reduce memory in Genotypes.read (see #19)

haptools/data/genotypes.py

@@ -92,29 +92,29 @@ def read(self, region: str = None, samples: list[str] = None):
         # load all info into memory
         vcf = VCF(str(self.fname), samples=samples)
         self.samples = tuple(vcf.samples)
-        variants = list(vcf(region))
+        self.variants = []
+        self.data = []
+        for variant in vcf(region):
+            # save meta information about each variant
+            self.variants.append((variant.ID, variant.CHROM, variant.POS, variant.aaf))
+            # extract the genotypes to a matrix of size n x p x 3
+            # the last dimension has three items:
+            # 1) presence of REF in strand one
+            # 2) presence of REF in strand two
+            # 3) whether the genotype is phased
+            self.data.append(variant.genotypes)
         vcf.close()
-        # save meta information about each variant
+        # convert to np array for speedy operations later on
         self.variants = np.array(
-            [
-                (variant.ID, variant.CHROM, variant.POS, variant.aaf)
-                for variant in variants
-            ],
+            self.variants,
             dtype=[
                 ("id", "U50"),
                 ("chrom", "U10"),
                 ("pos", np.uint),
                 ("aaf", np.float64),
             ],
         )
-        # extract the genotypes to a np matrix of size n x p x 3
-        # the last dimension has three items:
-        # 1) presence of REF in strand one
-        # 2) presence of REF in strand two
-        # 3) whether the genotype is phased
-        self.data = np.array(
-            [variant.genotypes for variant in variants], dtype=np.uint8
-        )
+        self.data = np.array(self.data, dtype=np.uint8)
         if self.data.shape == (0, 0, 0):
             raise ValueError(
                 "Failed to load genotypes. If you specified a region, check that the"