Python bindings: 3 UX bugs (path expansion, duplicate FASTA, partial VCF variant)

[bobvh]

Bug 1: Path expansion — ~ not expanded

Repository("~/my_repo") fails silently on macOS. Repository("/Users/bvh/my_repo") works.

~ should be expanded to the user's home directory. Likely affects any binding method that accepts a path argument.

Expected: ~/my_repo resolves the same as the absolute path.
Actual: Silent failure.

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Bug 2: Importing the same FASTA file twice raises RuntimeError

RuntimeError: '<filename>': contents already exist

Notebook cells are routinely re-run. Importing the same sequence to the same sample a second time should be idempotent (no-op or a warning), not a hard error.

Expected: Second import of identical FASTA is a no-op or emits a warning.
Actual: RuntimeError is raised, breaking notebook re-runs.

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Bug 3: update_with_vcf — partial out-of-bounds variant raises RuntimeError with unclear state

When a variant in the VCF partially falls outside the reference region, a RuntimeError is raised. It is not clear which variants made it into the database before the error and which did not.

Expected: Out-of-bounds variants are skipped with a warning message. A strict=True option (default False) should be available to raise an error instead and ensure no partial writes occur.
Actual: RuntimeError with no indication of DB state.