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Add pick to empty CSQ if no CSQ is present in the input #104

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Dec 17, 2024
Merged

Add pick to empty CSQ if no CSQ is present in the input #104

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8ece202
Add pick to empty CSQ if no CSQ is present in the input
bartcharbon Dec 17, 2024
49ffc36
Bump version
bartcharbon Dec 17, 2024
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -13,7 +13,7 @@

<groupId>org.molgenis</groupId>
<artifactId>vip-decision-tree</artifactId>
<version>5.1.2</version>
<version>5.1.3</version>

<name>vip-decision-tree</name>
<description>Decision tree module for filtering and labelling VCF files</description>
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5 changes: 5 additions & 0 deletions src/main/java/org/molgenis/vcf/decisiontree/runner/VepHelper.java
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Expand Up @@ -2,6 +2,7 @@

import static java.util.Collections.singletonList;
import static org.molgenis.vcf.decisiontree.runner.info.VepMetadataMapperImpl.ALLELE_NUM;
import static org.molgenis.vcf.decisiontree.runner.info.VepMetadataMapperImpl.PICK;

import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
Expand Down Expand Up @@ -52,6 +53,10 @@ public VcfRecord createEmptyCsqRecord(VcfRecord vcfRecord,
values.add("");
}
values.set(fields.get(ALLELE_NUM).getIndex(), alleleIndex.toString());
NestedField pick = fields.get(PICK);
if(pick != null) {
values.set(pick.getIndex(), "1");
}
VariantContext variantContext = vcfRecord.getVariantContext();
VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variantContext);
variantContextBuilder.attribute(nestedHeaderLine.getParentField().getId(),
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1 change: 1 addition & 0 deletions src/main/java/org/molgenis/vcf/decisiontree/runner/info/VepMetadataMapperImpl.java
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Expand Up @@ -20,6 +20,7 @@
public class VepMetadataMapperImpl implements VepMetadataMapper {

public static final String ALLELE_NUM = "ALLELE_NUM";
public static final String PICK = "PICK";
private static final String INFO_DESCRIPTION_PREFIX = "Consequence annotations from Ensembl VEP. Format: ";

private final FieldMetadataService fieldMetadataService;
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8 changes: 4 additions & 4 deletions src/test/resources/example-classified.vcf
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Expand Up @@ -45,7 +45,7 @@
#CHROM POS ID REF ALT QUAL FILTER INFO
1 10042538 . C T . PASS CSQ=LP|T|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP,|T|NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||HGNC|17877|1|0.0001|0|0.0001|0|0|0|0.0001|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0.43|0|0.41|LP
1 10042539 . C A,T . PASS CSQ=LP|A|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP,LB|T|missense_variant&NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|2||2|||HGNC|17877|2|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LB
1 10042540 . C G . PASS CLINVAR=LP;CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP
1 10042541 . C G . PASS CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB
1 10042542 . C G . . CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB
1 10042543 . C G . PASS CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP;FLAG1
1 10042540 . C G . PASS CLINVAR=LP;CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP
1 10042541 . C G . PASS CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB
1 10042542 . C G . . CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB
1 10042543 . C G . PASS CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP;FLAG1
8 changes: 4 additions & 4 deletions src/test/resources/example-classified_paths-labels.vcf
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Expand Up @@ -47,7 +47,7 @@
#CHROM POS ID REF ALT QUAL FILTER INFO
1 10042538 . C T . PASS CSQ=LP|T|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP|filter&vkgl&exit_lp|,|T|NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1|||HGNC|17877|1|0.0001|0|0.0001|0|0|0|0.0001|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0.43|0|0.41|LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&exit_lp|
1 10042539 . C A,T . PASS CSQ=LP|A|missense_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000377205|protein_coding|5/5||||763|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|1||1||1|HGNC|17877|1|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LP|filter&vkgl&exit_lp|,LB|T|missense_variant&NMD_transcript_variant|MODERATE|NMNAT1|ENSG00000173614|Transcript|ENST00000462686|nonsense_mediated_decay|5/6||||762|619|207|R/W|Cgg/Tgg|rs142968179&CM127756|2||2|||HGNC|17877|2|3.58e-05|0|2.891e-05|0|0|0|6.157e-05|0.0001629|0|pathogenic||1&1|26103963&22842229&22842230||0|0|0|0|LB|filter&vkgl&exit_lb|
1 10042540 . C G . PASS CLINVAR=LP;CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP|filter&vkgl&clinVar&exit_lp|
1 10042541 . C G . PASS CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
1 10042542 . C G . . CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
1 10042543 . C G . PASS CSQ=|||||||||||||||||||1||||||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lp|;FLAG1
1 10042540 . C G . PASS CLINVAR=LP;CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP|filter&vkgl&clinVar&exit_lp|
1 10042541 . C G . PASS CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
1 10042542 . C G . . CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LB|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lb|
1 10042543 . C G . PASS CSQ=|||||||||||||||||||1||||1||||||||||||||||||||||LP|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&flag&exit_lp|;FLAG1