Add new view test to bcftools_validation that checks combination of region, includes, and sample filters

Author: tomwhite

tests/test_bcftools_validation.py

@@ -86,6 +86,10 @@ def run_vcztools(args: str, expect_error=False) -> tuple[str, str]:
         ("view --no-version -s ^NA00003,NA00002", "sample.vcf.gz"),
         ("view --no-version -s ^NA00003,NA00002,NA00003", "sample.vcf.gz"),
         ("view --no-version -S ^tests/data/txt/samples.txt", "sample.vcf.gz"),
+        (
+            "view --no-version -r '20:1230236-' -i 'FMT/DP>3' -s 'NA00002,NA00003'",
+            "sample.vcf.gz"
+        )
     ],
     # This is necessary when trying to run individual tests, as the arguments above
     # make for unworkable command lines

vcztools/vcf_writer.py

@@ -222,6 +222,7 @@ def c_chunk_to_vcf(
     for name, array in chunk_data.items():
         if (
             name.startswith("call_")
+            and not name == "call_mask"
             and not name.startswith("call_genotype")
             and num_samples != 0
         ):