Refactor

szhan · Feb 25, 2024 · 0cb2daa · 0cb2daa
1 parent e8c8849
commit 0cb2daa
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -695,9 +695,9 @@ def compute_alt_allele_frequencies():
 
 def write_vcf(ref_ts, imputed_alleles, imputed_allele_probs, out_file, chr_name="1"):
     """
-    n = number of diploid individuals
-    h = number of query haplotypes in the individuals (2 * n)
     x = number of imputed sites
+    n = number of diploid individuals
+    q = number of query haplotypes in the individuals (2 * n)
 
     :param tskit.TreeSequence ref_ts: Tree sequence with reference haplotypes.
     :param numpy.ndarray imputed_site_pos: Physical positions of imputed sites.
@@ -709,8 +709,8 @@ def write_vcf(ref_ts, imputed_alleles, imputed_allele_probs, out_file, chr_name=
     """
     assert imputed_alleles.shape == imputed_allele_probs.shape
     assert imputed_alleles.shape % 2 == 0, "Even number of haplotypes is expected."
-    h = imputed_alleles.shape[0]  # Number of query haplotypes
-    n = h / 2  # Number of diploid individuals
+    q = imputed_alleles.shape[0]  # Number of query haplotypes
+    n = q / 2  # Number of diploid individuals
     x = imputed_alleles.shape[1]  # Number of imputed sites.
     _HEADER = [
         "##fileformat=VCFv4.2",