public class ConsequenceTypeDeletionCalculator 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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ConsequenceTypeDeletionCalculator(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 |
solveCodingExonVariantInNegativeTranscript(boolean splicing,
String transcriptSequence,
int cdnaCodingStart,
int cdnaVariantStart,
int cdnaVariantEnd) |
protected void |
solveCodingExonVariantInPositiveTranscript(boolean splicing,
String transcriptSequence,
int cdnaCodingStart,
int cdnaVariantStart,
int cdnaVariantEnd) |
protected void |
solveExonVariantInNegativeTranscript(boolean splicing,
String transcriptSequence,
int cdnaVariantStart,
int cdnaVariantEnd,
int firstCdsPhase) |
protected void |
solveExonVariantInPositiveTranscript(boolean splicing,
String transcriptSequence,
int cdnaVariantStart,
int cdnaVariantEnd,
int firstCdsPhase) |
protected void |
solveStopCodonNegativeVariant(String transcriptSequence,
int cdnaCodingStart,
int cdnaVariantStart,
int cdnaVariantEnd) |
protected void |
solveStopCodonPositiveVariant(String transcriptSequence,
int cdnaCodingStart,
int cdnaVariantStart,
int cdnaVariantEnd) |
solveCodingNegativeTranscript, solveCodingPositiveTranscript, solveJunction, solveNonCodingNegativeTranscript, solveNonCodingPositiveTranscript, solveTranscriptFlankingRegions
addNonCodingSOs, decideStopCodonModificationAnnotation, getEnd, getReverseComplementaryCodon, getSequenceOntologyTerms, getStart, parseQueryParam, regionsOverlap, setCdsAndProteinPosition, setInsertionAlleleAminoacidChange, solveIntergenic, solveMiRNA, solveNegativeTranscript, solvePositiveTranscript, solveRegulatoryRegions, updateNegativeInsertionCodonArrays, updatePositiveInsertionCodonArrays
public ConsequenceTypeDeletionCalculator(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 ConsequenceTypeGenericRegionCalculator
protected void solveExonVariantInNegativeTranscript(boolean splicing, String transcriptSequence, int cdnaVariantStart, int cdnaVariantEnd, int firstCdsPhase)
solveExonVariantInNegativeTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveExonVariantInPositiveTranscript(boolean splicing, String transcriptSequence, int cdnaVariantStart, int cdnaVariantEnd, int firstCdsPhase)
solveExonVariantInPositiveTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveCodingExonVariantInNegativeTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveCodingExonVariantInNegativeTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveStopCodonNegativeVariant(String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveStopCodonNegativeVariant
in class ConsequenceTypeGenericRegionCalculator
protected void solveCodingExonVariantInPositiveTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveCodingExonVariantInPositiveTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveStopCodonPositiveVariant(String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveStopCodonPositiveVariant
in class ConsequenceTypeGenericRegionCalculator
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