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Finally QUAL-related annotations are being output when they should be
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output -- had to update test data with missing AS_QD
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@ldgauthier
ldgauthier committed Sep 17, 2019
1 parent 82433b1 commit 332c40f
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Showing 5 changed files with 183 additions and 168 deletions.
24 changes: 15 additions & 9 deletions ...in/java/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -200,12 +200,16 @@ public Map<String, Object> combineAnnotations(final List<Allele> allelesList, Ma
for (final InfoFieldAnnotation annotationType : infoAnnotations) {
if (annotationType instanceof ReducibleAnnotation) {
ReducibleAnnotation currentASannotation = (ReducibleAnnotation) annotationType;
if (annotationMap.containsKey(currentASannotation.getRawKeyNames().get(0))) {
final List<ReducibleAnnotationData<?>> annotationValue = (List<ReducibleAnnotationData<?>>) annotationMap.get(currentASannotation.getRawKeyNames().get(0));
final Map<String, Object> annotationsFromCurrentType = currentASannotation.combineRawData(allelesList, annotationValue);
combinedAnnotations.putAll(annotationsFromCurrentType);
//remove the combined annotations so that the next method only processes the non-reducible ones
annotationMap.remove(currentASannotation.getRawKeyNames());
for (final String rawKey : currentASannotation.getRawKeyNames()) {
if (annotationMap.containsKey(rawKey)) {
final List<ReducibleAnnotationData<?>> annotationValue = (List<ReducibleAnnotationData<?>>) annotationMap.get(currentASannotation.getRawKeyNames().get(0));
final Map<String, Object> annotationsFromCurrentType = currentASannotation.combineRawData(allelesList, annotationValue);
combinedAnnotations.putAll(annotationsFromCurrentType);
//remove the combined annotations so that the next method only processes the non-reducible ones
for (final String rk : currentASannotation.getRawKeyNames()) {
annotationMap.remove(rk);
}
}
}
}
}
Expand All @@ -232,12 +236,14 @@ public VariantContext finalizeAnnotations(VariantContext vc, VariantContext orig
variantAnnotations.putAll(annotationsFromCurrentType);
}
//clean up raw annotation data after annotations are finalized
if (!keepRawCombinedAnnotations) {
variantAnnotations.remove(currentASannotation.getRawKeyNames());
for (final String rawKey: currentASannotation.getRawKeyNames()) {
if (!keepRawCombinedAnnotations) {
variantAnnotations.remove(rawKey);
}
}
}
}
variantAnnotations.remove(GATKVCFConstants.AS_QUAL_KEY); //this is manual until we extend the annotation raw key to take multiple values
variantAnnotations.remove(GATKVCFConstants.AS_QUAL_KEY); //this is manual because the "rawKeys" get added by genotyping

// generate a new annotated VC
final VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(variantAnnotations);
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6 changes: 4 additions & 2 deletions .../org/broadinstitute/hellbender/tools/walkers/annotator/allelespecific/AS_QualByDepth.java
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Original file line number Diff line number Diff line change
Expand Up @@ -144,8 +144,10 @@ public Map<String, Object> finalizeRawData(VariantContext vc, VariantContext ori

final Map<String, Object> map = new HashMap<>();
map.put(getKeyNames().get(0), AnnotationUtils.encodeValueList(QDlist, "%.2f"));
//keep AS_QUALapprox for Gnarly Pipeline because we don't subset alts or output genotypes if there are more than 6 alts
map.put(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, StringUtils.join(alleleQualList, AnnotationUtils.LIST_DELIMITER));
if (vc.hasAttribute(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY)) {
//keep AS_QUALapprox for Gnarly Pipeline because we don't subset alts or output genotypes if there are more than 6 alts
map.put(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY, StringUtils.join(alleleQualList, AnnotationUtils.LIST_DELIMITER));
}
return map;
}

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42 changes: 21 additions & 21 deletions src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -74,27 +74,27 @@ public Object[][] gvcfsToGenotype() {
return new Object[][]{
//combine not supported yet, see https://github.com/broadinstitute/gatk/issues/2429 and https://github.com/broadinstitute/gatk/issues/2584
//{"combine.single.sample.pipeline.1.vcf", null, Arrays.asList("-V", getTestFile("combine.single.sample.pipeline.2.vcf").toString() , "-V", getTestFile("combine.single.sample.pipeline.3.vcf").toString()), b37_reference_20_21},
// {getTestFile("leadingDeletion.g.vcf"), getTestFile("leadingDeletionRestrictToStartExpected.vcf"), Arrays.asList("-L", "20:69512-69513", "--"+GenotypeGVCFs.ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME), b37_reference_20_21},
// {getTestFile("leadingDeletion.g.vcf"), getTestFile("leadingDeletionExpected.vcf"), Arrays.asList("-L", "20:69512-69513"), b37_reference_20_21},
// {getTestFile(BASE_PAIR_GVCF), getTestFile( BASE_PAIR_EXPECTED), NO_EXTRA_ARGS, b37_reference_20_21}, //base pair level gvcf
// {getTestFile("testUpdatePGT.gvcf"), getTestFile( "testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //testUpdatePGT
// {getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //single sample vcf
// {getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-L", "20"), b37_reference_20_21}, //single sample vcf with -L
// {getTestFile("combined_genotype_gvcf_exception.original.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //test that an input vcf with 0/0 already in GT field is overwritten
// {getTestFile("combined_genotype_gvcf_exception.nocall.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //same test as above but with ./.
