hotfix-4.5.x: heritableTraitList and genomicFeatureList are no longer initialised to null when parsing ClinVar variant summary txt
@@ -144,7 +144,7 @@ public class ClinVarIndexer extends ClinicalIndexer {
alleleOrigin = getAlleleOriginList(new ArrayList<>(originSet));
}
- List<HeritableTrait> heritableTraitList = null;
+ List<HeritableTrait> heritableTraitList = Collections.emptyList();
if (!EtlCommons.isMissing(lineFields[VARIANT_SUMMARY_PHENOTYPE_COLUMN])) {
Set<String> phenotypeSet = new HashSet<String>(Arrays.asList(lineFields[VARIANT_SUMMARY_PHENOTYPE_COLUMN]
.toLowerCase().split(";")));
@@ -152,7 +152,7 @@ public class ClinVarIndexer extends ClinicalIndexer {
.map((phenotype) -> new HeritableTrait(phenotype, null)).collect(Collectors.toList());
}
- List<GenomicFeature> genomicFeatureList = null;
+ List<GenomicFeature> genomicFeatureList = Collections.emptyList();
if (!EtlCommons.isMissing(lineFields[VARIANT_SUMMARY_GENE_COLUMN])) {
String[] geneList = lineFields[VARIANT_SUMMARY_GENE_COLUMN].split(",");
genomicFeatureList = new ArrayList<>(geneList.length);
