Package org.bdgenomics.formats.avro

Class VariantAnnotation.Builder

  • All Implemented Interfaces:
    org.apache.avro.data.RecordBuilder<VariantAnnotation>
    Enclosing class:
    VariantAnnotation
    public static class VariantAnnotation.Builder
extends org.apache.avro.specific.SpecificRecordBuilderBase<VariantAnnotation>
implements org.apache.avro.data.RecordBuilder<VariantAnnotation>
    RecordBuilder for VariantAnnotation instances.

    • Method Detail

      • getAncestralAllele

        public String getAncestralAllele()
        Gets the value of the 'ancestralAllele' field. Ancestral allele, VCF INFO reserved key AA, Number=1, shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setAncestralAllele

        public VariantAnnotation.Builder setAncestralAllele​(String value)
        Sets the value of the 'ancestralAllele' field. Ancestral allele, VCF INFO reserved key AA, Number=1, shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'ancestralAllele'.
        Returns:
        This builder.

      • hasAncestralAllele

        public boolean hasAncestralAllele()
        Checks whether the 'ancestralAllele' field has been set. Ancestral allele, VCF INFO reserved key AA, Number=1, shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'ancestralAllele' field has been set, false otherwise.

      • clearAncestralAllele

        public VariantAnnotation.Builder clearAncestralAllele()
        Clears the value of the 'ancestralAllele' field. Ancestral allele, VCF INFO reserved key AA, Number=1, shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getAlleleCount

        public Integer getAlleleCount()
        Gets the value of the 'alleleCount' field. Allele count, VCF INFO reserved key AC, Number=A, split for multi-allelic sites into a single integer value.
        Returns:
        The value.

      • setAlleleCount

        public VariantAnnotation.Builder setAlleleCount​(Integer value)
        Sets the value of the 'alleleCount' field. Allele count, VCF INFO reserved key AC, Number=A, split for multi-allelic sites into a single integer value.
        Parameters:
        value - The value of 'alleleCount'.
        Returns:
        This builder.

      • hasAlleleCount

        public boolean hasAlleleCount()
        Checks whether the 'alleleCount' field has been set. Allele count, VCF INFO reserved key AC, Number=A, split for multi-allelic sites into a single integer value.
        Returns:
        True if the 'alleleCount' field has been set, false otherwise.

      • clearAlleleCount

        public VariantAnnotation.Builder clearAlleleCount()
        Clears the value of the 'alleleCount' field. Allele count, VCF INFO reserved key AC, Number=A, split for multi-allelic sites into a single integer value.
        Returns:
        This builder.

      • getReadDepth

        public Integer getReadDepth()
        Gets the value of the 'readDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth) and the alternate allele (readDepth, this field).
        Returns:
        The value.

      • setReadDepth

        public VariantAnnotation.Builder setReadDepth​(Integer value)
        Sets the value of the 'readDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth) and the alternate allele (readDepth, this field).
        Parameters:
        value - The value of 'readDepth'.
        Returns:
        This builder.

      • hasReadDepth

        public boolean hasReadDepth()
        Checks whether the 'readDepth' field has been set. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth) and the alternate allele (readDepth, this field).
        Returns:
        True if the 'readDepth' field has been set, false otherwise.

      • clearReadDepth

        public VariantAnnotation.Builder clearReadDepth()
        Clears the value of the 'readDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth) and the alternate allele (readDepth, this field).
        Returns:
        This builder.

      • getForwardReadDepth

        public Integer getForwardReadDepth()
        Gets the value of the 'forwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth) and the alternate allele (forwardReadDepth, this field).
        Returns:
        The value.

      • setForwardReadDepth

        public VariantAnnotation.Builder setForwardReadDepth​(Integer value)
        Sets the value of the 'forwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth) and the alternate allele (forwardReadDepth, this field).
        Parameters:
        value - The value of 'forwardReadDepth'.
        Returns:
        This builder.

      • hasForwardReadDepth

        public boolean hasForwardReadDepth()
        Checks whether the 'forwardReadDepth' field has been set. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth) and the alternate allele (forwardReadDepth, this field).
        Returns:
        True if the 'forwardReadDepth' field has been set, false otherwise.

