feat: add create_gnomad_sites_vcf tool

Port create_gnomad_sites_vcf.py from human-diversity-reference/scripts as a
defopt-compatible toolkit tool. Exports gnomAD variant sites above a given
population frequency threshold as a VCF file with per-population frequency
fields in the INFO column. Renames positional args path/vcf_path to
sites_table_path/output_vcf_path for clarity.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: ameynert

divref/divref/tools/create_gnomad_sites_vcf.py

@@ -0,0 +1,40 @@
+"""Tool to export gnomAD variants above a frequency threshold as a VCF file."""
+
+import hail as hl
+
+from divref.haplotype import HailPath
+
+
+def create_gnomad_sites_vcf(
+    *,
+    sites_table_path: HailPath,
+    output_vcf_path: HailPath,
+    min_popmax: float,
+) -> None:
+    """
+    Export gnomAD variant sites above a population frequency threshold as VCF.
+
+    Filters the gnomAD variant annotations table to sites where at least one
+    population's allele frequency meets or exceeds min_popmax, restructures
+    per-population frequency fields into VCF INFO format, and exports as VCF.
+
+    Args:
+        sites_table_path: Path to the gnomAD variant annotations Hail table
+            (from extract_gnomad_afs).
+        output_vcf_path: Output path for the VCF file.
+        min_popmax: Minimum allele frequency in any population to include a site.
+    """
+    hl.init()
+
+    ht = hl.read_table(sites_table_path)
+    pops: list[str] = ht.pops.collect()[0]
+
+    filt = ht.filter(hl.max(ht.pop_freqs[0].map(lambda x: x.AF)) >= min_popmax)
+    filt = filt.annotate(
+        info=hl.struct(**{
+            f"{pop}_{fd}": filt.pop_freqs[i][fd]
+            for i, pop in enumerate(pops)
+            for fd in filt.pop_freqs[i]
+        })
+    )
+    hl.export_vcf(filt, output_vcf_path)