Handle absent optional reference column.

pyhegp was crashing if the optional reference column was absent. We
handle it correctly now. And, we add several test cases to catch this
in the future.

11 files changed, 599 insertions, 35 deletions

diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py
index 4e0bd84..3133c25 100644
--- a/pyhegp/pyhegp.py
+++ b/pyhegp/pyhegp.py
@@ -49,14 +49,22 @@ def hegp_encrypt(plaintext, key):
 def hegp_decrypt(ciphertext, key):
     return np.transpose(key) @ ciphertext
 
+def drop_metadata_columns(genotype):
+    return (genotype.drop(columns=["chromosome", "position"])
+            # The reference column is optional. Do not error out if it
+            # does not exist.
+            .drop(columns=["reference"], errors="ignore"))
+
 def genotype_summary(genotype):
-    matrix = genotype.drop(columns=["chromosome", "position", "reference"]).to_numpy()
+    matrix = drop_metadata_columns(genotype).to_numpy()
     return Summary(genotype.shape[0],
                    pd.DataFrame({"chromosome": genotype.chromosome,
-                                 "position": genotype.position,
-                                 "reference": genotype.reference,
-                                 "mean": np.mean(matrix, axis=1),
-                                 "std": np.std(matrix, axis=1)}))
+                                 "position": genotype.position}
+                                | ({"reference": genotype.reference}
+                                   if "reference" in genotype.columns
+                                   else {})
+                                | {"mean": np.mean(matrix, axis=1),
+                                   "std": np.std(matrix, axis=1)}))
 
 def pool_stats(list_of_stats):
     sums = [stats.n*stats.mean for stats in list_of_stats]
@@ -70,13 +78,17 @@ def pool_stats(list_of_stats):
 
 def pool_summaries(summaries):
     def pool_summaries2(summary1, summary2):
+        metadata_columns = (["chromosome", "position"]
+                            + (["reference"]
+                               if "reference" in summary1.data.columns
+                               else []))
         # Drop any SNPs that are not in both summaries.
         data = pd.merge(summary1.data.rename(columns={"mean": "mean1",
                                                       "std": "std1"}),
                         summary2.data.rename(columns={"mean": "mean2",
                                                       "std": "std2"}),
                         how="inner",
-                        on=("chromosome", "position", "reference"))
+                        on=metadata_columns)
         pooled_stats = pool_stats([Stats(summary1.n,
                                          data.mean1.to_numpy(),
                                          data.std2.to_numpy()),
@@ -84,13 +96,16 @@ def pool_summaries(summaries):
                                          data.mean2.to_numpy(),
                                          data.std2.to_numpy())])
         return Summary(pooled_stats.n,
-                       pd.concat((data[["chromosome", "position", "reference"]],
+                       pd.concat((data[metadata_columns],
                                   pd.DataFrame({"mean": pooled_stats.mean,
                                                 "std": pooled_stats.std})),
                                  axis="columns"))
     pooled_summary = reduce(pool_summaries2, summaries)
     return Summary(pooled_summary.n,
-                   pooled_summary.data.drop(columns=["reference"]))
+                   # The reference column is optional. Do not raise an
+                   # error if it is absent.
+                   pooled_summary.data.drop(columns=["reference"],
+                                            errors="ignore"))
 
 def encrypt_genotype(genotype, key, summary):
     # Drop SNPs that have a zero standard deviation. Such SNPs have no
@@ -102,8 +117,7 @@ def encrypt_genotype(genotype, key, summary):
     common_genotype = pd.merge(genotype,
                                summary.data[["chromosome", "position"]],
                                on=("chromosome", "position"))
-    sample_names = (common_genotype.drop(