      • clearForwardReadDepth

        public VariantAnnotation.Builder clearForwardReadDepth()
        Clears the value of the 'forwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth) and the alternate allele (forwardReadDepth, this field).
        Returns:
        This builder.

      • getReverseReadDepth

        public Integer getReverseReadDepth()
        Gets the value of the 'reverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth) and the alternate allele (reverseReadDepth, this field).
        Returns:
        The value.

      • setReverseReadDepth

        public VariantAnnotation.Builder setReverseReadDepth​(Integer value)
        Sets the value of the 'reverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth) and the alternate allele (reverseReadDepth, this field).
        Parameters:
        value - The value of 'reverseReadDepth'.
        Returns:
        This builder.

      • hasReverseReadDepth

        public boolean hasReverseReadDepth()
        Checks whether the 'reverseReadDepth' field has been set. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth) and the alternate allele (reverseReadDepth, this field).
        Returns:
        True if the 'reverseReadDepth' field has been set, false otherwise.

      • clearReverseReadDepth

        public VariantAnnotation.Builder clearReverseReadDepth()
        Clears the value of the 'reverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth) and the alternate allele (reverseReadDepth, this field).
        Returns:
        This builder.

      • getReferenceReadDepth

        public Integer getReferenceReadDepth()
        Gets the value of the 'referenceReadDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth, this field) and the alternate allele (readDepth).
        Returns:
        The value.

      • setReferenceReadDepth

        public VariantAnnotation.Builder setReferenceReadDepth​(Integer value)
        Sets the value of the 'referenceReadDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth, this field) and the alternate allele (readDepth).
        Parameters:
        value - The value of 'referenceReadDepth'.
        Returns:
        This builder.

      • hasReferenceReadDepth

        public boolean hasReferenceReadDepth()
        Checks whether the 'referenceReadDepth' field has been set. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth, this field) and the alternate allele (readDepth).
        Returns:
        True if the 'referenceReadDepth' field has been set, false otherwise.

      • clearReferenceReadDepth

        public VariantAnnotation.Builder clearReferenceReadDepth()
        Clears the value of the 'referenceReadDepth' field. Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReadDepth, this field) and the alternate allele (readDepth).
        Returns:
        This builder.

      • getReferenceForwardReadDepth

        public Integer getReferenceForwardReadDepth()
        Gets the value of the 'referenceForwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth, this field) and the alternate allele (forwardReadDepth).
        Returns:
        The value.

      • setReferenceForwardReadDepth

        public VariantAnnotation.Builder setReferenceForwardReadDepth​(Integer value)
        Sets the value of the 'referenceForwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth, this field) and the alternate allele (forwardReadDepth).
        Parameters:
        value - The value of 'referenceForwardReadDepth'.
        Returns:
        This builder.

      • hasReferenceForwardReadDepth

        public boolean hasReferenceForwardReadDepth()
        Checks whether the 'referenceForwardReadDepth' field has been set. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth, this field) and the alternate allele (forwardReadDepth).
        Returns:
        True if the 'referenceForwardReadDepth' field has been set, false otherwise.

      • clearReferenceForwardReadDepth

        public VariantAnnotation.Builder clearReferenceForwardReadDepth()
        Clears the value of the 'referenceForwardReadDepth' field. Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceForwardReadDepth, this field) and the alternate allele (forwardReadDepth).
        Returns:
        This builder.

      • getReferenceReverseReadDepth

        public Integer getReferenceReverseReadDepth()
        Gets the value of the 'referenceReverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth, this field) and the alternate allele (reverseReadDepth).
        Returns:
        The value.

      • setReferenceReverseReadDepth

        public VariantAnnotation.Builder setReferenceReverseReadDepth​(Integer value)
        Sets the value of the 'referenceReverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth, this field) and the alternate allele (reverseReadDepth).
        Parameters:
        value - The value of 'referenceReverseReadDepth'.
        Returns:
        This builder.

      • hasReferenceReverseReadDepth

        public boolean hasReferenceReverseReadDepth()
        Checks whether the 'referenceReverseReadDepth' field has been set. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth, this field) and the alternate allele (reverseReadDepth).
        Returns:
        True if the 'referenceReverseReadDepth' field has been set, false otherwise.