// {getTestFile(BASE_PAIR_GVCF), getTestFile("ndaTest.gatk3.7_30_ga4f720357.expected.vcf"), Collections.singletonList("--annotate-with-num-discovered-alleles"), b37_reference_20_21}, //annotating with the number of alleles discovered option
// {getTestFile(BASE_PAIR_GVCF), getTestFile("maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("--max-alternate-alleles", "1"), b37_reference_20_21 }, //restricting the max number of alt alleles
// {getTestFile(BASE_PAIR_GVCF), getTestFile("standardConfTest.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-stand-call-conf", "300"),b37_reference_20_21}, //set minimum calling threshold
// {getTestFile("spanningDel.combined.g.vcf"), getTestFile( "spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},
// {getTestFile("spanningDel.delOnly.g.vcf"), getTestFile( "spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},
// {getTestFile("spanningDel.depr.delOnly.g.vcf"), getTestFile( "spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf" ), NO_EXTRA_ARGS, b37_reference_20_21},
// {getTestFile("ad-bug-input.vcf"), getTestFile( "ad-bug-gatk3.7_30_ga4f720357-output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //Bad AD Propagation Haploid Bug
// {CEUTRIO_20_21_GATK3_4_G_VCF, getTestFile(CEUTRIO_20_21_EXPECTED_VCF), Arrays.asList("--dbsnp", largeFileTestDir + "dbsnp_138.b37.20.21.vcf"), b37_reference_20_21},
// {getTestFile("CEUTrio.20.21.missingIndel.g.vcf"), getTestFile( "CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("--dbsnp", "src/test/resources/large/dbsnp_138.b37.20.21.vcf"), b37_reference_20_21},
// {new File(largeFileTestDir + "gvcfs/gatk3.7_30_ga4f720357.24_sample.21.g.vcf"), new File( largeFileTestDir + "gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf"), NO_EXTRA_ARGS, b38_reference_20_21},
// {getTestFile("chr21.bad.pl.g.vcf"), getTestFile( "chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-L", "chr21:28341770-28341790"), b38_reference_20_21},
// {new File(largeFileTestDir + "gvcfs/combined.gatk3.7_30_ga4f720357.g.vcf.gz"), new File(largeFileTestDir + "gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b38_reference_20_21},
// //Tests for Allele-Specific Annotations
{getTestFile("leadingDeletion.g.vcf"), getTestFile("leadingDeletionRestrictToStartExpected.vcf"), Arrays.asList("-L", "20:69512-69513", "--"+GenotypeGVCFs.ONLY_OUTPUT_CALLS_STARTING_IN_INTERVALS_FULL_NAME), b37_reference_20_21},
{getTestFile("leadingDeletion.g.vcf"), getTestFile("leadingDeletionExpected.vcf"), Arrays.asList("-L", "20:69512-69513"), b37_reference_20_21},
{getTestFile(BASE_PAIR_GVCF), getTestFile( BASE_PAIR_EXPECTED), NO_EXTRA_ARGS, b37_reference_20_21}, //base pair level gvcf
{getTestFile("testUpdatePGT.gvcf"), getTestFile( "testUpdatePGT.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //testUpdatePGT
{getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //single sample vcf
{getTestFile("gvcfExample1.vcf"), getTestFile( "gvcfExample1.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-L", "20"), b37_reference_20_21}, //single sample vcf with -L
{getTestFile("combined_genotype_gvcf_exception.original.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //test that an input vcf with 0/0 already in GT field is overwritten
{getTestFile("combined_genotype_gvcf_exception.nocall.vcf"), getTestFile( "combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //same test as above but with ./.
