public class IARCTP53Indexer extends ClinicalIndexer
HAPLOTYPE_FIELD_NAME, HAPLOTYPE_STRING_SEPARATOR, jsonObjectWriter, logger, mapper, normalize, normalizer, numberIndexedRecords, numberNewVariants, numberVariantUpdates, rdb, totalNumberRecords
Constructor and Description |
---|
IARCTP53Indexer(Path germlineFile,
Path germlineReferencesFile,
Path somaticFile,
Path somaticReferencesFile,
boolean normalize,
Path genomeSequenceFilePath,
String assembly,
org.rocksdb.RocksDB rdb) |
Modifier and Type | Method and Description |
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void |
index() |
org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer.SequenceLocation |
parsePosition(String[] fields,
boolean isGermline) |
addHaplotypeProperty, createGeneGenomicFeature, getAlleleOriginList, getNormalisedVariantString, getVariantAnnotation, getVariantClassification
public IARCTP53Indexer(Path germlineFile, Path germlineReferencesFile, Path somaticFile, Path somaticReferencesFile, boolean normalize, Path genomeSequenceFilePath, String assembly, org.rocksdb.RocksDB rdb) throws IOException
IOException
public void index() throws org.rocksdb.RocksDBException
org.rocksdb.RocksDBException
public org.opencb.cellbase.lib.builders.clinical.variant.ClinicalIndexer.SequenceLocation parsePosition(String[] fields, boolean isGermline)
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