public abstract class ClinicalIndexer extends Object
Modifier and Type | Field and Description |
---|---|
protected Path |
genomeSequenceFilePath |
protected static String |
HAPLOTYPE_FIELD_NAME |
protected static char |
HAPLOTYPE_STRING_SEPARATOR |
protected static com.fasterxml.jackson.databind.ObjectWriter |
jsonObjectWriter |
protected static org.slf4j.Logger |
logger |
protected static com.fasterxml.jackson.databind.ObjectMapper |
mapper |
protected boolean |
normalize |
protected org.opencb.biodata.tools.variant.VariantNormalizer |
normalizer |
protected int |
numberIndexedRecords |
protected int |
numberNewVariants |
protected int |
numberVariantUpdates |
protected org.rocksdb.RocksDB |
rdb |
protected int |
totalNumberRecords |
Constructor and Description |
---|
ClinicalIndexer(Path genomeSequenceFilePath) |
Modifier and Type | Method and Description |
---|---|
protected void |
addHaplotypeProperty(List<org.opencb.biodata.models.variant.avro.EvidenceEntry> evidenceEntryList,
List<String> normalisedVariantStringList) |
protected org.opencb.biodata.models.variant.avro.GenomicFeature |
createGeneGenomicFeature(String gene) |
protected List<org.opencb.biodata.models.variant.avro.AlleleOrigin> |
getAlleleOriginList(List<String> sourceOriginList) |
protected List<String> |
getNormalisedVariantString(String chromosome,
int start,
String reference,
String alternate) |
protected org.opencb.biodata.models.variant.avro.VariantAnnotation |
getVariantAnnotation(byte[] key) |
protected org.opencb.biodata.models.variant.avro.VariantClassification |
getVariantClassification(List<String> classificationStringList) |
protected static final char HAPLOTYPE_STRING_SEPARATOR
protected static final String HAPLOTYPE_FIELD_NAME
protected static org.slf4j.Logger logger
protected int numberNewVariants
protected int numberVariantUpdates
protected int totalNumberRecords
protected int numberIndexedRecords
protected org.rocksdb.RocksDB rdb
protected static com.fasterxml.jackson.databind.ObjectMapper mapper
protected static com.fasterxml.jackson.databind.ObjectWriter jsonObjectWriter
protected Path genomeSequenceFilePath
protected boolean normalize
protected org.opencb.biodata.tools.variant.VariantNormalizer normalizer
public ClinicalIndexer(Path genomeSequenceFilePath) throws IOException
IOException
protected org.opencb.biodata.models.variant.avro.VariantAnnotation getVariantAnnotation(byte[] key) throws org.rocksdb.RocksDBException, IOException
org.rocksdb.RocksDBException
IOException
protected org.opencb.biodata.models.variant.avro.GenomicFeature createGeneGenomicFeature(String gene)
protected List<org.opencb.biodata.models.variant.avro.AlleleOrigin> getAlleleOriginList(List<String> sourceOriginList)
protected org.opencb.biodata.models.variant.avro.VariantClassification getVariantClassification(List<String> classificationStringList)
protected List<String> getNormalisedVariantString(String chromosome, int start, String reference, String alternate)
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