      • clearReferenceReverseReadDepth

        public VariantAnnotation.Builder clearReferenceReverseReadDepth()
        Clears the value of the 'referenceReverseReadDepth' field. Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for multi-allelic sites into single integer values for the reference allele (referenceReverseReadDepth, this field) and the alternate allele (reverseReadDepth).
        Returns:
        This builder.

      • getAlleleFrequency

        public Float getAlleleFrequency()
        Gets the value of the 'alleleFrequency' field. Minor allele frequency, VCF INFO reserved key AF, Number=A, split for multi-allelic sites into a single float value. Use this when frequencies are estimated from primary data, not calculated from called genotypes.
        Returns:
        The value.

      • setAlleleFrequency

        public VariantAnnotation.Builder setAlleleFrequency​(Float value)
        Sets the value of the 'alleleFrequency' field. Minor allele frequency, VCF INFO reserved key AF, Number=A, split for multi-allelic sites into a single float value. Use this when frequencies are estimated from primary data, not calculated from called genotypes.
        Parameters:
        value - The value of 'alleleFrequency'.
        Returns:
        This builder.

      • hasAlleleFrequency

        public boolean hasAlleleFrequency()
        Checks whether the 'alleleFrequency' field has been set. Minor allele frequency, VCF INFO reserved key AF, Number=A, split for multi-allelic sites into a single float value. Use this when frequencies are estimated from primary data, not calculated from called genotypes.
        Returns:
        True if the 'alleleFrequency' field has been set, false otherwise.

      • clearAlleleFrequency

        public VariantAnnotation.Builder clearAlleleFrequency()
        Clears the value of the 'alleleFrequency' field. Minor allele frequency, VCF INFO reserved key AF, Number=A, split for multi-allelic sites into a single float value. Use this when frequencies are estimated from primary data, not calculated from called genotypes.
        Returns:
        This builder.

      • getCigar

        public String getCigar()
        Gets the value of the 'cigar' field. CIGAR string describing how to align an alternate allele to the reference allele, VCF INFO reserved key CIGAR, Number=A, split for multi-allelic sites into a single string value.
        Returns:
        The value.

      • setCigar

        public VariantAnnotation.Builder setCigar​(String value)
        Sets the value of the 'cigar' field. CIGAR string describing how to align an alternate allele to the reference allele, VCF INFO reserved key CIGAR, Number=A, split for multi-allelic sites into a single string value.
        Parameters:
        value - The value of 'cigar'.
        Returns:
        This builder.

      • hasCigar

        public boolean hasCigar()
        Checks whether the 'cigar' field has been set. CIGAR string describing how to align an alternate allele to the reference allele, VCF INFO reserved key CIGAR, Number=A, split for multi-allelic sites into a single string value.
        Returns:
        True if the 'cigar' field has been set, false otherwise.

      • clearCigar

        public VariantAnnotation.Builder clearCigar()
        Clears the value of the 'cigar' field. CIGAR string describing how to align an alternate allele to the reference allele, VCF INFO reserved key CIGAR, Number=A, split for multi-allelic sites into a single string value.
        Returns:
        This builder.

      • getDbSnp

        public Boolean getDbSnp()
        Gets the value of the 'dbSnp' field. Membership in dbSNP, VCF INFO reserved key DB, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setDbSnp

        public VariantAnnotation.Builder setDbSnp​(Boolean value)
        Sets the value of the 'dbSnp' field. Membership in dbSNP, VCF INFO reserved key DB, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'dbSnp'.
        Returns:
        This builder.

      • hasDbSnp

        public boolean hasDbSnp()
        Checks whether the 'dbSnp' field has been set. Membership in dbSNP, VCF INFO reserved key DB, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'dbSnp' field has been set, false otherwise.

      • clearDbSnp

        public VariantAnnotation.Builder clearDbSnp()
        Clears the value of the 'dbSnp' field. Membership in dbSNP, VCF INFO reserved key DB, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getHapMap2

        public Boolean getHapMap2()
        Gets the value of the 'hapMap2' field. Membership in HapMap2, VCF INFO reserved key H2, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setHapMap2

        public VariantAnnotation.Builder setHapMap2​(Boolean value)
        Sets the value of the 'hapMap2' field. Membership in HapMap2, VCF INFO reserved key H2, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'hapMap2'.
        Returns:
        This builder.

