public class ConsequenceTypeInsertionCalculator extends ConsequenceTypeCalculator
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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ConsequenceTypeInsertionCalculator(GenomeDBAdaptor genomeDBAdaptor) |
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) |
protected void |
solveCodingNegativeTranscript() |
protected void |
solveCodingPositiveTranscript() |
protected void |
solveNonCodingNegativeTranscript() |
protected void |
solveNonCodingPositiveTranscript() |
addNonCodingSOs, decideStopCodonModificationAnnotation, getEnd, getReverseComplementaryCodon, getSequenceOntologyTerms, getStart, parseQueryParam, regionsOverlap, setCdsAndProteinPosition, setInsertionAlleleAminoacidChange, solveIntergenic, solveMiRNA, solveNegativeTranscript, solvePositiveTranscript, solveRegulatoryRegions, updateNegativeInsertionCodonArrays, updatePositiveInsertionCodonArrays
public ConsequenceTypeInsertionCalculator(GenomeDBAdaptor genomeDBAdaptor)
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 ConsequenceTypeCalculator
protected void solveNonCodingNegativeTranscript()
solveNonCodingNegativeTranscript
in class ConsequenceTypeCalculator
protected void solveCodingNegativeTranscript()
solveCodingNegativeTranscript
in class ConsequenceTypeCalculator
protected void solveNonCodingPositiveTranscript()
solveNonCodingPositiveTranscript
in class ConsequenceTypeCalculator
protected void solveCodingPositiveTranscript()
solveCodingPositiveTranscript
in class ConsequenceTypeCalculator
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