diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java index 6896c55cd..b7aa8f115 100644 --- a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java +++ b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java @@ -34,11 +34,12 @@ import java.io.File; import java.io.IOException; import java.nio.file.*; +import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.List; -import static org.opencb.cellbase.lib.EtlCommons.PHARMGKB_DATA; +import static org.opencb.cellbase.lib.EtlCommons.*; /** * Created by imedina on 03/02/15. @@ -347,16 +348,26 @@ private CellBaseBuilder buildConservation() { return new ConservationBuilder(conservationFilesDir, conservationChunkSize, serializer); } - private CellBaseBuilder buildClinicalVariants() { + private CellBaseBuilder buildClinicalVariants() throws CellBaseException { Path clinicalVariantFolder = downloadFolder.resolve(EtlCommons.CLINICAL_VARIANTS_FOLDER); - copyVersionFiles(Arrays.asList(clinicalVariantFolder.resolve("clinvarVersion.json"))); - copyVersionFiles(Arrays.asList(clinicalVariantFolder.resolve("gwasVersion.json"))); + + List versionFiles = new ArrayList<>(); + List versionFilenames = Arrays.asList(CLINVAR_VERSION_FILENAME, COSMIC_VERSION_FILENAME, GWAS_VERSION_FILENAME, + HGMD_VERSION_FILENAME); + for (String versionFilename : versionFilenames) { + Path versionFile = clinicalVariantFolder.resolve(versionFilename); + if (!versionFile.toFile().exists()) { + throw new CellBaseException("Could not build clinical variants because of the file " + versionFilename + " does not exist"); + } + versionFiles.add(versionFile); + } + copyVersionFiles(versionFiles); CellBaseSerializer serializer = new CellBaseJsonFileSerializer(buildFolder, EtlCommons.CLINICAL_VARIANTS_JSON_FILE.replace(".json.gz", ""), true); return new ClinicalVariantBuilder(clinicalVariantFolder, normalize, getFastaReferenceGenome(), buildCommandOptions.assembly == null ? getDefaultHumanAssembly() : buildCommandOptions.assembly, - serializer); + configuration, serializer); } private String getDefaultHumanAssembly() { diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml index 264732208..09f0eb976 100644 --- a/cellbase-core/src/main/resources/configuration.yml +++ b/cellbase-core/src/main/resources/configuration.yml @@ -183,6 +183,8 @@ download: ## Download file from https://www.ebi.ac.uk/gwas/docs/file-downloads to find the real version, which is 'e110_r2023-12-20' host: https://ftp.ebi.ac.uk/pub/databases/gwas/releases/2024/02/12/gwas-catalog-associations_ontology-annotated.tsv version: "2024-02-12" + files: + - All.vcf.gz hpo: ## NOTE: Download manually from here now host: https://hpo.jax.org/app/data/annotations diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java index 165007e3d..545c5cc61 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/EtlCommons.java @@ -87,26 +87,6 @@ public class EtlCommons { public static final String GWAS_NAME = "GWAS catalog"; public static final String GWAS_VERSION_FILENAME = "gwas" + SUFFIX_VERSION_FILENAME; - @Deprecated - public static final String CLINVAR_VERSION = "2022.11"; - @Deprecated - public static final String CLINVAR_DATE = "2022-11"; - @Deprecated - public static final String CLINVAR_XML_FILE = "ClinVarFullRelease_2022-11.xml.gz"; - @Deprecated - public static final String CLINVAR_EFO_FILE = "ClinVar_Traits_EFO_Names.csv"; - @Deprecated - public static final String CLINVAR_SUMMARY_FILE = "variant_summary.txt.gz"; - @Deprecated - public static final String CLINVAR_VARIATION_ALLELE_FILE = "variation_allele.txt.gz"; - public static final String IARCTP53_FILE = "IARC-TP53.zip"; - @Deprecated - public static final String GWAS_FILE = "gwas-catalog-associations_ontology-annotated.tsv"; - @Deprecated - public static final String COSMIC_FILE = "CosmicMutantExport.tsv.gz"; - @Deprecated - public static final String DBSNP_FILE = "All.vcf.gz"; - public static final String STRUCTURAL_VARIANTS_DATA = "svs"; public static final String REPEATS_DATA = "repeats"; public static final String OBO_DATA = "ontology"; diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java index 93098122b..7e5baa9e6 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinVarIndexer.java @@ -41,11 +41,6 @@ import java.util.stream.Collectors; import java.util.stream.Stream; -import static org.opencb.cellbase.lib.EtlCommons.CLINVAR_DATE; -import static org.opencb.cellbase.lib.EtlCommons.CLINVAR_VERSION; - -//import org.opencb.biodata.formats.variant.clinvar.v24jaxb.