Use any non-redundant meta information lines stored by bio2zarr

Author: tomwhite

tests/test_vcf_writer.py

@@ -327,6 +327,11 @@ def test_write_vcf__generate_header():
 ##contig=<ID=19>
 ##contig=<ID=20>
 ##contig=<ID=X>
+##fileDate=20090805
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
+##ALT=<ID=CNV,Description="Copy number variable region">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
 """  # noqa: E501
 

vcztools/vcf_writer.py

@@ -414,6 +414,12 @@ def _generate_header(
             file=output,
         )
 
+    # Other meta information lines not covered above
+    if "vcf_meta_information" in ds.attrs:
+        for key, value in ds.attrs["vcf_meta_information"]:
+            if key not in ("fileformat", "source"):
+                print(f"##{key}={value}", file=output)
+
     # [1.5 Header line syntax]
     print(
         "#CHROM",