phenopackets / phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.
http://phenopackets.org/phenopacket-tools/stable/
GNU General Public License v3.0
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Positions as String #67

Closed pnrobinson closed 2 years ago

pnrobinson commented 2 years ago

In the GenomicInterpretation, variant positions are emerging as strings. I am trying to trace down where this happens. At line 115 of Retinoblastoma, we are still ok

acmg_pathogenicity_classification: PATHOGENIC
therapeutic_actionability: ACTIONABLE
variation_descriptor {
  variation {
    copy_number {
      allele {
        sequence_location {
          sequence_id: "refseq:NC_000013.14"
          sequence_interval {
            start_number {
              value: 25981249
            }
            end_number {
              value: 61706822
            }
          }
        }
      }
      number {
        value: 1
      }
    }
  }
  extensions {
    name: "mosaicism"
    value: "40.0%"
  }
}
pnrobinson commented 2 years ago

This is required by JSON Schema