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Updates Code to handle multi-valued alts and remove default value for Genomic Source Class #97

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merged 2 commits into from
Mar 7, 2022

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Description

This PR is a combination of two commits:

  • Updates code to handle the case where a vcf record has multiple alts. Different FHIR variants must be created for each ALT.
  • Removes default value(Somatic) for the genomicSourceClass parameter.

Fixes #96

How Has This Been Tested?

The code has been tested by running all the unit tests using the command python -m unittest and the PEP 8 formatting was validated using pycodestyle.

  • Unit Tests
  • PEP 8 Formatting Validation

Records with multiple alts must be split into multiple variant records.
Updates Converter Class to have genomic source class as a required parameter without a default value.

type check for genomicSourceClass
@rhdolin rhdolin merged commit e6ea006 into elimuinformatics:master Mar 7, 2022
@Rohan-cod Rohan-cod deleted the multi-valued-alt branch March 25, 2022 12:48
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Successfully merging this pull request may close these issues.

Incorrect output when ALT is a multi-valued list
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