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Adding argument to GenotypeGVCFs to keep only RAW_GT_COUNT #7996

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merged 13 commits into from
Oct 24, 2022
Merged

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 Aug 19, 2022
4a8b3cf
making the argument more general
meganshand Aug 24, 2022
522cd29
making arg optional
meganshand Aug 24, 2022
470c858
WIP
meganshand Sep 21, 2022
bf9fffc
WIP - adding annotation list as argument
meganshand Sep 26, 2022
263d2d8
Integrate GenotypeGVCFsAnnotationArgumentCollection.
cmnbroad Sep 26, 2022
7462183
trying to fix annotation argument
meganshand Sep 30, 2022
aaad296
addressing comments
meganshand Sep 30, 2022
65e4309
fixing ReblockGvcf tests
meganshand Sep 30, 2022
27b3994
addressing argument collection comments
meganshand Oct 6, 2022
fdccc7b
Update src/main/java/org/broadinstitute/hellbender/cmdline/GATKPlugin…
meganshand Oct 13, 2022
8d314f6
addressing comments
meganshand Oct 14, 2022
f7b8aa9
cleaning up
meganshand Oct 18, 2022
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1 change: 0 additions & 1 deletion ...stitute/hellbender/cmdline/GATKPlugin/DefaultGATKVariantAnnotationArgumentCollection.java
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@@ -1,6 +1,5 @@
package org.broadinstitute.hellbender.cmdline.GATKPlugin;

import com.google.common.collect.Lists;
import org.broadinstitute.barclay.argparser.Advanced;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
Expand Down
17 changes: 15 additions & 2 deletions ...java/org/broadinstitute/hellbender/cmdline/GATKPlugin/GATKAnnotationPluginDescriptor.java
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Expand Up @@ -16,7 +16,6 @@
import org.broadinstitute.hellbender.utils.config.ConfigFactory;
import org.broadinstitute.hellbender.utils.config.GATKConfig;

import java.io.File;
import java.lang.reflect.Modifier;
import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -485,6 +484,21 @@ public List<Annotation> getResolvedInstances() {
return resolvedInstances;
}

/**
* Returns a map of the String to Annotations only in the resolved instances. Should only be used if
* getResolvedInstances() is not sufficient.
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I think the "Should be used...." warning can be removed. That comment was intended for a previous revision where you were exposing allDiscoveredAnnotations.

*
* @return a Map of Strings to Annotations of resolved instances
*/
public Map<String, Annotation> getResolvedInstancesMap() {
if (resolvedInstances == null) {
getResolvedInstances();
}
Map<String, Annotation> resolvedInstancesMap = new HashMap<>();
allDiscoveredAnnotations.keySet().stream().filter(s -> resolvedInstances.contains(allDiscoveredAnnotations.get(s))).
forEach(s -> resolvedInstancesMap.put(s, allDiscoveredAnnotations.get(s)));
return(resolvedInstancesMap);
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}

/**
* Return the class representing the instance of the plugin specified by {@code pluginName}
Expand All @@ -496,5 +510,4 @@ public List<Annotation> getResolvedInstances() {
public Class<?> getClassForPluginHelp(final String pluginName) {
return allDiscoveredAnnotations.containsKey(pluginName) ? allDiscoveredAnnotations.get(pluginName).getClass() : null;
}

}
34 changes: 29 additions & 5 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs.java
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Expand Up @@ -9,6 +9,8 @@
import htsjdk.variant.vcf.VCFHeaderLine;
import org.broadinstitute.barclay.argparser.*;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor;
import org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKReadFilterPluginDescriptor;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.cmdline.argumentcollections.DbsnpArgumentCollection;
import org.broadinstitute.hellbender.cmdline.programgroups.ShortVariantDiscoveryProgramGroup;
Expand All @@ -28,6 +30,7 @@
import org.broadinstitute.hellbender.tools.walkers.mutect.M2ArgumentCollection;
import org.broadinstitute.hellbender.utils.*;
import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;

import java.util.*;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -132,17 +135,17 @@ public final class GenotypeGVCFs extends VariantLocusWalker {
doc = "LOD threshold to emit variant to VCF.")
protected double tlodThreshold = 3.5; //allow for some lower quality variants


