public class ConsequenceTypeMNVCalculator 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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ConsequenceTypeMNVCalculator(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 |
solveJunction(Integer spliceSite1,
Integer spliceSite2,
String leftSpliceSiteTag,
String rightSpliceSiteTag,
boolean[] junctionSolution) |
solveCodingNegativeTranscript, solveCodingPositiveTranscript, solveExonVariantInNegativeTranscript, solveExonVariantInPositiveTranscript, solveNonCodingNegativeTranscript, solveNonCodingPositiveTranscript, solveStopCodonNegativeVariant, solveStopCodonPositiveVariant, solveTranscriptFlankingRegions
addNonCodingSOs, decideStopCodonModificationAnnotation, getEnd, getReverseComplementaryCodon, getSequenceOntologyTerms, getStart, parseQueryParam, regionsOverlap, setCdsAndProteinPosition, setInsertionAlleleAminoacidChange, solveIntergenic, solveMiRNA, solveNegativeTranscript, solvePositiveTranscript, solveRegulatoryRegions, updateNegativeInsertionCodonArrays, updatePositiveInsertionCodonArrays
public ConsequenceTypeMNVCalculator(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 solveCodingExonVariantInNegativeTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveCodingExonVariantInNegativeTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveCodingExonVariantInPositiveTranscript(boolean splicing, String transcriptSequence, int cdnaCodingStart, int cdnaVariantStart, int cdnaVariantEnd)
solveCodingExonVariantInPositiveTranscript
in class ConsequenceTypeGenericRegionCalculator
protected void solveJunction(Integer spliceSite1, Integer spliceSite2, String leftSpliceSiteTag, String rightSpliceSiteTag, boolean[] junctionSolution)
solveJunction
in class ConsequenceTypeGenericRegionCalculator
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