-        columns=["chromosome", "position", "reference"]).columns)
+    sample_names = drop_metadata_columns(common_genotype).columns
     genotype_matrix = common_genotype[sample_names].to_numpy().T
     encrypted_genotype_matrix = hegp_encrypt(standardize(
         genotype_matrix,
@@ -202,9 +216,7 @@ def encrypt_command(genotype_file, phenotype_file, summary_file, key_file, force
     else:
         summary = genotype_summary(genotype)
     key = random_key(np.random.default_rng(),
-                     len(genotype
-                         .drop(columns=["chromosome", "position", "reference"])
-                         .columns))
+                     len(drop_metadata_columns(genotype).columns))
     if key_file:
         write_key(key_file, key)
 
diff --git a/test-data/encrypt-test-genotype-without-reference.tsv b/test-data/encrypt-test-genotype-without-reference.tsv
new file mode 100644
index 0000000..8598e36
--- /dev/null
+++ b/test-data/encrypt-test-genotype-without-reference.tsv
@@ -0,0 +1,5 @@
+chromosome	position	sample1	sample2
+chr1	1	0	1
+chr2	19	2	3
+chrX	21	4	5
+chrX	22	4	5
diff --git a/test-data/encrypt-test-summary-without-reference b/test-data/encrypt-test-summary-without-reference
new file mode 100644
index 0000000..71a77a3
--- /dev/null
+++ b/test-data/encrypt-test-summary-without-reference
@@ -0,0 +1,6 @@
+# pyhegp summary file version 1
+# number-of-samples 10
+chromosome	position	mean	standard-deviation
+chr1	1	0	1
+chr2	19	2	3
+chrX	21	4	5
diff --git a/test-data/genotype-without-reference.tsv b/test-data/genotype-without-reference.tsv
new file mode 100644
index 0000000..cd7cbbd
--- /dev/null
+++ b/test-data/genotype-without-reference.tsv
@@ -0,0 +1,101 @@
+chromosome	position	Q_CFW-SW/100.0a	Q_CFW-SW/100.0c	Q_CFW-SW/100.0d	Q_CFW-SW/100.0e	Q_CFW-SW/100.0f	Q_CFW-SW/100.0g	Q_CFW-SW/100.0h	Q_CFW-SW/100.0i	Q_CFW-SW/100.0j	Q_CFW-SW/100.0l	Q_CFW-SW/100.0m	Q_CFW-SW/100.0n	Q_CFW-SW/100.0o	Q_CFW-SW/100.0p	Q_CFW-SW/100.0q	Q_CFW-SW/100.0r	Q_CFW-SW/10.0b	Q_CFW-SW/10.0c	Q_CFW-SW/10.0d	Q_CFW-SW/10.0f
+chr11	3200246	0.4043	0.3655	0.3375	-0.614	0.3452	0.3836	0.3901	0.2411	-0.1418	0.3629	-1.8435	0.3742	-0.5826	0.4141	-0.0555	0.2733	0.408	0.388	-3.6091	0.381
+chr11	3205355	0.395	0.3545	0.3325	-0.5421	0.3433	0.3751	0.3806	0.2034	-0.1	0.3539	-1.9966	0.3681	-0.4778	0.4084	-0.0767	0.2807	0.3991	0.384	-3.5452	0.3728
+chr11	3218908	0.3977	0.3207	0.3134	-0.4491	0.3267	0.3576	0.3449	0.1215	-0.0346	0.3294	-2.3341	0.3548	-0.2218	0.3769	-0.0873	0.3071	0.3728	0.3672	-3.5468	0.3528
+chr11	3414044	-0.3616	-0.328	-0.3234	0.074	-0.2713	-0.2976	-0.339	1.0335	-0.2665	-0.3005	3.5125	-0.3327	-0.2604	-0.3458	0.239	-0.3538	-0.3239	-0.3452	3.6101	-0.3177
+chr11	3460427	-0.341	-0.3363	-0.3346	0.073	-0.2652	-0.2791	-0.3456	1.3293	-0.2961	-0.3032	3.5493	-0.3261	-0.2861	-0.3472	0.051	-0.3419	-0.33	-0.3332	3.664	-0.3154
+chr11	3462290	-0.3552	-0.3281	-0.3287	0.0912	-0.2708	-0.2841	-0.3331	1.3928	-0.2856	-0.3056	3.5419	-0.3303	-0.2974	-0.3477	0.0408	-0.3514	-0.323	-0.343	3.6699	-0.3101
+chr11	3462323	-0.3524	-0.3296	-0.3298	0.0874	-0.2697	-0.2832	-0.3357	1.3896	-0.2873	-0.3051	3.542	-0.3294	-0.2953	-0.3476	0.0418	-0.3495	-0.3244	-0.3411	3.6675	-0.3111
+chr11	3462325	-0.3533	-0.3291	-0.3294	0.0885	-0.27	-0.2835	-0.3349	1.3909	-0.2867	-0.3052	3.5419	-0.3297	-0.296	-0.3476	0.0414	-0.3501	-0.324	-0.3417	3.6682	-0.3108
+chr11	3462348	-0.361	-0.3244	-0.326	0.0986	-0.2731	-0.2864	-0.3279	1.4031	-0.2807	-0.3064	3.541	-0.3318	-0.3018	-0.3476	0.0372	-0.3551	-0.32	-0.3469	3.6751	-0.3079
+chr11	3464016	-0.3461	-0.334	-0.3331	0.08	-0.2672	-0.2805	-0.3413	1.3757	-0.2937	-0.3044	3.543	-0.328	-0.2906	-0.3479	0.0464	-0.3455	-0.3279	-0.3369	3.6601	-0.3138
+chr11	3554197	0.3393	0.3346	0.0862	-0.1332	0.2532	0.2705	0.3409	-0.5622	0.3082	0.2896	-3.4878	0.3228	0.3214	0.3396	0.017	0.3492	0.3396	0.3289	-3.5317	0.3086
+chr11	3558414	-0.3648	-0.3172	0.0754	0.1639	-0.2644	-0.286	-0.3239	0.5833	-0.2805	-0.2923	3.3617	-0.3305	-0.342	-0.3407	-0.0391	-0.3686	-0.3297	-0.3505	3.5287	-0.2993
+chr11	3619052	-0.3394	-0.3269	1.0859	0.2534	-0.2429	-0.2508	-0.3166	0.2133	-0.3278	-0.2838	1.7148	-0.3089	-0.3337	-0.3288	-0.0442	-0.3453	-0.3142	-0.3346	2.9131	-0.2884
+chr11	3883306	-0.3207	-0.2844	2.6043	0.0664	-0.227	-0.2504	-8e-04	-0.2199	-0.3104	-0.2247	0.2938	-0.3079	-0.2412	-0.3312	-0.2698	-0.3016	-0.2836	-0.2786	-0.2529	-0.3149