/**
* Margin of error in allele fraction to consider a somatic variant homoplasmic, i.e. if there is less than a 0.1% reference allele fraction, those reads are likely errors
*/
@Argument(fullName=CombineGVCFs.ALLELE_FRACTION_DELTA_LONG_NAME, doc = "Margin of error in allele fraction to consider a somatic variant homoplasmic")
protected double afTolerance = 1e-3; //based on Q30 as a "good" base quality score

/**
* If specified, keep the combined raw annotations (e.g. AS_SB_TABLE) after genotyping. This is applicable to Allele-Specific annotations
* If specified, keep all the combined raw annotations (e.g. AS_SB_TABLE) after genotyping. This is applicable to Allele-Specific annotations. See {@link ReducibleAnnotation}
*/
@Argument(fullName=KEEP_COMBINED_LONG_NAME, shortName = KEEP_COMBINED_SHORT_NAME, doc = "If specified, keep the combined raw annotations")
@Argument(fullName=KEEP_COMBINED_LONG_NAME, shortName = KEEP_COMBINED_SHORT_NAME, doc = "If specified, keep the combined raw annotations",
mutex = {GenotypeGVCFsAnnotationArgumentCollection.KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME})
protected boolean keepCombined = false;

@ArgumentCollection
Expand Down Expand Up @@ -172,6 +175,9 @@ public final class GenotypeGVCFs extends VariantLocusWalker {
@ArgumentCollection
private final DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();

// @ArgumentCollection deliberately omitted since this is passed to the annotation plugin
final GenotypeGVCFsAnnotationArgumentCollection genotypeGVCFsAnnotationArgs = new GenotypeGVCFsAnnotationArgumentCollection();

// the annotation engine
private VariantAnnotatorEngine annotationEngine;

Expand Down Expand Up @@ -221,6 +227,16 @@ protected GenomicsDBOptions getGenomicsDBOptions() {
@Override
public boolean useVariantAnnotations() { return true;}

@Override
public List<? extends CommandLinePluginDescriptor<?>> getPluginDescriptors() {
GATKReadFilterPluginDescriptor readFilterDescriptor = new GATKReadFilterPluginDescriptor(getDefaultReadFilters());
return useVariantAnnotations()?
Arrays.asList(readFilterDescriptor, new GATKAnnotationPluginDescriptor(
genotypeGVCFsAnnotationArgs,
getDefaultVariantAnnotations(), getDefaultVariantAnnotationGroups())):
Collections.singletonList(readFilterDescriptor);
}

@Override
public List<Class<? extends Annotation>> getDefaultVariantAnnotationGroups() {
return Arrays.asList(StandardAnnotation.class);
Expand Down Expand Up @@ -261,8 +277,9 @@ public void onTraversalStart() {
intervals = hasUserSuppliedIntervals() ? intervalArgumentCollection.getIntervals(getBestAvailableSequenceDictionary()) :
Collections.emptyList();

Collection<Annotation> variantAnnotations = makeVariantAnnotations();
annotationEngine = new VariantAnnotatorEngine(variantAnnotations, dbsnp.dbsnp, Collections.emptyList(), false, keepCombined);
final Collection<Annotation> variantAnnotations = makeVariantAnnotations();
final Set<Annotation> annotationsToKeep = getAnnotationsToKeep();
annotationEngine = new VariantAnnotatorEngine(variantAnnotations, dbsnp.dbsnp, Collections.emptyList(), false, keepCombined, annotationsToKeep);

merger = new ReferenceConfidenceVariantContextMerger(annotationEngine, getHeaderForVariants(), somaticInput, false, true);