      • hasHapMap2

        public boolean hasHapMap2()
        Checks whether the 'hapMap2' field has been set. Membership in HapMap2, VCF INFO reserved key H2, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'hapMap2' field has been set, false otherwise.

      • clearHapMap2

        public VariantAnnotation.Builder clearHapMap2()
        Clears the value of the 'hapMap2' field. Membership in HapMap2, VCF INFO reserved key H2, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getHapMap3

        public Boolean getHapMap3()
        Gets the value of the 'hapMap3' field. Membership in HapMap3, VCF INFO reserved key H3, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setHapMap3

        public VariantAnnotation.Builder setHapMap3​(Boolean value)
        Sets the value of the 'hapMap3' field. Membership in HapMap3, VCF INFO reserved key H3, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'hapMap3'.
        Returns:
        This builder.

      • hasHapMap3

        public boolean hasHapMap3()
        Checks whether the 'hapMap3' field has been set. Membership in HapMap3, VCF INFO reserved key H3, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'hapMap3' field has been set, false otherwise.

      • clearHapMap3

        public VariantAnnotation.Builder clearHapMap3()
        Clears the value of the 'hapMap3' field. Membership in HapMap3, VCF INFO reserved key H3, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getValidated

        public Boolean getValidated()
        Gets the value of the 'validated' field. Validated by follow up experiment, VCF INFO reserved key VALIDATED, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setValidated

        public VariantAnnotation.Builder setValidated​(Boolean value)
        Sets the value of the 'validated' field. Validated by follow up experiment, VCF INFO reserved key VALIDATED, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'validated'.
        Returns:
        This builder.

      • hasValidated

        public boolean hasValidated()
        Checks whether the 'validated' field has been set. Validated by follow up experiment, VCF INFO reserved key VALIDATED, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'validated' field has been set, false otherwise.

      • clearValidated

        public VariantAnnotation.Builder clearValidated()
        Clears the value of the 'validated' field. Validated by follow up experiment, VCF INFO reserved key VALIDATED, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getThousandGenomes

        public Boolean getThousandGenomes()
        Gets the value of the 'thousandGenomes' field. Membership in 1000 Genomes, VCF INFO reserved key 1000G, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        The value.

      • setThousandGenomes

        public VariantAnnotation.Builder setThousandGenomes​(Boolean value)
        Sets the value of the 'thousandGenomes' field. Membership in 1000 Genomes, VCF INFO reserved key 1000G, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Parameters:
        value - The value of 'thousandGenomes'.
        Returns:
        This builder.

      • hasThousandGenomes

        public boolean hasThousandGenomes()
        Checks whether the 'thousandGenomes' field has been set. Membership in 1000 Genomes, VCF INFO reserved key 1000G, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        True if the 'thousandGenomes' field has been set, false otherwise.

      • clearThousandGenomes

        public VariantAnnotation.Builder clearThousandGenomes()
        Clears the value of the 'thousandGenomes' field. Membership in 1000 Genomes, VCF INFO reserved key 1000G, Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alternate alleles in the same VCF record.
        Returns:
        This builder.

      • getSomatic

        public Boolean getSomatic()
        Gets the value of the 'somatic' field. True if this variant call is somatic; in this case, the reference allele will have been observed in another sample. VCF INFO reserved key "SOMATIC", Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alleles in the same VCF record.
        Returns:
        The value.

      • setSomatic

        public VariantAnnotation.Builder setSomatic​(Boolean value)
        Sets the value of the 'somatic' field. True if this variant call is somatic; in this case, the reference allele will have been observed in another sample. VCF INFO reserved key "SOMATIC", Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alleles in the same VCF record.
        Parameters:
        value - The value of 'somatic'.
        Returns:
        This builder.

      • hasSomatic

        public boolean hasSomatic()
        Checks whether the 'somatic' field has been set. True if this variant call is somatic; in this case, the reference allele will have been observed in another sample. VCF INFO reserved key "SOMATIC", Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alleles in the same VCF record.
        Returns:
        True if the 'somatic' field has been set, false otherwise.