+chr11	4017210	-0.3655	-0.3608	1.5442	-0.0087	-0.2506	-0.3213	0.215	-0.3742	-0.396	-0.2641	0.2322	-0.3503	-0.2296	-0.405	-0.3226	-0.3643	-0.2958	-0.3026	-0.4183	-0.3808
+chr11	4017211	-0.3685	-0.356	1.5489	-0.0107	-0.2535	-0.3241	0.2125	-0.3624	-0.3916	-0.261	0.2295	-0.3533	-0.2325	-0.4005	-0.3256	-0.3673	-0.2987	-0.3055	-0.4064	-0.3776
+chr11	4017223	-0.3824	-0.3338	1.5704	-0.02	-0.2667	-0.3373	0.2009	-0.3071	-0.3708	-0.2466	0.2171	-0.3669	-0.2459	-0.3794	-0.3394	-0.3812	-0.3125	-0.3194	-0.3509	-0.3623
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+chr11	4024616	-0.7473	1.1971	0.937	-0.4412	-0.7211	-0.7083	-0.6358	2.9722	1.1229	0.7712	-0.7234	-0.733	-0.7373	1.1363	-0.723	-0.7502	-0.7397	-0.7496	2.9891	0.8355
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+chr11	4156678	-0.7124	0.9335	0.9412	-0.6338	-0.7107	-0.7118	-0.7025	2.5787	0.9332	0.9266	-0.7122	-0.7121	-0.7116	0.9333	-0.7095	-0.7124	-0.7123	-0.7124	2.5787	0.9332
+chr11	4157061	-0.7159	1.0851	1.0835	-0.7163	-0.7164	-0.716	-0.7183	2.8866	1.0854	1.0774	-0.7172	-0.716	-0.7165	1.0853	-0.7162	-0.7162	-0.7163	-0.7163	2.8866	1.0854
+chr11	4157575	-0.7172	0.9675	0.9739	-0.6531	-0.7159	-0.7168	-0.7093	2.6516	0.9672	0.962	-0.7171	-0.717	-0.7166	0.9673	-0.7149	-0.7172	-0.7172	-0.7172	2.6516	0.9672
+chr11	4157625	-0.7124	0.9339	0.9416	-0.6342	-0.7108	-0.7119	-0.7027	2.5796	0.9336	0.9288	-0.7123	-0.7122	-0.7116	0.9337	-0.7096	-0.7124	-0.7124	-0.7124	2.5796	0.9336
+chr11	4157692	-0.7123	0.9332	0.941	-0.6338	-0.7107	-0.7118	-0.7025	2.5781	0.9329	0.9282	-0.7122	-0.7121	-0.7115	0.933	-0.7095	-0.7124	-0.7123	-0.7123	2.5782	0.9329
+chr11	4157786	-0.7124	0.9338	0.9415	-0.6342	-0.7108	-0.7119	-0.7026	2.5793	0.9334	0.9289	-0.7122	-0.7122	-0.7116	0.9336	-0.7096	-0.7124	-0.7123	-0.7124	2.5793	0.9334
+chr11	4157829	-0.7125	0.9344	0.9421	-0.6345	-0.7109	-0.712	-0.7027	2.5807	0.9341	0.9296	-0.7124	-0.7123	-0.7117	0.9342	-0.7097	-0.7126	-0.7125	-0.7125	2.5807	0.9341
+chr11	4157846	-0.712	0.9311	0.9389	-0.6327	-0.7104	-0.7115	-0.702	2.5735	0.9308	0.9264	-0.7118	-0.7117	-0.7112	0.9309	-0.7091	-0.712	-0.7119	-0.712	2.5736	0.9308
+chr11	4158681	-0.7117	0.9288	0.9369	-0.6316	-0.71	-0.7112	-0.7016	2.5687	0.9285	0.9257	-0.7115	-0.7114	-0.7109	0.9287	-0.7088	-0.7117	-0.7116	-0.7117	2.5688	0.9285
+chr11	4159249	-0.7176	1.0827	1.0845	-0.7156	-0.7175	-0.7176	-0.7171	2.883	1.0827	1.0799	-0.7174	-0.7176	-0.7175	1.0827	-0.7175	-0.7176	-0.7176	-0.7176	2.883	1.0827
+chr11	4159512	-0.7124	0.9326	0.9407	-0.6341	-0.7108	-0.7119	-0.7025	2.5774	0.9325	0.9312	-0.7122	-0.7122	-0.7116	0.9326	-0.7096	-0.7124	-0.7123	-0.7124	2.5774	0.9325
+chr11	4159576	-0.7181	0.974	0.9804	-0.6574	-0.7169	-0.7177	-0.7105	2.6659	0.9739	0.9725	-0.718	-0.7179	-0.7175	0.974	-0.7159	-0.7181	-0.7181	-0.7181	2.6659	0.9739
+chr11	4160767	-0.7174	1.084	1.0858	-0.7164	-0.7173	-0.7174	-0.7169	2.8852	1.0839	1.0831	-0.7172	-0.7174	-0.7173	1.0839	-0.7173	-0.7173	-0.7173	-0.7173	2.8852	1.0839
+chr11	4161449	-0.7208	1.009	1.0136	-0.677	-0.72	-0.7205	-0.7157	2.7387	1.0089	1.0085	-0.7209	-0.7207	-0.7204	1.009	-0.7193	-0.7209	-0.7208	-0.7209	2.7387	1.0089
+chr11	4163009	-0.7123	0.9296	0.9385	-0.6333	-0.7106	-0.7118	-0.7017	2.5713	0.9295	0.9297	-0.7118	-0.7121	-0.7113	0.9296	-0.7094	-0.7123	-0.7122	-0.7122	2.5713	0.9295
+chr11	4164110	-0.7171	1.0839	1.085	-0.7166	-0.7171	-0.7171	-0.7173	2.885	1.084	1.0831	-0.7172	-0.7171	-0.7171	1.084	-0.7171	-0.7171	-0.7171	-0.7171	2.885	1.084
+chr11	4165583	-0.719	0.9823	0.9883	-0.6632	-0.7179	-0.7187	-0.7121	2.6835	0.9822	0.9821	-0.719	-0.7189	-0.7184	0.9823	-0.717	-0.7191	-0.719	-0.719	2.6835	0.9822
+chr11	4166188	-0.7173	1.0834	1.0848	-0.7165	-0.7173	-0.7173	-0.7172	2.884	1.0833	1.0827	-0.7173	-0.7173	-0.7173	1.0833	-0.7173	-0.7173	-0.7173	-0.7173	2.884	1.0833
+chr11	4169047	-0.7169	1.075	1.0725	-0.7124	-0.7176	-0.7171	-0.7197	2.8675	1.0753	1.0742	-0.7188	-0.717	-0.7178	1.0753	-0.7171	-0.7173	-0.7174	-0.7174	2.8676	1.0753
+chr11	4169344	-0.7172	1.0836	1.085	-0.7169	-0.7172	-0.7172	-0.7171	2.8844	1.0836	1.0833	-0.7172	-0.7172	-0.7172	1.0836	-0.7172	-0.7172	-0.7172	-0.7172	2.8844	1.0836
+chr11	4173901	-0.7189	1.0782	1.0815	-0.7145	-0.7184	-0.7188	-0.7169	2.8749	1.078	1.0782	-0.718	-0.7188	-0.7184	1.078	-0.7186	-0.7187	-0.7186	-0.7186	2.8749	1.078
