From ee0b1836f33004c62d05408c4ee2b69086652131 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Wed, 28 Jan 2026 00:23:56 +0000
Subject: Do not drop zero standard deviation SNPs with --only-center.

---
 tests/test_pyhegp.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

(limited to 'tests/test_pyhegp.py')

diff --git a/tests/test_pyhegp.py b/tests/test_pyhegp.py
index 569ebe5..3192bf7 100644
--- a/tests/test_pyhegp.py
+++ b/tests/test_pyhegp.py
@@ -178,6 +178,19 @@ def test_encrypt_genotype_does_not_produce_na(genotype, key, only_center):
 def test_encrypt_phenotype_does_not_produce_na(phenotype, key):
     assert not encrypt_phenotype(phenotype, key).isna().any(axis=None)
 
+def test_encrypt_with_only_center_does_not_drop_snps(tmp_path):
+    genotype_file = Path("test-data/genotype-with-zero-stddev-snp.tsv")
+    shutil.copy(genotype_file, tmp_path)
+    result = CliRunner().invoke(main, ["encrypt",
+                                       "--only-center",
+                                       str(tmp_path / genotype_file.name)])
+    assert result.exit_code == 0
+    with genotype_file.open("rb") as file:
+        genotype = read_genotype(file)
+    with (tmp_path / f"{genotype_file.name}.hegp").open("rb") as file:
+        encrypted_genotype = read_genotype(file)
+    assert len(genotype) == len(encrypted_genotype)
+
 @pytest.mark.parametrize("summary_files",
                          [[Path("test-data/pool-test-summary1"),
                            Path("test-data/pool-test-summary2")],
-- 
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