*; - /** * Created by fjlopez on 28/09/16. */ @@ -78,11 +73,15 @@ public class ClinVarIndexer extends ClinicalIndexer { private static final String DIPLOTYPE = "Diplotype"; private static final String VARIANT = "Variant"; private static final char CLINICAL_SIGNIFICANCE_SEPARATOR = '/'; + private final Path clinvarXMLFiles; private final Path clinvarSummaryFile; private final Path clinvarVariationAlleleFile; private final Path clinvarEFOFile; + + private final String version; private final String assembly; + private int numberSomaticRecords = 0; private int numberGermlineRecords = 0; private int numberNoDiseaseTrait = 0; @@ -94,15 +93,15 @@ public class ClinVarIndexer extends ClinicalIndexer { private static final Set RECESSIVE_TERM_SET = new HashSet<>(Arrays.asList(ModeOfInheritance.biallelic)); - public ClinVarIndexer(Path clinvarXMLFiles, Path clinvarSummaryFile, Path clinvarVariationAlleleFile, - Path clinvarEFOFile, boolean normalize, Path genomeSequenceFilePath, String assembly, - RocksDB rdb) throws IOException { + public ClinVarIndexer(Path clinvarXMLFiles, Path clinvarSummaryFile, Path clinvarVariationAlleleFile, Path clinvarEFOFile, + String version, boolean normalize, Path genomeSequenceFilePath, String assembly, RocksDB rdb) throws IOException { super(genomeSequenceFilePath); this.rdb = rdb; this.clinvarXMLFiles = clinvarXMLFiles; this.clinvarSummaryFile = clinvarSummaryFile; this.clinvarVariationAlleleFile = clinvarVariationAlleleFile; this.clinvarEFOFile = clinvarEFOFile; + this.version = version; this.normalize = normalize; this.genomeSequenceFilePath = genomeSequenceFilePath; this.assembly = assembly; @@ -310,7 +309,7 @@ private void addNewEntries(VariantAnnotation variantAnnotation, String variation String mateVariantString, String clinicalHaplotypeString, Map traitsToEfoTermsMap) { - EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_NAME, CLINVAR_VERSION, CLINVAR_DATE); + EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_NAME, version, null); // Create a set to avoid situations like germline;germline;germline List alleleOrigin = null; if (!EtlCommons.isMissing(lineFields[VARIANT_SUMMARY_ORIGIN_COLUMN])) { @@ -391,7 +390,7 @@ private void addNewEntries(VariantAnnotation variantAnnotation, PublicSetType pu throws JsonProcessingException { List additionalProperties = new ArrayList<>(3); - EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_NAME, CLINVAR_VERSION, CLINVAR_DATE); + EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.CLINVAR_NAME, version, null); // String accession = publicSet.getReferenceClinVarAssertion().getClinVarAccession().getAcc(); VariantClassification variantClassification = getVariantClassification( diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilder.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilder.java index 4736d7abd..7529bbdd2 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilder.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilder.java @@ -19,8 +19,9 @@ import com.fasterxml.jackson.databind.ObjectMapper; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.VariantAnnotation; +import org.opencb.cellbase.core.config.CellBaseConfiguration; +import org.opencb.cellbase.core.exception.CellBaseException; import org.opencb.cellbase.core.serializer.CellBaseSerializer; -import org.opencb.cellbase.lib.EtlCommons; import org.opencb.cellbase.lib.builders.CellBaseBuilder; import org.rocksdb.Options; import org.rocksdb.RocksDB; @@ -38,108 +39,82 @@ */ public class ClinicalVariantBuilder extends CellBaseBuilder { - private final Path clinvarXMLFile; - private final Path clinvarSummaryFile; - private final Path clinvarVariationAlleleFile; - private final Path clinvarEFOFile; - private final Path cosmicFile; - private final Path gwasFile; - private final Path dbsnpFile; + private final Path clinicalVariantFolder; private final String