description: This cross-version extension represents MolecularSequence.variant from http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1 for use in FHIR R5.
package_name: hl7.fhir.uv.xver-r4.r5
derivation: constraint
name: Ext_R4_MolecularSequence_variant
type: Extension
elements:
  extension:
    base: {max: '*', min: 0, path: Extension.extension}
    array: true
    index: 0
    slicing:
      rules: closed
      ordered: false
      discriminator:
      - {path: url, type: value}
      min: 0
      slices:
        start:
          match: {url: start}
          schema:
            short: Start position of the variant on the  reference sequence
            base: {max: '*', min: 0, path: Extension.extension}
            index: 1
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: start}
                index: 2
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: Start position of the variant on the  reference sequence
                choices: [valueInteger]
                index: 4
              valueInteger:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: integer
                short: Start position of the variant on the  reference sequence
                choiceOf: value
                index: 5
            required: [url]
        end:
          match: {url: end}
          schema:
            short: End position of the variant on the reference sequence
            base: {max: '*', min: 0, path: Extension.extension}
            index: 6
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: end}
                index: 7
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: End position of the variant on the reference sequence
                choices: [valueInteger]
                index: 9
              valueInteger:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: integer
                short: End position of the variant on the reference sequence
                choiceOf: value
                index: 10
            required: [url]
        observedAllele:
          match: {url: observedAllele}
          schema:
            short: Allele that was observed
            base: {max: '*', min: 0, path: Extension.extension}
            index: 11
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: observedAllele}
                index: 12
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: Allele that was observed
                choices: [valueString]
                index: 14
              valueString:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: string
                short: Allele that was observed
                choiceOf: value
                index: 15
            required: [url]
        referenceAllele:
          match: {url: referenceAllele}
          schema:
            short: Allele in the reference sequence
            base: {max: '*', min: 0, path: Extension.extension}
            index: 16
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: referenceAllele}
                index: 17
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: Allele in the reference sequence
                choices: [valueString]
                index: 19
              valueString:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: string
                short: Allele in the reference sequence
                choiceOf: value
                index: 20
            required: [url]
        cigar:
          match: {url: cigar}
          schema:
            short: Extended CIGAR string for aligning the sequence with reference bases
            base: {max: '*', min: 0, path: Extension.extension}
            index: 21
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: cigar}
                index: 22
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: Extended CIGAR string for aligning the sequence with reference bases
                choices: [valueString]
                index: 24
              valueString:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: string
                short: Extended CIGAR string for aligning the sequence with reference bases
                choiceOf: value
                index: 25
            required: [url]
        variantPointer:
          match: {url: variantPointer}
          schema:
            short: Pointer to observed variant information
            base: {max: '*', min: 0, path: Extension.extension}
            index: 26
            elements:
              url:
                base: {max: '1', min: 1, path: Extension.url}
                pattern: {type: Uri, value: variantPointer}
                index: 27
              value:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                short: Pointer to observed variant information
                choices: [valueReference]
                index: 29
              valueReference:
                base: {max: '1', min: 0, path: 'Extension.value[x]'}
                type: Reference
                short: Pointer to observed variant information
                choiceOf: value
                index: 30
            required: [url]
  url:
    base: {max: '1', min: 1, path: Extension.url}
    pattern: {type: Uri, value: 'http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.variant'}
    index: 31
package_version: 0.0.1-snapshot-2
extensions:
  start:
    url: start
    short: Start position of the variant on the  reference sequence
    base: {max: '*', min: 0, path: Extension.extension}
    index: 1
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: start}
        index: 2
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: Start position of the variant on the  reference sequence
        choices: [valueInteger]
        index: 4
      valueInteger:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: integer
        short: Start position of the variant on the  reference sequence
        choiceOf: value
        index: 5
    required: [url]
  end:
    url: end
    short: End position of the variant on the reference sequence
    base: {max: '*', min: 0, path: Extension.extension}
    index: 6
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: end}
        index: 7
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: End position of the variant on the reference sequence
        choices: [valueInteger]
        index: 9
      valueInteger:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: integer
        short: End position of the variant on the reference sequence
        choiceOf: value
        index: 10
    required: [url]
  observedAllele:
    url: observedAllele
    short: Allele that was observed
    base: {max: '*', min: 0, path: Extension.extension}
    index: 11
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: observedAllele}
        index: 12
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: Allele that was observed
        choices: [valueString]
        index: 14
      valueString:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: string
        short: Allele that was observed
        choiceOf: value
        index: 15
    required: [url]
  referenceAllele:
    url: referenceAllele
    short: Allele in the reference sequence
    base: {max: '*', min: 0, path: Extension.extension}
    index: 16
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: referenceAllele}
        index: 17
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: Allele in the reference sequence
        choices: [valueString]
        index: 19
      valueString:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: string
        short: Allele in the reference sequence
        choiceOf: value
        index: 20
    required: [url]
  cigar:
    url: cigar
    short: Extended CIGAR string for aligning the sequence with reference bases
    base: {max: '*', min: 0, path: Extension.extension}
    index: 21
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: cigar}
        index: 22
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: Extended CIGAR string for aligning the sequence with reference bases
        choices: [valueString]
        index: 24
      valueString:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: string
        short: Extended CIGAR string for aligning the sequence with reference bases
        choiceOf: value
        index: 25
    required: [url]
  variantPointer:
    url: variantPointer
    short: Pointer to observed variant information
    base: {max: '*', min: 0, path: Extension.extension}
    index: 26
    elements:
      url:
        base: {max: '1', min: 1, path: Extension.url}
        pattern: {type: Uri, value: variantPointer}
        index: 27
      value:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        short: Pointer to observed variant information
        choices: [valueReference]
        index: 29
      valueReference:
        base: {max: '1', min: 0, path: 'Extension.value[x]'}
        type: Reference
        short: Pointer to observed variant information
        choiceOf: value
        index: 30
    required: [url]
class: extension
kind: complex-type
url: http://hl7.org/fhir/4.0/StructureDefinition/extension-MolecularSequence.variant
base: http://hl7.org/fhir/StructureDefinition/Extension|5.0.0
version: 0.0.1-snapshot-2
required: [url]