{getTestFile(BASE_PAIR_GVCF), getTestFile("ndaTest.gatk3.7_30_ga4f720357.expected.vcf"), Collections.singletonList("--annotate-with-num-discovered-alleles"), b37_reference_20_21}, //annotating with the number of alleles discovered option
{getTestFile(BASE_PAIR_GVCF), getTestFile("maxAltAllelesTest.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("--max-alternate-alleles", "1"), b37_reference_20_21 }, //restricting the max number of alt alleles
{getTestFile(BASE_PAIR_GVCF), getTestFile("standardConfTest.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-stand-call-conf", "300"),b37_reference_20_21}, //set minimum calling threshold
{getTestFile("spanningDel.combined.g.vcf"), getTestFile( "spanningDel.combined.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},
{getTestFile("spanningDel.delOnly.g.vcf"), getTestFile( "spanningDel.delOnly.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b37_reference_20_21},
{getTestFile("spanningDel.depr.delOnly.g.vcf"), getTestFile( "spanningDel.depr.delOnly.gatk3.7_30_ga4f720357.expected.vcf" ), NO_EXTRA_ARGS, b37_reference_20_21},
{getTestFile("ad-bug-input.vcf"), getTestFile( "ad-bug-gatk3.7_30_ga4f720357-output.vcf"), NO_EXTRA_ARGS, b37_reference_20_21}, //Bad AD Propagation Haploid Bug
{CEUTRIO_20_21_GATK3_4_G_VCF, getTestFile(CEUTRIO_20_21_EXPECTED_VCF), Arrays.asList("--dbsnp", largeFileTestDir + "dbsnp_138.b37.20.21.vcf"), b37_reference_20_21},
{getTestFile("CEUTrio.20.21.missingIndel.g.vcf"), getTestFile( "CEUTrio.20.21.missingIndel.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("--dbsnp", "src/test/resources/large/dbsnp_138.b37.20.21.vcf"), b37_reference_20_21},
{new File(largeFileTestDir + "gvcfs/gatk3.7_30_ga4f720357.24_sample.21.g.vcf"), new File( largeFileTestDir + "gvcfs/gatk3.7_30_ga4f720357.24_sample.21.expected.vcf"), NO_EXTRA_ARGS, b38_reference_20_21},
{getTestFile("chr21.bad.pl.g.vcf"), getTestFile( "chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList("-L", "chr21:28341770-28341790"), b38_reference_20_21},
{new File(largeFileTestDir + "gvcfs/combined.gatk3.7_30_ga4f720357.g.vcf.gz"), new File(largeFileTestDir + "gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf"), NO_EXTRA_ARGS, b38_reference_20_21},
//Tests for Allele-Specific Annotations
{new File(ALLELE_SPECIFIC_DIRECTORY, "NA12878.AS.chr20snippet.g.vcf"), getTestFile( "AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList( "-A", "ClippingRankSumTest", "-G", "AS_StandardAnnotation", "-G", "StandardAnnotation"), b37_reference_20_21},
{new File(ALLELE_SPECIFIC_DIRECTORY, "NA12878.AS.chr20snippet.g.vcf"), getTestFile( "AS_Annotations.gatk3.7_30_ga4f720357.expected.vcf"), Arrays.asList( "-A", "ClippingRankSumTest", "-G", "AS_StandardAnnotation", "-G", "StandardAnnotation"), b37_reference_20_21},
{new File(ALLELE_SPECIFIC_DIRECTORY, "NA12878.AS.chr20snippet.g.vcf"), getTestFile( "AS_Annotations.keepRawCombined.expected.vcf"), Arrays.asList( "-A", "ClippingRankSumTest", "-G", "AS_StandardAnnotation", "-G", "StandardAnnotation", "-keep-combined"), b37_reference_20_21},
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