From fe5f6451188b08e624085bd508a1c5c23af75090 Mon Sep 17 00:00:00 2001
From: Shing Zhan <shing.zhan@gmail.com>
Date: Fri, 23 Feb 2024 14:00:19 +0000
Subject: [PATCH] Rename variables

---
 python/tests/beagle_numba.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
index aa3b59d6bc..f5f5363d88 100644
--- a/python/tests/beagle_numba.py
+++ b/python/tests/beagle_numba.py
@@ -539,8 +539,8 @@ def run_tsimpute(
     typed_cm = convert_to_genetic_map_positions(typed_pos, genetic_map)
     untyped_cm = convert_to_genetic_map_positions(untyped_pos, genetic_map)
     # Get rates at genotyped markers.
-    rho = rho[typed_idx]
-    mu = mu[typed_idx]
+    transition_probs = rho[typed_idx]
+    mismatch_probs = mu[typed_idx]
     # Subset haplotypes.
     ref_ts_typed = ref_ts.delete_sites(site_ids=untyped_idx)
     ref_ts_untyped = ref_ts.delete_sites(site_ids=typed_idx)
@@ -552,8 +552,8 @@ def run_tsimpute(
     # WARN: Be careful with argument `acgt_alleles`!!!
     ls_hmm = _tskit.LsHmm(
         ref_ts_typed._ll_tree_sequence,
-        recombination_rate=rho,
-        mutation_rate=mu,
+        recombination_rate=transition_probs,  # Transition probabilities
+        mutation_rate=mismatch_probs,  # Mismatch probabilities
         acgt_alleles=True,
         precision=precision,
     )