      • clearSomatic

        public VariantAnnotation.Builder clearSomatic()
        Clears the value of the 'somatic' field. True if this variant call is somatic; in this case, the reference allele will have been observed in another sample. VCF INFO reserved key "SOMATIC", Number=0. Until Number=A and Number=R flags are supported by the VCF specification, this value is shared across all alleles in the same VCF record.
        Returns:
        This builder.

      • getTranscriptEffects

        public List<TranscriptEffect> getTranscriptEffects()
        Gets the value of the 'transcriptEffects' field. Zero or more transcript effects, predicted by a tool such as SnpEff or Ensembl VEP, one per transcript (or other feature). VCF INFO key ANN, split for multi-allelic sites. See http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf.
        Returns:
        The value.

      • setTranscriptEffects

        public VariantAnnotation.Builder setTranscriptEffects​(List<TranscriptEffect> value)
        Sets the value of the 'transcriptEffects' field. Zero or more transcript effects, predicted by a tool such as SnpEff or Ensembl VEP, one per transcript (or other feature). VCF INFO key ANN, split for multi-allelic sites. See http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf.
        Parameters:
        value - The value of 'transcriptEffects'.
        Returns:
        This builder.

      • hasTranscriptEffects

        public boolean hasTranscriptEffects()
        Checks whether the 'transcriptEffects' field has been set. Zero or more transcript effects, predicted by a tool such as SnpEff or Ensembl VEP, one per transcript (or other feature). VCF INFO key ANN, split for multi-allelic sites. See http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf.
        Returns:
        True if the 'transcriptEffects' field has been set, false otherwise.

      • clearTranscriptEffects

        public VariantAnnotation.Builder clearTranscriptEffects()
        Clears the value of the 'transcriptEffects' field. Zero or more transcript effects, predicted by a tool such as SnpEff or Ensembl VEP, one per transcript (or other feature). VCF INFO key ANN, split for multi-allelic sites. See http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf.
        Returns:
        This builder.

      • getAttributes

        public Map<String,​String> getAttributes()
        Gets the value of the 'attributes' field. Additional variant attributes that do not fit into the standard fields above. The values are stored as strings, even for flag, integer, and float types. VCF INFO key values with Number=., Number=0, Number=1, and Number=[n] are shared across all alternate alleles in the same VCF record. VCF INFO key values with Number=A are split for multi-allelic sites into a single value. VCF INFO key values with Number=R are split into an array of two values, [reference allele, alternate allele], separated by commas, e.g. "0,1".
        Returns:
        The value.

      • setAttributes

        public VariantAnnotation.Builder setAttributes​(Map<String,​String> value)
        Sets the value of the 'attributes' field. Additional variant attributes that do not fit into the standard fields above. The values are stored as strings, even for flag, integer, and float types. VCF INFO key values with Number=., Number=0, Number=1, and Number=[n] are shared across all alternate alleles in the same VCF record. VCF INFO key values with Number=A are split for multi-allelic sites into a single value. VCF INFO key values with Number=R are split into an array of two values, [reference allele, alternate allele], separated by commas, e.g. "0,1".
        Parameters:
        value - The value of 'attributes'.
        Returns:
        This builder.

      • hasAttributes

        public boolean hasAttributes()
        Checks whether the 'attributes' field has been set. Additional variant attributes that do not fit into the standard fields above. The values are stored as strings, even for flag, integer, and float types. VCF INFO key values with Number=., Number=0, Number=1, and Number=[n] are shared across all alternate alleles in the same VCF record. VCF INFO key values with Number=A are split for multi-allelic sites into a single value. VCF INFO key values with Number=R are split into an array of two values, [reference allele, alternate allele], separated by commas, e.g. "0,1".
        Returns:
        True if the 'attributes' field has been set, false otherwise.

      • clearAttributes

        public VariantAnnotation.Builder clearAttributes()
        Clears the value of the 'attributes' field. Additional variant attributes that do not fit into the standard fields above. The values are stored as strings, even for flag, integer, and float types. VCF INFO key values with Number=., Number=0, Number=1, and Number=[n] are shared across all alternate alleles in the same VCF record. VCF INFO key values with Number=A are split for multi-allelic sites into a single value. VCF INFO key values with Number=R are split into an array of two values, [reference allele, alternate allele], separated by commas, e.g. "0,1".
        Returns:
        This builder.