Fix off-by-one error for VCF regions

Author: tomwhite

vcztools/regions.py

@@ -18,14 +18,20 @@ def parse_targets_string(targets: str) -> tuple[str, Optional[int], Optional[int
         return contig, None, None
 
 
-def pslice_to_slice(
+def region_to_slice(
     all_contigs: List[str],
     variant_contig: Any,
     variant_position: Any,
     contig: str,
     start: Optional[int] = None,
     end: Optional[int] = None,
 ) -> slice:
+    """Convert a VCF region to a Python slice."""
+
+    # subtract one from start since VCF is 1-based (fully closed),
+    # but Python slices are 0-based (half open)
+    start = None if start is None else start - 1
+
     contig_index = all_contigs.index(contig)
     contig_range = np.searchsorted(variant_contig, [contig_index, contig_index + 1])
 

vcztools/vcf_writer.py

@@ -5,7 +5,7 @@
 from typing import MutableMapping, Optional, TextIO, Union
 
 import numpy as np
-from vcztools.regions import parse_targets_string, pslice_to_slice
+from vcztools.regions import parse_targets_string, region_to_slice
 import zarr
 
 from . import _vcztools
@@ -168,7 +168,14 @@ def write_vcf(
             variant_mask = np.ones(pos.shape[0], dtype=bool)
         else:
             contig, start, end = parse_targets_string(variant_targets)
-            variant_slice = pslice_to_slice(root["contig_id"][:].astype("U").tolist(), root["variant_contig"], pos, contig, start, end)
+            variant_slice = region_to_slice(
+                root["contig_id"][:].astype("U").tolist(),
+                root["variant_contig"],
+                pos,
+                contig,
+                start,
+                end,
+            )
             variant_mask = np.zeros(pos.shape[0], dtype=bool)
             variant_mask[variant_slice] = 1
         # Use zarr arrays to get mask chunks aligned with the main data