Add fallback for proxy VCF construction failures on small/single-sample objects

[ywge03]

Summary

This PR keeps the existing proxy_match() proxy-construction logic as the default path, and adds a compatibility fallback that is only used when the original implementation fails during proxy VCF construction.

The goal is to fix a failure mode I encountered in my environment without changing behavior for users whose workflows already succeed with the current implementation.

In particular, the original code path is still attempted first. The fallback is only triggered if VariantAnnotation genotype-slot replacement fails during construction of the proxy VCF object.

Background

proxy_match() currently builds a proxy VCF object and then modifies its geno slot after construction by:

• appending the PR geno header field
• flipping ES values when allele orientation requires sign reversal
• inserting a new PR genotype matrix to track the proxy rsID used

In my case, this post-construction S4 replacement pattern failed with a subscript/dimension-related error during manipulation of geno(prox). The failure appears to be associated with small or effectively single-sample VCF-like objects, where VariantAnnotation's replacement behavior can be fragile.

The functional intent of the original code is correct, so this PR does not replace that logic globally. Instead, it preserves the original implementation and adds a narrowly scoped fallback for the failing case.

What this PR changes

This PR updates only the proxy VCF construction section inside proxy_match().

The new behavior is:

1. Attempt the original implementation exactly as before.

2. If that succeeds, return the result unchanged.

3. If that fails, catch the error and rebuild the proxy VCF using a compatibility path that:

   • extracts genotype fields as plain matrices first
   • applies effect-sign flipping before VCF construction
   • inserts the PR matrix before VCF construction
   • then creates the VCF object once, instead of relying on post-hoc geno slot replacement

This means existing successful cases continue using the original code path, and only problematic cases use the fallback.

[remlapmot]

Thanks for this.