+chr11	4174384	-0.7174	1.0824	1.0838	-0.7165	-0.7174	-0.7174	-0.7173	2.8822	1.0824	1.0822	-0.7174	-0.7174	-0.7174	1.0824	-0.7174	-0.7174	-0.7174	-0.7174	2.8822	1.0824
+chr11	4177048	-0.7173	1.0818	1.0827	-0.7163	-0.7174	-0.7173	-0.7176	2.881	1.0818	1.0816	-0.7175	-0.7173	-0.7174	1.0818	-0.7173	-0.7174	-0.7174	-0.7174	2.881	1.0818
+chr11	4178320	-0.7127	0.932	0.9397	-0.637	-0.7111	-0.7122	-0.7032	2.5766	0.9319	0.9332	-0.7126	-0.7126	-0.7118	0.932	-0.7101	-0.7127	-0.7127	-0.7127	2.5766	0.9319
+chr11	4178518	-0.7173	1.083	1.0843	-0.717	-0.7173	-0.7173	-0.7173	2.8834	1.083	1.0829	-0.7173	-0.7173	-0.7173	1.083	-0.7173	-0.7173	-0.7173	-0.7173	2.8834	1.083
+chr11	4183635	-0.7212	1.0541	1.0574	-0.703	-0.7207	-0.721	-0.7185	2.8293	1.0541	1.0546	-0.7209	-0.7211	-0.7208	1.0541	-0.7205	-0.7211	-0.7211	-0.7211	2.8293	1.0541
+chr11	4185242	-0.7173	1.0826	1.0836	-0.7172	-0.7174	-0.7173	-0.7175	2.8825	1.0826	1.0825	-0.7174	-0.7173	-0.7174	1.0826	-0.7173	-0.7173	-0.7174	-0.7174	2.8825	1.0826
+chr11	4209116	-0.7166	1.0819	1.0809	-0.717	-0.7171	-0.7168	-0.7183	2.8809	1.0821	1.0817	-0.7176	-0.7167	-0.7171	1.0821	-0.7169	-0.7169	-0.7169	-0.7169	2.8809	1.0821
+chr11	4211694	-0.7214	1.0487	1.0515	-0.7011	-0.7209	-0.7213	-0.7187	2.8188	1.0487	1.0497	-0.7213	-0.7214	-0.721	1.0487	-0.7208	-0.7214	-0.7214	-0.7213	2.8188	1.0487
+chr11	4228604	-0.718	1.0783	1.0782	-0.7154	-0.718	-0.718	-0.7179	2.8746	1.0783	1.0784	-0.7181	-0.718	-0.718	1.0783	-0.7179	-0.718	-0.718	-0.718	2.8746	1.0783
+chr11	4229176	-0.7175	1.0824	1.0825	-0.7173	-0.7174	-0.7175	-0.7173	2.8822	1.0824	1.0824	-0.7174	-0.7175	-0.7174	1.0824	-0.7174	-0.7174	-0.7174	-0.7174	2.8822	1.0824
+chr11	4229195	-0.7173	1.0823	1.0821	-0.7173	-0.7173	-0.7173	-0.7175	2.882	1.0823	1.0823	-0.7174	-0.7173	-0.7173	1.0824	-0.7173	-0.7173	-0.7173	-0.7173	2.882	1.0824
+chr11	4230918	-0.7175	1.0814	1.0811	-0.7169	-0.7175	-0.7175	-0.7176	2.8804	1.0815	1.0827	-0.7176	-0.7175	-0.7175	1.0815	-0.7175	-0.7175	-0.7175	-0.7175	2.8804	1.0815
+chr11	4237235	-0.7217	1.0411	1.0425	-0.6978	-0.7212	-0.7216	-0.7187	2.8039	1.0416	1.0465	-0.7217	-0.7217	-0.7213	1.0411	-0.7211	-0.7217	-0.7217	-0.7217	2.8039	1.0411
+chr11	4238100	-0.7218	1.0417	1.0433	-0.6981	-0.7212	-0.7216	-0.7186	2.8051	1.0422	1.0474	-0.7216	-0.7218	-0.7213	1.0417	-0.7211	-0.7218	-0.7218	-0.7217	2.8051	1.0417
+chr11	4246351	-0.7189	1.0638	1.0612	-0.7087	-0.7193	-0.719	-0.7199	2.847	1.0643	1.0699	-0.7202	-0.7191	-0.7194	1.0639	-0.719	-0.7193	-0.7193	-0.7193	2.847	1.064
+chr11	4246985	-0.7219	1.0396	1.041	-0.6971	-0.7212	-0.7217	-0.7186	2.8009	1.0403	1.047	-0.7218	-0.7218	-0.7213	1.0395	-0.7212	-0.7218	-0.7218	-0.7217	2.8009	1.0395
+chr11	4261375	-0.7176	1.0824	1.0813	-0.7174	-0.7176	-0.7176	-0.7173	2.8823	1.0823	1.0909	-0.7175	-0.7176	-0.7175	1.0823	-0.7176	-0.7176	-0.7176	-0.7176	2.8823	1.0823
+chr11	4273327	-0.7175	1.0831	1.0711	-0.7175	-0.7175	-0.7175	-0.7176	2.8838	1.0832	1.0925	-0.7176	-0.7175	-0.7175	1.0828	-0.7175	-0.7175	-0.7175	-0.7175	2.8839	1.0832
+chr11	4283717	0.7233	-1.1344	0.391	0.7222	0.7241	0.7246	0.715	-2.9824	-1.1255	-1.1348	0.7251	0.722	0.7227	0.3988	0.7242	0.7249	0.7253	0.7249	-2.9836	-1.1298
+chr11	4284110	0.7062	-1.1375	0.5957	0.7058	0.7066	0.7066	0.7038	-2.9797	-1.1346	-1.1381	0.7068	0.7058	0.7059	0.6075	0.7065	0.7067	0.7068	0.7067	-2.9807	-1.1376
+chr11	4285090	0.7024	-1.0934	0.683	0.6975	0.7021	0.7022	0.7056	-2.8862	-1.1106	-1.0931	0.7035	0.7028	0.7026	0.6985	0.7024	0.7034	0.703	0.703	-2.8865	-1.0925
+chr11	4286016	0.6998	-1.1324	0.6815	0.699	0.6994	0.6997	0.699	-2.9626	-1.133	-1.1317	0.6996	0.6997	0.6992	0.698	0.6996	0.6996	0.6997	0.6997	-2.9627	-1.1315
+chr11	4288936	0.7042	-1.0649	0.6806	0.6939	0.7021	0.7037	0.7027	-2.8246	-1.0924	-1.064	0.7039	0.704	0.7031	0.7012	0.7032	0.704	0.704	0.7041	-2.8247	-1.061
+chr11	4301371	0.6999	-1.1332	0.6817	0.6989	0.6992	0.6998	0.698	-2.9638	-1.1331	-1.1326	0.6994	0.6997	0.699	0.6981	0.6996	0.6994	0.6996	0.6996	-2.964	-1.1323
+chr11	4310171	0.6995	-1.1496	0.6833	0.6991	0.6993	0.6995	0.7	-2.96	-1.1325	-1.1305	0.6997	0.6996	0.6991	0.6988	0.6995	0.6997	0.6996	0.6996	-2.9604	-1.1308
+chr11	4330042	0.7035	-1.1568	0.6829	0.6965	0.7019	0.7033	0.7023	-2.8717	-1.109	-1.0874	0.7035	0.7036	0.7021	0.7013	0.703	0.7035	0.7036	0.7037	-2.8725	-1.0853
