/** * Convert org.opencb.biodata.models.variant.Variant into a htsjdk.variant.variantcontext.VariantContext * some assumptions: * * splitted multiallelic variants will produce only one variantContexts. Merging is done * * If some normalization has been applied, the source entries may have an attribute ORI like: "POS:REF:ALT_0(,ALT_N)*:ALT_IDX" * * @param variant A variant object to be converted * @param studyConfiguration StudyConfiguration * @param annotations Variant annotation * @return The variant in HTSJDK format * TODO: Move to a separated converter */ public VariantContext convertVariantToVariantContext(Variant variant, StudyConfiguration studyConfiguration, List<String> annotations) { //, StudyConfiguration return convertVariantToVariantContext(variant, annotations); }
@Override public boolean write(List<Variant> batch) { for (Variant variant : batch) { try { VariantContext variantContext = convertVariantToVariantContext(variant, annotations); if (variantContext != null) { writer.add(variantContext); } } catch (RuntimeException e) { logger.error("Error exporting variant " + variant, e); failedVariants++; converterErrorListener.get().accept(variant, e); } } return true; }