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[TEST] Add tests for edgecases #117

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eldariont opened this issue May 4, 2021 · 0 comments
Open

[TEST] Add tests for edgecases #117

eldariont opened this issue May 4, 2021 · 0 comments

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@eldariont
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We should add tests for at least the following edge-cases:

  • SVs located at the very beginning of a chromosome
  • SVs located at the very end of a chromosome (need the genome as input to check that)
  • DELs that delete the entire chromosome

For these edge-cases we need to confirm that iGenVar:

  • does not crash
  • produces valid VCF
  • respects the specification (e.g. choosing the right padding base as described here:
    For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event)
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