public class CosmicIndexer extends ClinicalIndexer
genomeSequenceFilePath, HAPLOTYPE_FIELD_NAME, HAPLOTYPE_STRING_SEPARATOR, jsonObjectWriter, logger, mapper, normalize, normalizer, numberIndexedRecords, numberNewVariants, numberVariantUpdates, rdb, totalNumberRecords
Constructor and Description |
---|
CosmicIndexer(Path cosmicFile,
boolean normalize,
Path genomeSequenceFilePath,
String assembly,
org.rocksdb.RocksDB rdb) |
Modifier and Type | Method and Description |
---|---|
void |
index() |
boolean |
parsePosition(org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer.SequenceLocation sequenceLocation,
String line) |
boolean |
sameSomaticDocument(org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry1,
org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry2) |
addHaplotypeProperty, createGeneGenomicFeature, getAlleleOriginList, getNormalisedVariantString, getVariantAnnotation, getVariantClassification
public CosmicIndexer(Path cosmicFile, boolean normalize, Path genomeSequenceFilePath, String assembly, org.rocksdb.RocksDB rdb) throws IOException
IOException
public void index() throws org.rocksdb.RocksDBException
org.rocksdb.RocksDBException
public boolean sameSomaticDocument(org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry1, org.opencb.biodata.models.variant.avro.EvidenceEntry evidenceEntry2)
public boolean parsePosition(org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer.SequenceLocation sequenceLocation, String line)
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