FragmentLength.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/FragmentLength.java @@ -1,15 +1,12 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; -import com.google.common.primitives.Doubles; import com.google.common.primitives.Ints; import htsjdk.variant.variantcontext.VariantContext; -import org.apache.commons.math3.stat.descriptive.rank.Median; import org.broadinstitute.hellbender.utils.GATKProtectedMathUtils; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.read.GATKRead; import java.util.List; -import java.util.OptionalDouble; import java.util.OptionalInt; /** @@ -17,7 +14,7 @@ * * Created by David Benjamin on 3/20/17. */ -public class FragmentLength extends PerAlleleAnnotation { +public class FragmentLength extends PerAlleleAnnotation implements StandardMutectAnnotation { public static final String KEY = "MFRL"; @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQuality.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQuality.java index 9eed1fcdcae..9b35ff0025d 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQuality.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/MappingQuality.java @@ -1,17 +1,12 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; -import com.google.common.primitives.Doubles; import com.google.common.primitives.Ints; import htsjdk.variant.variantcontext.VariantContext; -import org.apache.commons.math3.stat.descriptive.rank.Median; import org.broadinstitute.hellbender.utils.GATKProtectedMathUtils; import org.broadinstitute.hellbender.utils.Utils; -import org.broadinstitute.hellbender.utils.read.AlignmentUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; -import org.broadinstitute.hellbender.utils.read.ReadUtils; import java.util.List; -import java.util.OptionalDouble; import java.util.OptionalInt; /** @@ -19,7 +14,7 @@ * * Created by David Benjamin on 3/20/17. */ -public class MappingQuality extends PerAlleleAnnotation { +public class MappingQuality extends PerAlleleAnnotation implements StandardMutectAnnotation { public static final String KEY = "MMQ"; @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCounts.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCounts.java index 18ee9f38465..5c5882dad16 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCounts.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/OxoGReadCounts.java @@ -14,15 +14,11 @@ import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines; -import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; import java.util.stream.Collectors; -import static org.broadinstitute.hellbender.utils.BaseUtils.Base.A; -import static org.broadinstitute.hellbender.utils.BaseUtils.Base.C; - /** * Count of read pairs in the F1R2 and F2R1 configurations supporting the reference and alternate alleles @@ -36,7 +32,7 @@ * "Discovery and characterization of artefactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation." * by Costello et al.

    */ -public final class OxoGReadCounts extends GenotypeAnnotation { +public final class OxoGReadCounts extends GenotypeAnnotation implements StandardMutectAnnotation { @Override public List getKeyNames() { diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java index 821d310800f..0ffd5bd2b22 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ReadPosition.java @@ -16,7 +16,7 @@ * * Created by David Benjamin on 3/20/17. */ -public class ReadPosition extends PerAlleleAnnotation { +public class ReadPosition extends PerAlleleAnnotation implements StandardMutectAnnotation { public static final String KEY = "MPOS"; @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardSomaticAnnotation.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardMutectAnnotation.java similarity index 58% rename from src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardSomaticAnnotation.java rename to src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardMutectAnnotation.java index bb5196717c5..ed1e3f27377 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardSomaticAnnotation.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StandardMutectAnnotation.java @@ -1,7 +1,7 @@ package org.broadinstitute.hellbender.tools.walkers.annotator; /** - * This is a marker interface used to indicate which annotations are "Standard" for MuTect only. + * This is a marker interface used to indicate which annotations are "Standard" for Mutect2 only. */ -public interface StandardSomaticAnnotation { +public interface StandardMutectAnnotation extends Annotation { } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandArtifact.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandArtifact.java index c850e0f1509..abefd5eabcf 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandArtifact.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/StrandArtifact.java @@ -21,7 +21,7 @@ * * Created by tsato on 4/19/17. */ -public class StrandArtifact extends GenotypeAnnotation implements StandardSomaticAnnotation { +public class StrandArtifact extends GenotypeAnnotation implements StandardMutectAnnotation { public static final String POSTERIOR_PROBABILITIES_KEY = "SA_POST_PROB"; public static final String MAP_ALLELE_FRACTIONS_KEY = "SA_MAP_AF"; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java index b7d92d59108..51b6b55599f 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/TandemRepeat.java @@ -24,7 +24,7 @@ * * */ -public final class TandemRepeat extends InfoFieldAnnotation { +public final class TandemRepeat extends InfoFieldAnnotation implements StandardMutectAnnotation { @Override public Map annotate(final ReferenceContext ref, diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/UniqueAltReadCount.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/UniqueAltReadCount.java index 27b100b6d31..2bb88cc8413 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/UniqueAltReadCount.