Merge pull request malariagen#1149 from khushthecoder/GH940-fix-region-start-zero-truthiness

Fix malariagen#940: Replace truthiness checks with explicit None checks for reg…

Author: jonbrenas

malariagen_data/anoph/hap_data.py

@@ -143,7 +143,7 @@ def _haplotype_sites_for_region(
         )
 
         # Deal with a region.
-        if region.start or region.end:
+        if region.start is not None or region.end is not None:
             if field == "POS":
                 pos = ret
             else:
@@ -385,7 +385,7 @@ def haplotypes(
                 x = _simple_xarray_concat(ly, dim=DIM_SAMPLE)
 
                 # Handle region.
-                if r.start or r.end:
+                if r.start is not None or r.end is not None:
                     pos = x["variant_position"].values
                     loc_region = _locate_region(r, pos)
                     x = x.isel(variants=loc_region)

malariagen_data/anoph/snp_data.py

@@ -253,7 +253,7 @@ def _site_filters_for_region(
             inline_array=inline_array,
             chunks=chunks,
         )
-        if region.start or region.end:
+        if region.start is not None or region.end is not None:
             pos = self._snp_sites_for_contig(
                 contig=region.contig,
                 field="POS",
@@ -353,7 +353,7 @@ def _snp_sites_for_region(
         )
 
         # Deal with a region.
-        if region.start or region.end:
+        if region.start is not None or region.end is not None:
             if field == "POS":
                 pos = ret
             else:
@@ -506,7 +506,7 @@ def snp_genotypes(
                 x = _da_concat(ly, axis=1)
 
                 # Locate region - do this only once, optimisation.
-                if r.start or r.end:
+                if r.start is not None or r.end is not None:
                     pos = self._snp_sites_for_contig(
                         contig=contig,
                         field="POS",
@@ -670,7 +670,7 @@ def snp_variants(
             )
 
             # Handle region.
-            if r.start or r.end:
+            if r.start is not None or r.end is not None:
                 pos = x["variant_position"].values
                 loc_region = _locate_region(r, pos)
                 x = x.isel(variants=loc_region)
@@ -1141,7 +1141,7 @@ def _raw_snp_calls(
                 x = xr.merge([v, x], compat="override", join="override")
 
                 # Handle region, do this only once - optimisation.
-                if r.start or r.end:
+                if r.start is not None or r.end is not None:
                     pos = x["variant_position"].values
                     loc_region = _locate_region(r, pos)
                     x = x.isel(variants=loc_region)