assembly; private final Path genomeSequenceFilePath; - private final Path hgmdFile; private boolean normalize; - public ClinicalVariantBuilder(Path clinicalVariantFolder, boolean normalize, Path genomeSequenceFilePath, - String assembly, CellBaseSerializer serializer) { - this(clinicalVariantFolder.resolve(EtlCommons.CLINVAR_XML_FILE), - clinicalVariantFolder.resolve(EtlCommons.CLINVAR_SUMMARY_FILE), - clinicalVariantFolder.resolve(EtlCommons.CLINVAR_VARIATION_ALLELE_FILE), - clinicalVariantFolder.resolve(EtlCommons.CLINVAR_EFO_FILE), - clinicalVariantFolder.resolve(EtlCommons.COSMIC_FILE), - clinicalVariantFolder.resolve(EtlCommons.GWAS_FILE), - clinicalVariantFolder.resolve(EtlCommons.DBSNP_FILE), - clinicalVariantFolder.resolve(EtlCommons.HGMD_FILE), - normalize, - genomeSequenceFilePath, assembly, serializer); - } + private final CellBaseConfiguration configuration; - public ClinicalVariantBuilder(Path clinvarXMLFile, Path clinvarSummaryFile, Path clinvarVariationAlleleFile, - Path clinvarEFOFile, Path cosmicFile, Path gwasFile, Path dbsnpFile, Path hgmdFile, - boolean normalize, Path genomeSequenceFilePath, String assembly, - CellBaseSerializer serializer) { + public ClinicalVariantBuilder(Path clinicalVariantFolder, boolean normalize, Path genomeSequenceFilePath, + String assembly, CellBaseConfiguration configuration, CellBaseSerializer serializer) { super(serializer); - this.clinvarXMLFile = clinvarXMLFile; - this.clinvarSummaryFile = clinvarSummaryFile; - this.clinvarVariationAlleleFile = clinvarVariationAlleleFile; - this.clinvarEFOFile = clinvarEFOFile; - this.cosmicFile = cosmicFile; - this.gwasFile = gwasFile; - this.dbsnpFile = dbsnpFile; - this.hgmdFile = hgmdFile; + this.clinicalVariantFolder = clinicalVariantFolder; this.normalize = normalize; this.genomeSequenceFilePath = genomeSequenceFilePath; this.assembly = assembly; + this.configuration = configuration; } - public void parse() throws IOException, RocksDBException { - + public void parse() throws IOException, RocksDBException, CellBaseException { RocksDB rdb = null; Options dbOption = null; String dbLocation = null; try { - Object[] dbConnection = getDBConnection(clinvarXMLFile.getParent().toString() + "/integration.idx", true); + Object[] dbConnection = getDBConnection(clinicalVariantFolder.toString() + "/integration.idx", true); rdb = (RocksDB) dbConnection[0]; dbOption = (Options) dbConnection[1]; dbLocation = (String) dbConnection[2]; // COSMIC // IMPORTANT: COSMIC must be indexed first (before ClinVar, IARC TP53, DOCM, HGMD,...)!!! - if (this.cosmicFile != null && Files.exists(this.cosmicFile)) { - CosmicIndexer cosmicIndexer = new CosmicIndexer(cosmicFile, normalize, genomeSequenceFilePath, assembly, rdb); + Path cosmicFile = clinicalVariantFolder.resolve(configuration.getDownload().getCosmic().getFiles().get(0)); + if (cosmicFile != null && Files.exists(cosmicFile)) { + CosmicIndexer cosmicIndexer = new CosmicIndexer(cosmicFile, configuration.getDownload().getCosmic().getVersion(), + normalize, genomeSequenceFilePath, assembly, rdb); cosmicIndexer.index(); } else { - logger.warn("Cosmic file {} missing. Skipping Cosmic data", cosmicFile); + throw new CellBaseException("Could not build clinical variants: the COSMIC file " + cosmicFile + " is missing"); } // ClinVar - if (this.clinvarXMLFile != null && this.clinvarSummaryFile != null - && this.clinvarVariationAlleleFile != null && Files.exists(clinvarXMLFile) - && Files.exists(clinvarSummaryFile) && Files.exists(clinvarVariationAlleleFile)) { - ClinVarIndexer clinvarIndexer = new ClinVarIndexer(clinvarXMLFile.getParent().resolve("clinvar_chunks"), clinvarSummaryFile, - clinvarVariationAlleleFile, clinvarEFOFile, normalize, genomeSequenceFilePath, assembly, rdb); - clinvarIndexer.index(); - } else { - logger.warn("One or more of required ClinVar files are missing. Skipping ClinVar data.