Expand All @@ -279,6 +296,13 @@ public void onTraversalStart() {

}

private Set<Annotation> getAnnotationsToKeep() {
final GATKAnnotationPluginDescriptor pluginDescriptor = getCommandLineParser().getPluginDescriptor(GATKAnnotationPluginDescriptor.class);
final List<String> annotationStringsToKeep = genotypeGVCFsAnnotationArgs.getKeepSpecifiedCombinedAnnotationNames();
final Map<String, Annotation> resolvedInstancesMap = pluginDescriptor.getResolvedInstancesMap();
return annotationStringsToKeep.stream().map(resolvedInstancesMap::get).collect(Collectors.toSet());
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@cmnbroad cmnbroad Oct 11, 2022 •
edited

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I think you need to be a bit more defensive in how you reconcile the "resolved" entries returned by getResolvedInstancesMap() with the entries in annotationStringsToKeep. You're not guaranteed that resolvedInstancesMap will contain an entry for every annotation the user specified in annotationStringsToKeep, so you need to handle the case where resolvedInstancesMap::get returns null here.

For instance, I don't think there is anything that will detect that the user made up some non-existent annotation name and specified it as a keeper, since they're just strings up until this point. Also, it's possible for the user to have both excluded an annotation AND specified it as a keeper (in which case it won't be in the resolved list). This code needs to detect and reject those cases so it doesn't wind up handing the annotator engine null annotations, preferably with some tests to ensure they're rejected properly.

You probably won't be able to tell exactly WHY a null is returned here, but I think rejecting that case with an error message saying something like, the annotation zzz either does not exist or was excluded. It's a bit of a pain - a lot of the logic in the plugin descriptor is to do exactly this kind of reconciliation and error reporting, but since the keep list is specific to GenotypeGVCFs, reconciling part of it has to be done here.

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I moved the "missing annotation" check here and added a test.

}

@Override
public void apply(final Locatable loc, List<VariantContext> variants, ReadsContext reads, ReferenceContext ref, FeatureContext features) {

Expand Down
27 changes: 27 additions & 0 deletions ...rg/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsAnnotationArgumentCollection.java
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package org.broadinstitute.hellbender.tools.walkers;

import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.hellbender.cmdline.GATKPlugin.DefaultGATKVariantAnnotationArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;

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

public class GenotypeGVCFsAnnotationArgumentCollection extends DefaultGATKVariantAnnotationArgumentCollection {
private static final long serialVersionUID = 1L;

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";

/**
* 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<>();

public List<String> getKeepSpecifiedCombinedAnnotationNames() {return Collections.unmodifiableList(keepSpecifiedCombined);}
}
35 changes: 34 additions & 1 deletion ...in/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java
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Expand Up @@ -4,12 +4,14 @@
import htsjdk.variant.vcf.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.engine.FeatureContext;
import org.broadinstitute.hellbender.engine.FeatureDataSource;
import org.broadinstitute.hellbender.engine.FeatureInput;
import org.broadinstitute.hellbender.engine.ReferenceContext;
import org.broadinstitute.hellbender.exceptions.GATKException;
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsAnnotationArgumentCollection;
import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotation;
import org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific.ReducibleAnnotationData;
import org.broadinstitute.hellbender.utils.Utils;
Expand Down Expand Up @@ -43,6 +45,7 @@ public final class VariantAnnotatorEngine {
private boolean expressionAlleleConcordance;
private final boolean useRawAnnotations;
private final boolean keepRawCombinedAnnotations;
private final List<String> rawAnnotationsToKeep;

