Changelog

Source: NEWS.md

gwasvcf 0.1.6

• Updates to 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 (thanks @ywge03)

gwasvcf 0.1.5

• proxy_match() is now robust to VCFs with multiple samples (thanks @jwr-git)

gwasvcf 0.1.4

• Add sqlite3 to DESCRIPTION SystemRequirements for create_pval_index_from_vcf()
• Update some URLs within the package documentation

gwasvcf 0.1.3

• Fix for security message in get_ld_proxies() (thanks @mattlee821)

gwasvcf 0.1.2

• New gwasvcf_to_summaryset() function to create a gwasglue2 SummarySet object from a vcf file
• Fixed error in get_ld_proxies() related with argument validate, deprecated in as_tibble() (tibble 2.0.0)