Merge pull request #6 from molgenis/fix/5

fix #5: VIM and VID status fields have different types
molgenis · Dec 7, 2020 · 6fcaa5e · 6fcaa5e
2 parents 34df2a8 + ae4bfbf
commit 6fcaa5e
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/Annotator.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/Annotator.java
@@ -40,7 +40,7 @@ VCFHeader annotateHeader(VCFHeader vcfHeader) {
         VCFHeaderLineType.Integer,
         "Inheritance Denovo status."));
     vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(INHERITANCE_MATCH, 1,
-        VCFHeaderLineType.String,
+        VCFHeaderLineType.Integer,
         "Inheritance Match status."));
     vcfHeader.addMetaDataLine(new VCFFormatHeaderLine(MATCHING_GENES, VCFHeaderLineCount.UNBOUNDED,
         VCFHeaderLineType.String,

diff --git a/src/test/java/org/molgenis/vcf/inheritance/matcher/AnnotatorTest.java b/src/test/java/org/molgenis/vcf/inheritance/matcher/AnnotatorTest.java
@@ -42,7 +42,7 @@ void annotateHeader() {
         VCFHeaderLineType.Integer,
         "Inheritance Denovo status."));
     verify(vcfHeader).addMetaDataLine(new VCFFormatHeaderLine(INHERITANCE_MATCH, 1,
-        VCFHeaderLineType.String,
+        VCFHeaderLineType.Integer,
         "Inheritance Match status."));
     verify(vcfHeader).addMetaDataLine(new VCFFormatHeaderLine(MATCHING_GENES, VCFHeaderLineCount.UNBOUNDED,
         VCFHeaderLineType.String,

diff --git a/src/test/resources/expected.vcf b/src/test/resources/expected.vcf
@@ -6,7 +6,7 @@
 ##FORMAT=<ID=VIC,Number=1,Type=Integer,Description="Inheritance Compound status.">
 ##FORMAT=<ID=VID,Number=1,Type=Integer,Description="Inheritance Denovo status.">
 ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
-##FORMAT=<ID=VIM,Number=1,Type=String,Description="Inheritance Match status.">
+##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|SYMBOL|Gene|InheritanceModesGene">
 ##INFO=<ID=Compounds,Number=.,Type=String,Description="List of compound pairs for this variant.The list is splitted on ',' family id is separated with compoundswith ':'. Compounds are separated with '|'.">
 ##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">

diff --git a/src/test/resources/expected_probands.vcf b/src/test/resources/expected_probands.vcf
@@ -6,7 +6,7 @@
 ##FORMAT=<ID=VIC,Number=1,Type=Integer,Description="Inheritance Compound status.">
 ##FORMAT=<ID=VID,Number=1,Type=Integer,Description="Inheritance Denovo status.">
 ##FORMAT=<ID=VIG,Number=.,Type=String,Description="Genes with an inheritance match.">
-##FORMAT=<ID=VIM,Number=1,Type=String,Description="Inheritance Match status.">
+##FORMAT=<ID=VIM,Number=1,Type=Integer,Description="Inheritance Match status.">
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|SYMBOL|Gene|InheritanceModesGene">
 ##INFO=<ID=Compounds,Number=.,Type=String,Description="List of compound pairs for this variant.The list is splitted on ',' family id is separated with compoundswith ':'. Compounds are separated with '|'.">
 ##INFO=<ID=GeneticModels,Number=.,Type=String,Description="':'-separated list of genetic models for this variant.">