private final static Logger logger = LogManager.getLogger(VariantAnnotatorEngine.class);
private final static OneShotLogger jumboAnnotationsLogger = new OneShotLogger(VariantAnnotatorEngine.class);
Expand All @@ -59,17 +62,21 @@ public final class VariantAnnotatorEngine {
* @param useRaw When this is set to true, the annotation engine will call {@link ReducibleAnnotation#annotateRawData(ReferenceContext, VariantContext, AlleleLikelihoods)}
* on annotations that extend {@link ReducibleAnnotation}, instead of {@link InfoFieldAnnotation#annotate(ReferenceContext, VariantContext, AlleleLikelihoods)},
* @param keepCombined If true, retain the combined raw annotation values instead of removing them after finalizing
* @param rawAnnotationsToKeep List of raw annotations to keep even when others are removed
*/
public VariantAnnotatorEngine(final Collection<Annotation> annotationList,
final FeatureInput<VariantContext> dbSNPInput,
final List<FeatureInput<VariantContext>> featureInputs,
final boolean useRaw,
boolean keepCombined){
final boolean keepCombined,
final Collection<Annotation> rawAnnotationsToKeep){
Utils.nonNull(featureInputs, "comparisonFeatureInputs is null");
infoAnnotations = new ArrayList<>();
genotypeAnnotations = new ArrayList<>();
jumboInfoAnnotations = new ArrayList<>();
jumboGenotypeAnnotations = new ArrayList<>();
final List<String> variantAnnotationKeys = new ArrayList<>();
final List<String> rawVariantAnnotationKeysToKeep = new ArrayList<>();
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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.

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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)

for (Annotation annot : annotationList) {
if (annot instanceof InfoFieldAnnotation) {
infoAnnotations.add((InfoFieldAnnotation) annot);
Expand All @@ -82,11 +89,19 @@ public VariantAnnotatorEngine(final Collection<Annotation> annotationList,
} else {
throw new GATKException.ShouldNeverReachHereException("Unexpected annotation type: " + annot.getClass().getName());
}
variantAnnotationKeys.addAll(((VariantAnnotation) annot).getKeyNames());
}
variantOverlapAnnotator = initializeOverlapAnnotator(dbSNPInput, featureInputs);
reducibleKeys = new LinkedHashSet<>();
useRawAnnotations = useRaw;
keepRawCombinedAnnotations = keepCombined;
for (final Annotation rawAnnot : rawAnnotationsToKeep) {
if (!annotationList.contains(rawAnnot)) {
throw new UserException("Requested --" + GenotypeGVCFsAnnotationArgumentCollection.KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME + ": " + rawAnnot + " is not available. Add requested annotation with --" + StandardArgumentDefinitions.ANNOTATION_LONG_NAME + ".");
}
rawVariantAnnotationKeysToKeep.addAll(((VariantAnnotation) rawAnnot).getKeyNames());
}
this.rawAnnotationsToKeep = rawVariantAnnotationKeysToKeep;
for (InfoFieldAnnotation annot : infoAnnotations) {
if (annot instanceof ReducibleAnnotation) {
for (final String rawKey : ((ReducibleAnnotation) annot).getRawKeyNames()) {
Expand All @@ -96,6 +111,14 @@ public VariantAnnotatorEngine(final Collection<Annotation> annotationList,
}
}

public VariantAnnotatorEngine(final Collection<Annotation> annotationList,
final FeatureInput<VariantContext> dbSNPInput,
final List<FeatureInput<VariantContext>> featureInputs,
final boolean useRaw,
boolean keepCombined){
this(annotationList, dbSNPInput, featureInputs, useRaw, keepCombined, Collections.emptyList());
}

private VariantOverlapAnnotator initializeOverlapAnnotator(final FeatureInput<VariantContext> dbSNPInput, final List<FeatureInput<VariantContext>> featureInputs) {
final Map<FeatureInput<VariantContext>, String> overlaps = new LinkedHashMap<>();
for ( final FeatureInput<VariantContext> fi : featureInputs) {
Expand Down Expand Up @@ -253,6 +276,14 @@ public Map<String, Object> combineAnnotations(final List<Allele> allelesList, Ma
public VariantContext finalizeAnnotations(VariantContext vc, VariantContext originalVC) {
final Map<String, Object> variantAnnotations = new LinkedHashMap<>(vc.getAttributes());