+chr11	4908477	-0.2937	-0.2945	-0.2933	-0.2939	-0.2938	-0.2937	-0.2943	-0.2937	-0.2939	-0.2945	-0.2937	3.3684	-0.2934	-0.2937	-0.2934	3.3681	-0.2937	-0.2934	-0.2938	-0.2937
+chr11	4941705	-0.2927	-0.289	-0.3024	-0.2936	-0.2913	-0.2911	-0.293	-0.2925	-0.2917	-0.2893	-0.2991	3.3273	-0.3012	-0.2917	-0.3011	3.3298	-0.2983	-0.2982	-0.2917	-0.2924
+chr11	4944016	-0.2944	-0.2943	-0.2946	-0.2944	-0.2943	-0.2943	-0.2944	-0.2944	-0.2944	-0.2943	-0.2945	3.3274	-0.2946	-0.2944	-0.2946	3.3274	-0.2945	-0.2945	-0.2944	-0.2944
+chr11	4945582	-0.2944	-0.2943	-0.2946	-0.2944	-0.2943	-0.2944	-0.2944	-0.2944	-0.2944	-0.2943	-0.2945	3.3273	-0.2946	-0.2944	-0.2946	3.3273	-0.2945	-0.2945	-0.2944	-0.2944
+chr11	4949541	-0.2948	-0.2942	-0.294	-0.2943	-0.2945	-0.295	-0.2941	-0.2947	-0.2946	-0.2942	-0.2934	3.3271	-0.2941	-0.295	-0.294	3.3267	-0.2941	-0.2944	-0.2948	-0.2948
+chr11	4971995	-0.2958	-0.2957	-0.2949	-0.2955	-0.2957	-0.296	-0.2954	-0.2957	-0.2957	-0.2957	-0.2948	3.3243	-0.295	-0.2959	-0.295	3.3241	-0.2952	-0.2954	-0.2958	-0.2958
diff --git a/test-data/genotype0-without-reference.tsv b/test-data/genotype0-without-reference.tsv
new file mode 100644
index 0000000..5b408cd
--- /dev/null
+++ b/test-data/genotype0-without-reference.tsv
@@ -0,0 +1,101 @@
+chromosome	position	Q_CFW-SW/100.0a	Q_CFW-SW/100.0c	Q_CFW-SW/100.0d	Q_CFW-SW/100.0e	Q_CFW-SW/100.0f
+chr11	3200246	0.4043	0.3655	0.3375	-0.614	0.3452
+chr11	3205355	0.395	0.3545	0.3325	-0.5421	0.3433
+chr11	3218908	0.3977	0.3207	0.3134	-0.4491	0.3267
+chr11	3414044	-0.3616	-0.328	-0.3234	0.074	-0.2713
+chr11	3460427	-0.341	-0.3363	-0.3346	0.073	-0.2652
+chr11	3462290	-0.3552	-0.3281	-0.3287	0.0912	-0.2708
+chr11	3462323	-0.3524	-0.3296	-0.3298	0.0874	-0.2697
+chr11	3462325	-0.3533	-0.3291	-0.3294	0.0885	-0.27
+chr11	3462348	-0.361	-0.3244	-0.326	0.0986	-0.2731
+chr11	3464016	-0.3461	-0.334	-0.3331	0.08	-0.2672
+chr11	3554197	0.3393	0.3346	0.0862	-0.1332	0.2532
+chr11	3558414	-0.3648	-0.3172	0.0754	0.1639	-0.2644
+chr11	3619052	-0.3394	-0.3269	1.0859	0.2534	-0.2429
+chr11	3883306	-0.3207	-0.2844	2.6043	0.0664	-0.227
+chr11	4017210	-0.3655	-0.3608	1.5442	-0.0087	-0.2506
+chr11	4017211	-0.3685	-0.356	1.5489	-0.0107	-0.2535
+chr11	4017223	-0.3824	-0.3338	1.5704	-0.02	-0.2667
+chr11	4017385	-0.3677	-0.3524	1.5514	-0.0141	-0.2529
+chr11	4022004	-0.3702	-0.3553	1.5401	-0.0114	-0.2548
+chr11	4024616	-0.7473	1.1971	0.937	-0.4412	-0.7211
+chr11	4110988	0.8081	-1.0677	-1.2622	0.66	0.7659
+chr11	4124677	0.8076	-0.9793	-1.1824	0.6428	0.7643
+chr11	4139413	-0.7222	1.0853	1.0928	-0.7139	-0.7198
+chr11	4139426	-0.717	1.0865	1.0815	-0.714	-0.7171
+chr11	4140742	-0.7174	1.0856	1.0817	-0.7139	-0.7173
+chr11	4141532	-0.7187	1.0779	1.0748	-0.7101	-0.7185
+chr11	4141701	-0.7173	1.0861	1.0826	-0.7144	-0.7172
+chr11	4141949	-0.7188	1.077	1.0742	-0.7098	-0.7186
+chr11	4142088	-0.7176	1.0803	1.0756	-0.7115	-0.7178
+chr11	4142629	-0.7175	1.0852	1.0823	-0.7143	-0.7174
+chr11	4142987	-0.7215	1.0388	1.0379	-0.6896	-0.7209
+chr11	4143502	-0.7178	1.0846	1.0826	-0.7143	-0.7175
+chr11	4143779	-0.717	1.0858	1.0825	-0.7149	-0.7171
+chr11	4143838	-0.7169	1.086	1.0824	-0.715	-0.717
+chr11	4143850	-0.7174	1.0853	1.0828	-0.7147	-0.7173
+chr11	4144873	-0.7173	1.0832	1.08	-0.7137	-0.7174
+chr11	4146736	-0.7189	1.072	1.0698	-0.7082	-0.7189
+chr11	4147532	-0.7188	1.0764	1.0753	-0.7106	-0.7186
+chr11	4147579	-0.7181	1.0791	1.0773	-0.712	-0.7181
+chr11	4148004	-0.7169	1.0852	1.0828	-0.7152	-0.717
+chr11	4148006	-0.717	1.0857	1.0837	-0.7155	-0.717
+chr11	4149618	-0.7171	1.0848	1.0834	-0.7153	-0.7171
+chr11	4151366	-0.7118	0.9346	0.9387	-0.633	-0.7105
+chr11	4151391	-0.7119	0.9356	0.9395	-0.6336	-0.7106
+chr11	4151936	-0.7173	1.0841	1.0834	-0.7152	-0.7173
+chr11	4156606	-0.7123	0.9336	0.9411	-0.6338	-0.7107
+chr11	4156658	-0.7125	0.9334	0.9414	-0.6337	-0.7108
+chr11	4156678	-0.7124	0.9335	0.9412	-0.6338	-0.7107
+chr11	4157061	-0.7159	1.0851	1.0835	-0.7163	-0.7164
+chr11	4157575	-0.7172	0.9675	0.9739	-0.6531	-0.7159
+chr11	4157625	-0.7124	0.9339	0.9416	-0.6342	-0.7108
+chr11	4157692	-0.7123	0.9332	0.941	-0.6338	-0.7107
+chr11	4157786	-0.7124	0.9338	0.9415	-0.6342	-0.7108
+chr11	4157829	-0.7125	0.9344	0.9421	-0.6345	-0.7109
+chr11	4157846	-0.712	0.9311	0.9389	-0.6327	-0.7104
+chr11	4158681	-0.7117	0.9288	0.9369	-0.6316	-0.71