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/UniqueAltReadCount.java @@ -35,7 +35,7 @@ * We filter the variant if the count is lower than a user-specified threshold. * Mutect2FilteringEngine::applyDuplicatedAltReadFilter is the accompanying filter. */ -public class UniqueAltReadCount extends GenotypeAnnotation implements StandardSomaticAnnotation { +public class UniqueAltReadCount extends GenotypeAnnotation { public static final String UNIQUE_ALT_READ_SET_COUNT_KEY = "UNIQ_ALT_READ_COUNT"; @Override diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java index 9c586c3a532..f435ceb965c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java @@ -4,6 +4,7 @@ import htsjdk.variant.variantcontext.*; import htsjdk.variant.vcf.*; import org.broadinstitute.barclay.argparser.CommandLineException; +import org.broadinstitute.hellbender.cmdline.argumentcollections.VariantAnnotationArgumentCollection; import org.broadinstitute.hellbender.engine.FeatureContext; import org.broadinstitute.hellbender.engine.FeatureInput; import org.broadinstitute.hellbender.engine.ReferenceContext; @@ -79,6 +80,26 @@ public static VariantAnnotatorEngine ofSelectedMinusExcluded(final List return new VariantAnnotatorEngine(AnnotationManager.ofSelectedMinusExcluded(annotationGroupsToUse, annotationsToUse, annotationsToExclude), dbSNPInput, comparisonFeatureInputs); } + /** + * An overload of {@link org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine#ofSelectedMinusExcluded ofSelectedMinusExcluded} + * except that it accepts a {@link org.broadinstitute.hellbender.cmdline.argumentcollections.VariantAnnotationArgumentCollection} as input. + * @param argumentCollection VariantAnnotationArgumentCollection containing requested annotations. + * @param dbSNPInput input for variants from a known set from DbSNP or null if not provided. + * The annotation engine will mark variants overlapping anything in this set using {@link htsjdk.variant.vcf.VCFConstants#DBSNP_KEY}. + * @param comparisonFeatureInputs list of inputs with known variants. + * The annotation engine will mark variants overlapping anything in those sets using the name given by {@link FeatureInput#getName()}. + * Note: the DBSNP FeatureInput should be passed in separately, and not as part of this List - an GATKException will be thrown otherwise. + * Note: there are no non-DBSNP comparison FeatureInputs an empty List should be passed in here, rather than null. + * @return a VariantAnnotatorEngine initialized with the requested annotations + */ + public static VariantAnnotatorEngine ofSelectedMinusExcluded(final VariantAnnotationArgumentCollection argumentCollection, + final FeatureInput dbSNPInput, + final List> comparisonFeatureInputs) { + return ofSelectedMinusExcluded(argumentCollection.annotationGroupsToUse, + argumentCollection.annotationsToUse, + argumentCollection.annotationsToExclude, + dbSNPInput, comparisonFeatureInputs); + } private VariantOverlapAnnotator initializeOverlapAnnotator(final FeatureInput dbSNPInput, final List> featureInputs) { final Map, String> overlaps = new LinkedHashMap<>(); for ( final FeatureInput fi : featureInputs) { @@ -94,6 +115,7 @@ private VariantOverlapAnnotator initializeOverlapAnnotator(final FeatureInput annotationsToExclude = new ArrayList<>(); - @Advanced @Argument(fullName = "smithWaterman", shortName = "smithWaterman", doc = "Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true) public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.FASTEST_AVAILABLE; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java index 482220f85a0..9624387f024 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java @@ -2,10 +2,15 @@ import org.broadinstitute.barclay.argparser.Advanced; import org.broadinstitute.barclay.argparser.Argument; +import org.broadinstitute.barclay.argparser.ArgumentCollection; +import org.broadinstitute.hellbender.cmdline.argumentcollections.VariantAnnotationArgumentCollection; +import org.broadinstitute.hellbender.tools.walkers.annotator.StandardAnnotation; +import org.broadinstitute.hellbender.tools.walkers.annotator.StandardHCAnnotation; import java.io.Serializable; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.List; /** @@ -15,21 +20,15 @@ public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgume private static final long serialVersionUID = 1L; /** - * Which annotations to add to the output VCF file. The single value 'none' removes the default annotations. - * See the VariantAnnotator -list argument to view available annotations. + * When HaplotypeCaller is run with -ERC GVCF or -ERC BP_RESOLUTION, some annotations are excluded from the + * output by default because they will only be meaningful once they have been recalculated by GenotypeGVCFs. As + * of version 3.3 this concerns ChromosomeCounts, FisherStrand, StrandOddsRatio and QualByDepth. */ - @Advanced - @Argument(fullName = "annotation", shortName = "A", doc = "One or more specific annotations to apply to variant calls", optional = true) - public List annotationsToUse = new ArrayList<>(); - - /** - * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. See - * the VariantAnnotator -list argument to view available groups. Note that this usage is not recommended because - * it obscures the specific requirements of individual annotations. 