//save annotations that have been requested to be kept
final Map<String, Object> savedRawAnnotations = new LinkedHashMap<>();
for(final String rawAnnot : rawAnnotationsToKeep) {
if (variantAnnotations.containsKey(rawAnnot)) {
savedRawAnnotations.put(rawAnnot, variantAnnotations.get(rawAnnot));
}
}

// go through all the requested info annotationTypes
for (final InfoFieldAnnotation annotationType : infoAnnotations) {
if (annotationType instanceof ReducibleAnnotation) {
Expand Down Expand Up @@ -280,6 +311,8 @@ public VariantContext finalizeAnnotations(VariantContext vc, VariantContext orig
variantAnnotations.remove(GATKVCFConstants.VARIANT_DEPTH_KEY);
variantAnnotations.remove(GATKVCFConstants.RAW_GENOTYPE_COUNT_KEY);
}
//add back raw annotations that have specifically been requested to keep
variantAnnotations.putAll(savedRawAnnotations);

// generate a new annotated VC
final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(variantAnnotations);
Expand Down
6 changes: 3 additions & 3 deletions ...broadinstitute/hellbender/tools/walkers/annotator/allelespecific/ReducibleAnnotation.java
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Expand Up @@ -3,21 +3,21 @@
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCompoundHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.hellbender.engine.ReferenceContext;
import org.broadinstitute.hellbender.tools.walkers.annotator.Annotation;
import org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods;
import org.broadinstitute.hellbender.utils.read.GATKRead;
import org.broadinstitute.hellbender.utils.variant.GATKVCFHeaderLines;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

/**
* An interface for annotations that are calculated using raw data across samples, rather than the median (or median of median) of samples values
* The Raw annotation keeps some summary (one example might be a histogram of the raw values for each sample) of the individual sample (or allele)
* level annotation. As the annotations are combined across multiple samples the raw annotation continues to contain individual values while
* the final reduced annotation will typically be a summary statistic from these raw values.
*
*/
public interface ReducibleAnnotation extends Annotation {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
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Expand Up @@ -159,7 +159,7 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf
addInfoLine(new VCFInfoHeaderLine(INBREEDING_COEFFICIENT_KEY, 1, VCFHeaderLineType.Float, "Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"));
addInfoLine(new VCFInfoHeaderLine(AS_INBREEDING_COEFFICIENT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Allele-specific inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"));
addInfoLine(new VCFInfoHeaderLine(EXCESS_HET_KEY, 1, VCFHeaderLineType.Float, "Phred-scaled p-value for exact test of excess heterozygosity"));
addInfoLine(new VCFInfoHeaderLine(RAW_GENOTYPE_COUNT_KEY, 3, VCFHeaderLineType.Integer, "Counts of genotypes w.r.t. the reference allele: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"));
addInfoLine(new VCFInfoHeaderLine(RAW_GENOTYPE_COUNT_KEY, 3, VCFHeaderLineType.Integer, "Counts of genotypes w.r.t. the reference allele in the following order: 0/0, 0/*, */*, i.e. all alts lumped together; for use in calculating excess heterozygosity"));
addInfoLine(new VCFInfoHeaderLine(LIKELIHOOD_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods"));
addInfoLine(new VCFInfoHeaderLine(MAP_QUAL_RANK_SUM_KEY, 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"));
addInfoLine(new VCFInfoHeaderLine(AS_MAP_QUAL_RANK_SUM_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "allele specific Z-score From Wilcoxon rank sum test of each Alt vs. Ref read mapping qualities"));
Expand Down
5 changes: 2 additions & 3 deletions src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
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Expand Up @@ -43,8 +43,6 @@
import java.security.NoSuchAlgorithmException;
import java.util.*;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
import java.util.function.IntUnaryOperator;
import java.util.stream.Collectors;
import java.util.stream.Stream;

Expand Down Expand Up @@ -930,7 +928,7 @@ public void testRawGtCountAnnotation() {
args.addReference(b37_reference_20_21)
.addVCF(reblockedGVCF)
.addOutput(output)
.add("keep-combined-raw-annotations", true)
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Note that this replaces the previous test in favor of this new one. Perhaps we should consider just adding a new test, so that we cover both 1) keeping all combined annotations, and 2) keeping only the specified raw annotations?

