public class ConsequenceTypeBNDCalculator extends ConsequenceTypeGenericRegionCalculator
BIG_VARIANT_SIZE_THRESHOLD, variantEnd, variantStart
CNV_EXTRA_PADDING, cnvExtraPadding, COMPLEMENTARY_START_CODON, consequenceType, DOWN_UP_STREAM_GENE_TAG, gene, genomeDBAdaptor, imprecise, IMPRECISE, logger, MT, NO_EXON_OVERLAP, SoNames, START_CODON, SV_EXTRA_PADDING, svExtraPadding, transcript, variant
Constructor and Description |
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ConsequenceTypeBNDCalculator() |
Modifier and Type | Method and Description |
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List<org.opencb.biodata.models.variant.avro.ConsequenceType> |
run(org.opencb.biodata.models.variant.Variant inputVariant,
List<org.opencb.biodata.models.core.Gene> geneList,
boolean[] overlapsRegulatoryRegion,
org.opencb.commons.datastore.core.QueryOptions queryOptions) |
solveCodingExonVariantInNegativeTranscript, solveCodingExonVariantInPositiveTranscript, solveCodingNegativeTranscript, solveCodingPositiveTranscript, solveExonVariantInNegativeTranscript, solveExonVariantInPositiveTranscript, solveJunction, solveNonCodingNegativeTranscript, solveNonCodingPositiveTranscript, solveStopCodonNegativeVariant, solveStopCodonPositiveVariant, solveTranscriptFlankingRegions
addNonCodingSOs, decideStopCodonModificationAnnotation, getEnd, getReverseComplementaryCodon, getSequenceOntologyTerms, getStart, parseQueryParam, regionsOverlap, setCdsAndProteinPosition, setInsertionAlleleAminoacidChange, solveIntergenic, solveMiRNA, solveNegativeTranscript, solvePositiveTranscript, solveRegulatoryRegions, updateNegativeInsertionCodonArrays, updatePositiveInsertionCodonArrays
public List<org.opencb.biodata.models.variant.avro.ConsequenceType> run(org.opencb.biodata.models.variant.Variant inputVariant, List<org.opencb.biodata.models.core.Gene> geneList, boolean[] overlapsRegulatoryRegion, org.opencb.commons.datastore.core.QueryOptions queryOptions)
run
in class ConsequenceTypeGenericRegionCalculator
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