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 = "group", shortName = "G", doc = "One or more classes/groups of annotations to apply to variant calls", optional = true) - public List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{"StandardAnnotation", "StandardHCAnnotation"})); + @ArgumentCollection + public VariantAnnotationArgumentCollection variantAnnotationArgumentCollection = new VariantAnnotationArgumentCollection( + Arrays.asList(StandardAnnotation.class.getSimpleName(), StandardHCAnnotation.class.getSimpleName()), + Collections.emptyList(), + Collections.emptyList()); /** * You can use this argument to specify that HC should process a single sample out of a multisample BAM file. This diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java index 1c277c1b7fa..cab298797ac 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java @@ -171,7 +171,7 @@ private void initialize(boolean createBamOutIndex, final boolean createBamOutMD5 initializeActiveRegionEvaluationGenotyperEngine(); if (annotationEngine == null) { - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.annotationGroupsToUse, hcArgs.annotationsToUse, hcArgs.annotationsToExclude, hcArgs.dbsnp.dbsnp, hcArgs.comps); + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(hcArgs.variantAnnotationArgumentCollection, hcArgs.dbsnp.dbsnp, hcArgs.comps); } @@ -225,13 +225,13 @@ private void validateAndInitializeArgs() { hcArgs.genotypeArgs.STANDARD_CONFIDENCE_FOR_CALLING = -0.0; // also, we don't need to output several of the annotations - hcArgs.annotationsToExclude.add(ChromosomeCounts.class.getSimpleName()); - hcArgs.annotationsToExclude.add(FisherStrand.class.getSimpleName()); - hcArgs.annotationsToExclude.add(StrandOddsRatio.class.getSimpleName()); - hcArgs.annotationsToExclude.add(QualByDepth.class.getSimpleName()); + hcArgs.variantAnnotationArgumentCollection.annotationsToExclude.add(ChromosomeCounts.class.getSimpleName()); + hcArgs.variantAnnotationArgumentCollection.annotationsToExclude.add(FisherStrand.class.getSimpleName()); + hcArgs.variantAnnotationArgumentCollection.annotationsToExclude.add(StrandOddsRatio.class.getSimpleName()); + hcArgs.variantAnnotationArgumentCollection.annotationsToExclude.add(QualByDepth.class.getSimpleName()); // but we definitely want certain other ones - hcArgs.annotationsToUse.add(StrandBiasBySample.class.getSimpleName()); + hcArgs.variantAnnotationArgumentCollection.annotationsToUse.add(StrandBiasBySample.class.getSimpleName()); logger.info("Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output"); if ( ! hcArgs.annotateAllSitesWithPLs ) { logger.info("All sites annotated with PLs forced to true for reference-model confidence output"); diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java index d34b76233f2..d5ef3c0a845 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java @@ -1,15 +1,15 @@ package org.broadinstitute.hellbender.tools.walkers.mutect; import htsjdk.variant.variantcontext.VariantContext; -import org.broadinstitute.barclay.argparser.Advanced; import org.broadinstitute.barclay.argparser.Argument; -import org.broadinstitute.barclay.argparser.Hidden; +import org.broadinstitute.barclay.argparser.ArgumentCollection; +import org.broadinstitute.hellbender.cmdline.argumentcollections.VariantAnnotationArgumentCollection; import org.broadinstitute.hellbender.engine.FeatureInput; +import org.broadinstitute.hellbender.tools.walkers.annotator.StandardMutectAnnotation; import org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerArgumentCollection; -import java.util.ArrayList; import java.util.Arrays; -import java.util.List; +import java.util.Collections; public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection { private static final long serialVersionUID = 9341L; @@ -100,24 +100,15 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection @Argument(fullName = "normal_lod", optional = true, doc = "LOD threshold for calling normal variant non-germline.") public double NORMAL_LOD_THRESHOLD = 2.2; - /** - * Which annotations to add to the output VCF file. By default the tool adds all of the following annotations. - * If an annotation that a filter depends upon is absent, then the particular filtering will not occur and no warning will be given. - */ - @Advanced - @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls.", optional = true) - protected List annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"Coverage", "DepthPerAlleleBySample", - "TandemRepeat", "OxoGReadCounts", "ReadPosition", "BaseQuality", "MappingQuality", - "FragmentLength", "StrandArtifact"})); /** - * Which groups of annotations to add to the output VCF file. The single value 'none' removes the default group. - * Note that this usage is not recommended because it obscures the specific requirements of individual annotations. + * Set of annotation arguments to use. * 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. - * For somatic analyses, the StandardSomaticAnnotation group currently contains one annotations: StrandArtifact. - * Note the latter is redundant to an annotation given by the --annotation argument default. */ - @Argument(fullName = "group", shortName = "G", doc = "One or more classes/groups of annotations to apply to variant calls", optional = true) - public List annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{})); + @ArgumentCollection + VariantAnnotationArgumentCollection variantAnnotationArgumentCollection = new VariantAnnotationArgumentCollection( + Arrays.asList(StandardMutectAnnotation.class.getSimpleName()), + Collections.emptyList(), + Collections.emptyList()); } diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java index 986ba13f7af..498872e691e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2Engine.java @@ -112,9 +112,7 @@ private void initialize(final boolean createBamOutIndex, final boolean createBam " sample name " + MTAC.normalSampleName); } - annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(MTAC.annotationGroupsToUse, - MTAC.annotationsToUse, - MTAC.annotationsToExclude, + annotationEngine = VariantAnnotatorEngine.ofSelectedMinusExcluded(MTAC.variantAnnotationArgumentCollection, MTAC.dbsnp.dbsnp, MTAC.comps);