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We've now made these two arguments (keep all combined and keeping only specified) mutually exclusive (not at the time of your review, but since then based on other comments). So I'm going to leave this test as is.

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Sorry, just to be clear, you mean you'll revert this test to its original behavior, right? In that case, will you add another test for the keep-specified behavior?

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The original behavior of --keep-combined-raw-annotations set to true while --keep-specified-raw-annotations is not empty is no longer allowed due to the mutex. So I think I am not reverting this test to the original behavior. Does that make sense? This test sets --keep-specified-raw-annotations to RawGtCount

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@samuelklee samuelklee Sep 30, 2022 •
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Sorry, by "original behavior" I mean the current behavior of the test as it is in master. This test sets --keep-combined-raw-annotations true and hence additionally retains RAW_MQandDP.

In contrast, you modify the test in your branch so that only RAW_GT_COUNT is retained and we check that RAW_MQandDP is not. This means the code path that is responsible for retaining RAW_MQandDP is no longer run in this test, at least (and is perhaps not run for this particular input test file in any test at all). Even though the original test does not explicitly check for any particular RAW_MQandDP output, this is still an effective drop in test coverage.

Probably not anything to sweat about, but that's all that I wanted to point out in my original comment. I'll leave it up to you to decide if --keep-combined-raw-annotations true is sufficiently covered by the other tests so that we don't have to worry about replacing the original test here.

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Oh! Sorry, I see what you're saying now. I think I originally added this test as a way of testing RawGTCount, rather than --keep-combined-raw-annotations true, so I overlooked that it did actually test the latter too. I do think the other tests sufficiently cover --keep-combined-raw-annotations true but I very much see how that is not clear from this change.

.add(GenotypeGVCFsAnnotationArgumentCollection.KEEP_SPECIFIED_RAW_COMBINED_ANNOTATION_LONG_NAME, "RawGtCount")
.add("A", "RawGtCount");
runCommandLine(args);

Expand All @@ -942,6 +940,7 @@ public void testRawGtCountAnnotation() {
Assert.assertEquals(rawGtCount.get(0), ".");
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What's going on with the hom-ref count? I see the TODO in the RawGtCount class but I don't understand the fundamental limitation.

Incidentally, perhaps we can go ahead and expand the header-line documentation of this annotation to explicitly give the hom-ref/het/hom-var order. Maybe this is obvious to everyone else, but why not document it for dummies like me?

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The issue is that RawGtCount is combined by GenomicsDB as a sum. There is no RawGtCount annotation on RefBlocks so the HomRef count always ends up being 0 in this case. It seems like ExcessHet isn't actually using RawGtCount as I expected. It recalculates the counts in GenotypeUtils.computeDiploidGenotypeCounts which doesn't seem to use RawGtCount so I'm not sure why RawGtCount is the rawKey associated with ExcessHet. Seems like this whole thing could be cleaned up so that we use the same method ExcessHet does to calculate the count of Het and HomVar genotypes at a site, but I'm not sure why we didn't do that in the first place.

Also I added the documentation to the header line.

Assert.assertEquals(rawGtCount.get(1), "2");
Assert.assertEquals(rawGtCount.get(2), "0");
Assert.assertFalse(vc.getAttributes().containsKey(GATKVCFConstants.RAW_MAPPING_QUALITY_WITH_DEPTH_KEY));
}

}
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