+chr11	4159249	-0.7176	1.0827	1.0845	-0.7156	-0.7175
+chr11	4159512	-0.7124	0.9326	0.9407	-0.6341	-0.7108
+chr11	4159576	-0.7181	0.974	0.9804	-0.6574	-0.7169
+chr11	4160767	-0.7174	1.084	1.0858	-0.7164	-0.7173
+chr11	4161449	-0.7208	1.009	1.0136	-0.677	-0.72
+chr11	4163009	-0.7123	0.9296	0.9385	-0.6333	-0.7106
+chr11	4164110	-0.7171	1.0839	1.085	-0.7166	-0.7171
+chr11	4165583	-0.719	0.9823	0.9883	-0.6632	-0.7179
+chr11	4166188	-0.7173	1.0834	1.0848	-0.7165	-0.7173
+chr11	4169047	-0.7169	1.075	1.0725	-0.7124	-0.7176
+chr11	4169344	-0.7172	1.0836	1.085	-0.7169	-0.7172
+chr11	4173901	-0.7189	1.0782	1.0815	-0.7145	-0.7184
+chr11	4174384	-0.7174	1.0824	1.0838	-0.7165	-0.7174
+chr11	4177048	-0.7173	1.0818	1.0827	-0.7163	-0.7174
+chr11	4178320	-0.7127	0.932	0.9397	-0.637	-0.7111
+chr11	4178518	-0.7173	1.083	1.0843	-0.717	-0.7173
+chr11	4183635	-0.7212	1.0541	1.0574	-0.703	-0.7207
+chr11	4185242	-0.7173	1.0826	1.0836	-0.7172	-0.7174
+chr11	4209116	-0.7166	1.0819	1.0809	-0.717	-0.7171
+chr11	4211694	-0.7214	1.0487	1.0515	-0.7011	-0.7209
+chr11	4228604	-0.718	1.0783	1.0782	-0.7154	-0.718
+chr11	4229176	-0.7175	1.0824	1.0825	-0.7173	-0.7174
+chr11	4229195	-0.7173	1.0823	1.0821	-0.7173	-0.7173
+chr11	4230918	-0.7175	1.0814	1.0811	-0.7169	-0.7175
+chr11	4237235	-0.7217	1.0411	1.0425	-0.6978	-0.7212
+chr11	4238100	-0.7218	1.0417	1.0433	-0.6981	-0.7212
+chr11	4246351	-0.7189	1.0638	1.0612	-0.7087	-0.7193
+chr11	4246985	-0.7219	1.0396	1.041	-0.6971	-0.7212
+chr11	4261375	-0.7176	1.0824	1.0813	-0.7174	-0.7176
+chr11	4273327	-0.7175	1.0831	1.0711	-0.7175	-0.7175
+chr11	4283717	0.7233	-1.1344	0.391	0.7222	0.7241
+chr11	4284110	0.7062	-1.1375	0.5957	0.7058	0.7066
+chr11	4285090	0.7024	-1.0934	0.683	0.6975	0.7021
+chr11	4286016	0.6998	-1.1324	0.6815	0.699	0.6994
+chr11	4288936	0.7042	-1.0649	0.6806	0.6939	0.7021
+chr11	4301371	0.6999	-1.1332	0.6817	0.6989	0.6992
+chr11	4310171	0.6995	-1.1496	0.6833	0.6991	0.6993
+chr11	4330042	0.7035	-1.1568	0.6829	0.6965	0.7019
+chr11	4908477	-0.2937	-0.2945	-0.2933	-0.2939	-0.2938
+chr11	4941705	-0.2927	-0.289	-0.3024	-0.2936	-0.2913
+chr11	4944016	-0.2944	-0.2943	-0.2946	-0.2944	-0.2943
+chr11	4945582	-0.2944	-0.2943	-0.2946	-0.2944	-0.2943
+chr11	4949541	-0.2948	-0.2942	-0.294	-0.2943	-0.2945
+chr11	4971995	-0.2958	-0.2957	-0.2949	-0.2955	-0.2957
diff --git a/test-data/genotype1-without-reference.tsv b/test-data/genotype1-without-reference.tsv
new file mode 100644
index 0000000..c766ca5
--- /dev/null
+++ b/test-data/genotype1-without-reference.tsv
@@ -0,0 +1,101 @@
+chromosome	position	Q_CFW-SW/100.0g	Q_CFW-SW/100.0h	Q_CFW-SW/100.0i	Q_CFW-SW/100.0j	Q_CFW-SW/100.0l
+chr11	3200246	0.3836	0.3901	0.2411	-0.1418	0.3629
+chr11	3205355	0.3751	0.3806	0.2034	-0.1	0.3539
+chr11	3218908	0.3576	0.3449	0.1215	-0.0346	0.3294
+chr11	3414044	-0.2976	-0.339	1.0335	-0.2665	-0.3005
+chr11	3460427	-0.2791	-0.3456	1.3293	-0.2961	-0.3032
+chr11	3462290	-0.2841	-0.3331	1.3928	-0.2856	-0.3056
+chr11	3462323	-0.2832	-0.3357	1.3896	-0.2873	-0.3051
+chr11	3462325	-0.2835	-0.3349	1.3909	-0.2867	-0.3052
+chr11	3462348	-0.2864	-0.3279	1.4031	-0.2807	-0.3064
+chr11	3464016	-0.2805	-0.3413	1.3757	-0.2937	-0.3044
+chr11	3554197	0.2705	0.3409	-0.5622	0.3082	0.2896
+chr11	3558414	-0.286	-0.3239	0.5833	-0.2805	-0.2923
+chr11	3619052	-0.2508	-0.3166	0.2133	-0.3278	-0.2838
+chr11	3883306	-0.2504	-8e-04	-0.2199	-0.3104	-0.2247
+chr11	4017210	-0.3213	0.215	-0.3742	-0.396	-0.2641
+chr11	4017211	-0.3241	0.2125	-0.3624	-0.3916	-0.261
+chr11	4017223	-0.3373	0.2009	-0.3071	-0.3708	-0.2466
+chr11	4017385	-0.3236	0.2108	-0.3557	-0.3879	-0.2582
+chr11	4022004	-0.3259	0.2141	-0.3604	-0.3909	-0.2607
+chr11	4024616	-0.7083	-0.6358	2.9722	1.1229	0.7712
+chr11	4110988	0.7943	0.6125	-2.8791	-1.0382	-0.985
+chr11	4124677	0.795	0.6135	-2.7181	-0.9575	-0.9426
+chr11	4139413	-0.7216	-0.7119	2.8902	1.084	1.0653
+chr11	4139426	-0.717	-0.7172	2.8896	1.0862	1.0652
+chr11	4140742	-0.7173	-0.717	2.8881	1.0853	1.0651
+chr11	4141532	-0.7186	-0.7176	2.874	1.0776	1.0579
+chr11	4141701	-0.7172	-0.7169	2.889	1.0858	1.066
+chr11	4141949	-0.7187	-0.7176	2.8724	1.0767	1.0573
+chr11	4142088	-0.7176	-0.7181	2.8781	1.0802	1.0604
+chr11	4142629	-0.7174	-0.7169	2.8875	1.0849	1.0657
+chr11	4142987	-0.7213	-0.7178	2.7987	1.0385	1.0202