\n" - + "Please, ensure that these two files exist:\n" - + "{}\n" - + "{}", this.clinvarXMLFile.toString(), this.clinvarSummaryFile.toString()); - } + Path clinvarXMLFile = getPathFromHost(configuration.getDownload().getClinvar().getHost()); + Path clinvarSummaryFile = getPathFromHost(configuration.getDownload().getClinvarSummary().getHost()); + Path clinvarVariationAlleleFile = getPathFromHost(configuration.getDownload().getClinvarVariationAllele().getHost()); + Path clinvarEFOFile = getPathFromHost(configuration.getDownload().getClinvarEfoTerms().getHost()); + ClinVarIndexer clinvarIndexer = new ClinVarIndexer(clinvarXMLFile.getParent().resolve("clinvar_chunks"), clinvarSummaryFile, + clinvarVariationAlleleFile, clinvarEFOFile, configuration.getDownload().getClinvar().getVersion(), normalize, + genomeSequenceFilePath, assembly, rdb); + clinvarIndexer.index(); // HGMD - if (this.hgmdFile != null && Files.exists(hgmdFile)) { - HGMDIndexer hgmdIndexer = new HGMDIndexer(hgmdFile, normalize, genomeSequenceFilePath, assembly, rdb); + Path hgmdFile = clinicalVariantFolder.resolve(configuration.getDownload().getHgmd().getFiles().get(0)); + if (hgmdFile != null && Files.exists(hgmdFile)) { + HGMDIndexer hgmdIndexer = new HGMDIndexer(hgmdFile, configuration.getDownload().getHgmd().getVersion(), normalize, + genomeSequenceFilePath, assembly, rdb); hgmdIndexer.index(); } else { - logger.warn("The HGMD file {} is missing. Skipping HGMD data.", hgmdFile); + throw new CellBaseException("Could not build clinical variants: the HGMD file " + hgmdFile + " is missing"); } // GWAS catalog + Path gwasFile = clinicalVariantFolder.resolve(Paths.get(configuration.getDownload().getGwasCatalog().getHost()).getFileName()); if (gwasFile != null && Files.exists(gwasFile)) { + Path dbsnpFile = clinicalVariantFolder.resolve(configuration.getDownload().getHgmd().getFiles().get(0)); if (dbsnpFile != null && Files.exists(dbsnpFile)) { Path tabixFile = Paths.get(dbsnpFile.toAbsolutePath() + ".tbi"); if (tabixFile != null && Files.exists(tabixFile)) { GwasIndexer gwasIndexer = new GwasIndexer(gwasFile, dbsnpFile, genomeSequenceFilePath, assembly, rdb); gwasIndexer.index(); } else { - logger.warn("The dbSNP tabix file {} is missing. Skipping GWAS catalog data.", tabixFile); + throw new CellBaseException("Could not build clinical variants: the dbSNP tabix file " + tabixFile + " is missing"); } } else { - logger.warn("The dbSNP file {} is missing. Skipping GWAS catalog data.", dbsnpFile); + throw new CellBaseException("Could not build clinical variants: the dbSNP file " + dbsnpFile + " is missing"); } } else { - logger.warn("The GWAS catalog file {} is missing. Skipping GWAS catalog data.", gwasFile); + throw new CellBaseException("Could not build clinical variants: the GWAS catalog file " + gwasFile + " is missing"); } serializeRDB(rdb); @@ -153,6 +128,14 @@ public void parse() throws IOException, RocksDBException { } + private Path getPathFromHost(String host) throws CellBaseException { + Path path = clinicalVariantFolder.resolve(Paths.get(host).getFileName()); + if (!Files.exists(path)) { + throw new CellBaseException("Could not build clinical variants. The file " + path + " is missing"); + } + return path; + } + private void serializeRDB(RocksDB rdb) throws IOException { // DO NOT change the name of the rocksIterator variable - for some unexplainable reason Java VM crashes if it's // named "iterator" diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java index 5d8f14535..c77250173 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java @@ -37,13 +37,12 @@ public class CosmicIndexer extends ClinicalIndexer { private final Path cosmicFile; + private final String version; private final String assembly; + private Pattern mutationGRCh37GenomePositionPattern; private Pattern snvPattern; - @Deprecated - private static final String COSMIC_VERSION = "v95"; - private static final int GENE_NAMES_COLUMN = 0; private static final int HGNC_COLUMN = 3; private static final int PRIMARY_SITE_COLUMN = 7; @@ -85,10 +84,12 @@ public class CosmicIndexer extends ClinicalIndexer { private int rocksDBNewVariants = 0; private int rocksDBUpdateVariants = 0; - public CosmicIndexer(Path cosmicFile, boolean normalize, Path genomeSequenceFilePath, String assembly, RocksDB rdb) throws IOException { + public CosmicIndexer(Path cosmicFile, String version, boolean normalize, Path genomeSequenceFilePath, String assembly, RocksDB rdb) + throws IOException { super(genomeSequenceFilePath); this.cosmicFile = cosmicFile; + this.version = version; this.normalize = normalize; this.assembly = assembly; this.rdb = rdb; @@ -470,7 +471,7 @@ private EvidenceEntry buildCosmic(String[] fields) { String id = fields[ID_COLUMN]; String url = "https://cancer.sanger.ac.uk/cosmic/search?q=" + id; - EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.COSMIC_NAME, COSMIC_VERSION, null); + EvidenceSource evidenceSource = new EvidenceSource(EtlCommons.COSMIC_NAME, version, null); SomaticInformation somaticInformation = getSomaticInformation(fields); List genomicFeatureList = getGenomicFeature(fields); diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java index b7cb28cf1..2c0d2b3d2 100644 --- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java +++ b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/HGMDIndexer.java @@ -36,15 +36,17 @@ */ public class HGMDIndexer extends ClinicalIndexer { private final Path hgmdFile; + private final String version; private final String assembly; - public HGMDIndexer(Path hgmdFile, boolean normalize, Path genomeSequenceFilePath, String assembly, RocksDB rdb) + public HGMDIndexer(Path hgmdFile, String version, boolean normalize, Path genomeSequenceFilePath, String assembly, RocksDB rdb) throws IOException { super(genomeSequenceFilePath); - this.rdb = rdb; - this.assembly = assembly; this.hgmdFile = hgmdFile; + this.version = version; this.normalize = normalize; + this.assembly = assembly; + this.rdb = rdb; } public void index() throws RocksDBException, IOException { @@ -93,7 +95,7 @@ private void parseHgmdInfo(Variant variant) { } // Source - entry.setSource(new EvidenceSource(EtlCommons.HGMD_NAME, "2020.3", "2020")); + entry.setSource(new EvidenceSource(EtlCommons.HGMD_NAME, version, null)); // Assembly entry.setAssembly(assembly); diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilderTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilderTest.java index 7ad0892c1..fc5df3af3 100644 --- a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilderTest.java +++ b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/builders/clinical/variant/ClinicalVariantBuilderTest.java @@ -90,7 +90,7 @@ public void noNormaliseTest() throws Exception { clinicalVariantChunksFolder.resolve("ClinVarFullRelease_2020-02.xml.gz").toFile()); CellBaseSerializer serializer = new CellBaseJsonFileSerializer(Paths.get("/tmp/"), EtlCommons.CLINICAL_VARIANTS_DATA, true); - (new ClinicalVariantBuilder(clinicalVariantFolder, false, genomeSequenceFilePath, "GRCh37", serializer)).parse(); + (new ClinicalVariantBuilder(clinicalVariantFolder, false, genomeSequenceFilePath, "GRCh37", null, serializer)).parse(); List parsedVariantList = loadSerializedVariants("/tmp/" + EtlCommons.CLINICAL_VARIANTS_JSON_FILE); assertEquals(23, parsedVariantList.size()); @@ -146,7 +146,7 @@ public void parseMNVTest() throws Exception { Path genomeSequenceFilePath = clinicalVariantFolder.resolve("Homo_sapiens.GRCh37.75.dna.primary_assembly.chr17.fa.gz"); CellBaseSerializer serializer = new CellBaseJsonFileSerializer(Paths.get("/tmp/"), EtlCommons.CLINICAL_VARIANTS_DATA, true); - (new ClinicalVariantBuilder(clinicalVariantFolder, true, genomeSequenceFilePath, "GRCh37", serializer)).parse(); + (new ClinicalVariantBuilder(clinicalVariantFolder, true, genomeSequenceFilePath, "GRCh37", null, serializer)).parse(); List parsedVariantList = loadSerializedVariants("/tmp/" + EtlCommons.CLINICAL_VARIANTS_JSON_FILE); assertEquals(29, parsedVariantList.size()); @@ -231,7 +231,7 @@ public void parse() throws Exception { clinicalVariantChunksFolder.resolve("ClinVarFullRelease_2020-02.xml.gz").toFile()); CellBaseSerializer serializer = new CellBaseJsonFileSerializer(Paths.get("/tmp/"), EtlCommons.CLINICAL_VARIANTS_DATA, true); - (new ClinicalVariantBuilder(clinicalVariantFolder, true, genomeSequenceFilePath, "GRCh37", serializer)).parse(); + (new ClinicalVariantBuilder(clinicalVariantFolder, true, genomeSequenceFilePath, "GRCh37", null, serializer)).parse(); List parsedVariantList = loadSerializedVariants("/tmp/" + EtlCommons.CLINICAL_VARIANTS_JSON_FILE); assertEquals(29, parsedVariantList.size());