Make plink code follow original logic

Author: benjeffery

bio2zarr/plink.py

@@ -13,7 +13,7 @@
 class PlinkFormat:
     def __init__(self, path):
         self.path = path
-        self.bed = bed_reader.open_bed(path, num_threads=1)
+        self.bed = bed_reader.open_bed(path, num_threads=1, count_A1=False)
         self.num_records = self.bed.sid_count
         self.samples = list(self.bed.iid)
         self.num_samples = len(self.samples)
@@ -43,10 +43,11 @@ def iter_genotypes(self, shape, start, stop):
         gt = np.zeros(shape, dtype=np.int8)
         phased = np.zeros(shape[:-1], dtype=bool)
         for values in bed_chunk:
-            gt[values == -127] = -1  # Missing values
-            gt[values == 0] = [1, 1]  # Homozygous ALT (2 in PLINK)
-            gt[values == 1] = [1, 0]  # Heterozygous (1 in PLINK)
-            gt[values == 2] = [0, 0]  # Homozygous REF (0 in PLINK)
+            gt[:]= 0
+            gt[values == -127] = -1
+            gt[values == 2] = 1
+            gt[values == 1, 0] = 1
+
             yield gt, phased
 
     def generate_schema(