+chr11	4143502	-0.7177	-0.7167	2.8867	1.0844	1.0657
+chr11	4143779	-0.717	-0.7172	2.8885	1.0857	1.0669
+chr11	4143838	-0.7169	-0.7173	2.8888	1.0859	1.0671
+chr11	4143850	-0.7173	-0.7169	2.8879	1.0852	1.0666
+chr11	4144873	-0.7173	-0.7176	2.8836	1.0831	1.0648
+chr11	4146736	-0.7189	-0.7183	2.8629	1.072	1.0548
+chr11	4147532	-0.7187	-0.7177	2.8713	1.0763	1.0596
+chr11	4147579	-0.7181	-0.7177	2.8762	1.0791	1.0623
+chr11	4148004	-0.7169	-0.7174	2.8873	1.0853	1.0685
+chr11	4148006	-0.717	-0.7171	2.8882	1.0857	1.069
+chr11	4149618	-0.7171	-0.7172	2.8867	1.0848	1.069
+chr11	4151366	-0.7113	-0.7033	2.5804	0.9343	0.9214
+chr11	4151391	-0.7114	-0.7036	2.5826	0.9354	0.9224
+chr11	4151936	-0.7173	-0.7172	2.8854	1.0841	1.0697
+chr11	4156606	-0.7118	-0.7026	2.5788	0.9332	0.9265
+chr11	4156658	-0.7119	-0.7024	2.5786	0.9331	0.9265
+chr11	4156678	-0.7118	-0.7025	2.5787	0.9332	0.9266
+chr11	4157061	-0.716	-0.7183	2.8866	1.0854	1.0774
+chr11	4157575	-0.7168	-0.7093	2.6516	0.9672	0.962
+chr11	4157625	-0.7119	-0.7027	2.5796	0.9336	0.9288
+chr11	4157692	-0.7118	-0.7025	2.5781	0.9329	0.9282
+chr11	4157786	-0.7119	-0.7026	2.5793	0.9334	0.9289
+chr11	4157829	-0.712	-0.7027	2.5807	0.9341	0.9296
+chr11	4157846	-0.7115	-0.702	2.5735	0.9308	0.9264
+chr11	4158681	-0.7112	-0.7016	2.5687	0.9285	0.9257
+chr11	4159249	-0.7176	-0.7171	2.883	1.0827	1.0799
+chr11	4159512	-0.7119	-0.7025	2.5774	0.9325	0.9312
+chr11	4159576	-0.7177	-0.7105	2.6659	0.9739	0.9725
+chr11	4160767	-0.7174	-0.7169	2.8852	1.0839	1.0831
+chr11	4161449	-0.7205	-0.7157	2.7387	1.0089	1.0085
+chr11	4163009	-0.7118	-0.7017	2.5713	0.9295	0.9297
+chr11	4164110	-0.7171	-0.7173	2.885	1.084	1.0831
+chr11	4165583	-0.7187	-0.7121	2.6835	0.9822	0.9821
+chr11	4166188	-0.7173	-0.7172	2.884	1.0833	1.0827
+chr11	4169047	-0.7171	-0.7197	2.8675	1.0753	1.0742
+chr11	4169344	-0.7172	-0.7171	2.8844	1.0836	1.0833
+chr11	4173901	-0.7188	-0.7169	2.8749	1.078	1.0782
+chr11	4174384	-0.7174	-0.7173	2.8822	1.0824	1.0822
+chr11	4177048	-0.7173	-0.7176	2.881	1.0818	1.0816
+chr11	4178320	-0.7122	-0.7032	2.5766	0.9319	0.9332
+chr11	4178518	-0.7173	-0.7173	2.8834	1.083	1.0829
+chr11	4183635	-0.721	-0.7185	2.8293	1.0541	1.0546
+chr11	4185242	-0.7173	-0.7175	2.8825	1.0826	1.0825
+chr11	4209116	-0.7168	-0.7183	2.8809	1.0821	1.0817
+chr11	4211694	-0.7213	-0.7187	2.8188	1.0487	1.0497
+chr11	4228604	-0.718	-0.7179	2.8746	1.0783	1.0784
+chr11	4229176	-0.7175	-0.7173	2.8822	1.0824	1.0824
+chr11	4229195	-0.7173	-0.7175	2.882	1.0823	1.0823
+chr11	4230918	-0.7175	-0.7176	2.8804	1.0815	1.0827
+chr11	4237235	-0.7216	-0.7187	2.8039	1.0416	1.0465
+chr11	4238100	-0.7216	-0.7186	2.8051	1.0422	1.0474
+chr11	4246351	-0.719	-0.7199	2.847	1.0643	1.0699
+chr11	4246985	-0.7217	-0.7186	2.8009	1.0403	1.047
+chr11	4261375	-0.7176	-0.7173	2.8823	1.0823	1.0909
+chr11	4273327	-0.7175	-0.7176	2.8838	1.0832	1.0925
+chr11	4283717	0.7246	0.715	-2.9824	-1.1255	-1.1348
+chr11	4284110	0.7066	0.7038	-2.9797	-1.1346	-1.1381
+chr11	4285090	0.7022	0.7056	-2.8862	-1.1106	-1.0931
+chr11	4286016	0.6997	0.699	-2.9626	-1.133	-1.1317
+chr11	4288936	0.7037	0.7027	-2.8246	-1.0924	-1.064
+chr11	4301371	0.6998	0.698	-2.9638	-1.1331	-1.1326
+chr11	4310171	0.6995	0.7	-2.96	-1.1325	-1.1305
+chr11	4330042	0.7033	0.7023	-2.8717	-1.109	-1.0874
+chr11	4908477	-0.2937	-0.2943	-0.2937	-0.2939	-0.2945
+chr11	4941705	-0.2911	-0.293	-0.2925	-0.2917	-0.2893
+chr11	4944016	-0.2943	-0.2944	-0.2944	-0.2944	-0.2943
+chr11	4945582	-0.2944	-0.2944	-0.2944	-0.2944	-0.2943
+chr11	4949541	-0.295	-0.2941	-0.2947	-0.2946	-0.2942
+chr11	4971995	-0.296	-0.2954	-0.2957	-0.2957	-0.2957
diff --git a/test-data/genotype2-without-reference.tsv b/test-data/genotype2-without-reference.tsv
new file mode 100644
index 0000000..d237634
--- /dev/null
+++ b/test-data/genotype2-without-reference.tsv
@@ -0,0 +1,101 @@
+chromosome	position	Q_CFW-SW/100.0m	Q_CFW-SW/100.0n	Q_CFW-SW/100.0o	Q_CFW-SW/100.0p	Q_CFW-SW/100.0q
+chr11	3200246	-1.8435	0.3742	-0.5826	0.4141	-0.0555
+chr11	3205355	-1.9966	0.3681	-0.4778	0.4084	-0.0767
+chr11	3218908	-2.3341	0.3548	-0.2218	0.3769	-0.0873
+chr11	3414044	3.5125	-0.3327	-0.2604	-0.3458	0.239
+chr11	3460427	3.5493	-0.3261	-0.2861	-0.3472	0.051
+chr11	3462290	3.5419	-0.3303	-0.2974	-0.3477	0.0408
+chr11	3462323	3.542	-0.3294	-0.2953	-0.3476	0.0418
