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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)
The text was updated successfully, but these errors were encountered:
We should add tests for at least the following edge-cases:
For these edge-cases we need to confirm that iGenVar:
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)
The text was updated successfully, but these errors were encountered: