/** * Convert a bunch of lines from VEP int a single Variant Annotation * @param lines All line must refer to the same variant * @return */ public static VariantAnnotation parse(List<String> lines) { VariantAnnotation variantAnnotation = new VariantAnnotation(); return null; }
/** Sets the value of the 'accession' field */ public org.opencb.biodata.models.variant.avro.ClinVar.Builder setAccession(java.lang.String value) { validate(fields()[0], value); this.accession = value; fieldSetFlags()[0] = true; return this; }
/** Sets the value of the 'stain' field */ public org.opencb.biodata.models.variant.avro.Cytoband.Builder setStain(java.lang.String value) { validate(fields()[1], value); this.stain = value; fieldSetFlags()[1] = true; return this; }
/** Sets the value of the 'start' field */ public org.opencb.biodata.models.variant.avro.AlternateCoordinate.Builder setStart(java.lang.Integer value) { validate(fields()[1], value); this.start = value; fieldSetFlags()[1] = true; return this; }
/** Sets the value of the 'orientation' field */ public org.opencb.biodata.models.variant.avro.Breakend.Builder setOrientation(org.opencb.biodata.models.variant.avro.BreakendOrientation value) { validate(fields()[1], value); this.orientation = value; fieldSetFlags()[1] = true; return this; }
/** Sets the value of the 'siteSubtype' field */ public org.opencb.biodata.models.variant.avro.Cosmic.Builder setSiteSubtype(java.lang.String value) { validate(fields()[2], value); this.siteSubtype = value; fieldSetFlags()[2] = true; return this; }
/** Clears the value of the 'geneName' field */ public org.opencb.biodata.models.variant.avro.ConsequenceType.Builder clearGeneName() { geneName = null; fieldSetFlags()[0] = false; return this; }
/** Clears the value of the 'siteSubtype' field */ public org.opencb.biodata.models.variant.avro.Cosmic.Builder clearSiteSubtype() { siteSubtype = null; fieldSetFlags()[2] = false; return this; }
/** Clears the value of the 'effect' field */ public org.opencb.biodata.models.variant.avro.Drug.Builder clearEffect() { effect = null; fieldSetFlags()[2] = false; return this; }
/** Clears the value of the 'position' field */ public org.opencb.biodata.models.variant.avro.BreakendMate.Builder clearPosition() { position = null; fieldSetFlags()[1] = false; return this; }
/** Sets the value of the 'clinicalSignificance' field */ public org.opencb.biodata.models.variant.avro.ClinVar.Builder setClinicalSignificance(java.lang.String value) { validate(fields()[1], value); this.clinicalSignificance = value; fieldSetFlags()[1] = true; return this; }
/** Sets the value of the 'end' field */ public org.opencb.biodata.models.variant.avro.Cytoband.Builder setEnd(java.lang.Integer value) { validate(fields()[4], value); this.end = value; fieldSetFlags()[4] = true; return this; }
/** Sets the value of the 'type' field */ public org.opencb.biodata.models.variant.avro.AlternateCoordinate.Builder setType(org.opencb.biodata.models.variant.avro.VariantType value) { validate(fields()[5], value); this.type = value; fieldSetFlags()[5] = true; return this; }
/** Clears the value of the 'biotype' field */ public org.opencb.biodata.models.variant.avro.ConsequenceType.Builder clearBiotype() { biotype = null; fieldSetFlags()[4] = false; return this; }
/** Clears the value of the 'tumourOrigin' field */ public org.opencb.biodata.models.variant.avro.Cosmic.Builder clearTumourOrigin() { tumourOrigin = null; fieldSetFlags()[6] = false; return this; }
/** Sets the value of the 'geneNames' field */ public org.opencb.biodata.models.variant.avro.ClinVar.Builder setGeneNames(java.util.List<java.lang.String> value) { validate(fields()[3], value); this.geneNames = value; fieldSetFlags()[3] = true; return this; }
/** Clears the value of the 'exonOverlap' field */ public org.opencb.biodata.models.variant.avro.ConsequenceType.Builder clearExonOverlap() { exonOverlap = null; fieldSetFlags()[5] = false; return this; }
/** Sets the value of the 'reviewStatus' field */ public org.opencb.biodata.models.variant.avro.ClinVar.Builder setReviewStatus(java.lang.String value) { validate(fields()[4], value); this.reviewStatus = value; fieldSetFlags()[4] = true; return this; }
/** Clears the value of the 'cdnaPosition' field */ public org.opencb.biodata.models.variant.avro.ConsequenceType.Builder clearCdnaPosition() { cdnaPosition = null; fieldSetFlags()[7] = false; return this; }
/** Clears the value of the 'cdsPosition' field */ public org.opencb.biodata.models.variant.avro.ConsequenceType.Builder clearCdsPosition() { cdsPosition = null; fieldSetFlags()[8] = false; return this; }