+chr11	3462325	3.5419	-0.3297	-0.296	-0.3476	0.0414
+chr11	3462348	3.541	-0.3318	-0.3018	-0.3476	0.0372
+chr11	3464016	3.543	-0.328	-0.2906	-0.3479	0.0464
+chr11	3554197	-3.4878	0.3228	0.3214	0.3396	0.017
+chr11	3558414	3.3617	-0.3305	-0.342	-0.3407	-0.0391
+chr11	3619052	1.7148	-0.3089	-0.3337	-0.3288	-0.0442
+chr11	3883306	0.2938	-0.3079	-0.2412	-0.3312	-0.2698
+chr11	4017210	0.2322	-0.3503	-0.2296	-0.405	-0.3226
+chr11	4017211	0.2295	-0.3533	-0.2325	-0.4005	-0.3256
+chr11	4017223	0.2171	-0.3669	-0.2459	-0.3794	-0.3394
+chr11	4017385	0.2295	-0.3526	-0.2317	-0.3968	-0.3258
+chr11	4022004	0.2282	-0.3548	-0.2332	-0.3998	-0.3266
+chr11	4024616	-0.7234	-0.733	-0.7373	1.1363	-0.723
+chr11	4110988	0.6983	0.8009	0.7614	-1.0441	0.7859
+chr11	4124677	0.705	0.7998	0.7611	-0.9601	0.7821
+chr11	4139413	-0.7167	-0.7218	-0.7196	1.0836	-0.721
+chr11	4139426	-0.7172	-0.717	-0.7171	1.0857	-0.717
+chr11	4140742	-0.7173	-0.7173	-0.7174	1.0848	-0.7173
+chr11	4141532	-0.7185	-0.7186	-0.7186	1.0771	-0.7184
+chr11	4141701	-0.7172	-0.7172	-0.7172	1.0853	-0.7172
+chr11	4141949	-0.7186	-0.7188	-0.7187	1.0762	-0.7185
+chr11	4142088	-0.7182	-0.7176	-0.7179	1.0796	-0.7176
+chr11	4142629	-0.7173	-0.7175	-0.7174	1.0844	-0.7174
+chr11	4142987	-0.7215	-0.7214	-0.7213	1.038	-0.7204
+chr11	4143502	-0.7173	-0.7177	-0.7176	1.0839	-0.7176
+chr11	4143779	-0.7172	-0.717	-0.7171	1.0852	-0.7171
+chr11	4143838	-0.7171	-0.7169	-0.717	1.0854	-0.717
+chr11	4143850	-0.7172	-0.7174	-0.7173	1.0847	-0.7173
+chr11	4144873	-0.7176	-0.7173	-0.7175	1.0827	-0.7173
+chr11	4146736	-0.7193	-0.7189	-0.719	1.0718	-0.7187
+chr11	4147532	-0.7186	-0.7187	-0.7187	1.0762	-0.7185
+chr11	4147579	-0.7183	-0.7181	-0.7182	1.079	-0.718
+chr11	4148004	-0.7172	-0.7169	-0.717	1.0853	-0.7169
+chr11	4148006	-0.7171	-0.717	-0.717	1.0857	-0.717
+chr11	4149618	-0.7172	-0.7171	-0.7172	1.0848	-0.7171
+chr11	4151366	-0.7123	-0.7116	-0.7114	0.9344	-0.709
+chr11	4151391	-0.7125	-0.7117	-0.7115	0.9355	-0.7091
+chr11	4151936	-0.7173	-0.7173	-0.7173	1.0841	-0.7172
+chr11	4156606	-0.7122	-0.7121	-0.7116	0.9333	-0.7095
+chr11	4156658	-0.7122	-0.7122	-0.7116	0.9332	-0.7096
+chr11	4156678	-0.7122	-0.7121	-0.7116	0.9333	-0.7095
+chr11	4157061	-0.7172	-0.716	-0.7165	1.0853	-0.7162
+chr11	4157575	-0.7171	-0.717	-0.7166	0.9673	-0.7149
+chr11	4157625	-0.7123	-0.7122	-0.7116	0.9337	-0.7096
+chr11	4157692	-0.7122	-0.7121	-0.7115	0.933	-0.7095
+chr11	4157786	-0.7122	-0.7122	-0.7116	0.9336	-0.7096
+chr11	4157829	-0.7124	-0.7123	-0.7117	0.9342	-0.7097
+chr11	4157846	-0.7118	-0.7117	-0.7112	0.9309	-0.7091
+chr11	4158681	-0.7115	-0.7114	-0.7109	0.9287	-0.7088
+chr11	4159249	-0.7174	-0.7176	-0.7175	1.0827	-0.7175
+chr11	4159512	-0.7122	-0.7122	-0.7116	0.9326	-0.7096
+chr11	4159576	-0.718	-0.7179	-0.7175	0.974	-0.7159
+chr11	4160767	-0.7172	-0.7174	-0.7173	1.0839	-0.7173
+chr11	4161449	-0.7209	-0.7207	-0.7204	1.009	-0.7193
+chr11	4163009	-0.7118	-0.7121	-0.7113	0.9296	-0.7094
+chr11	4164110	-0.7172	-0.7171	-0.7171	1.084	-0.7171
+chr11	4165583	-0.719	-0.7189	-0.7184	0.9823	-0.717
+chr11	4166188	-0.7173	-0.7173	-0.7173	1.0833	-0.7173
+chr11	4169047	-0.7188	-0.717	-0.7178	1.0753	-0.7171
+chr11	4169344	-0.7172	-0.7172	-0.7172	1.0836	-0.7172
+chr11	4173901	-0.718	-0.7188	-0.7184	1.078	-0.7186
+chr11	4174384	-0.7174	-0.7174	-0.7174	1.0824	-0.7174
+chr11	4177048	-0.7175	-0.7173	-0.7174	1.0818	-0.7173
+chr11	4178320	-0.7126	-0.7126	-0.7118	0.932	-0.7101
+chr11	4178518	-0.7173	-0.7173	-0.7173	1.083	-0.7173
+chr11	4183635	-0.7209	-0.7211	-0.7208	1.0541	-0.7205
+chr11	4185242	-0.7174	-0.7173	-0.7174	1.0826	-0.7173
+chr11	4209116	-0.7176	-0.7167	-0.7171	1.0821	-0.7169
+chr11	4211694	-0.7213	-0.7214	-0.721	1.0487	-0.7208
+chr11	4228604	-0.7181	-0.718	-0.718	1.0783	-0.7179
+chr11	4229176	-0.7174	-0.7175	-0.7174	1.0824	-0.7174
+chr11	4229195	-0.7174	-0.7173	-0.7173	1.0824	-0.7173
+chr11	4230918	-0.7176	-0.7175	-0.7175	1.0815	-0.7175
+chr11	4237235	-0.7217	-0.7217	-0.7213	1.0411	-0.7211
+chr11	4238100	-0.7216	-0.7218	-0.7213	1.0417	-0.7211
+chr11	4246351	-0.7202	-0.7191	-0.7194	1.0639	-0.719
+chr11	4246985	-0.7218	-0.7218	-0.7213	1.0395	-0.7212
+chr11	4261375	-0.7175	-0.7176	-0.7175	1.0823	-0.7176
+chr11	4273327	-0.7176	-0.7175	-0.7175	1.0828	-0.7175
+chr11	4283717	0.7251	0.722	0.7227	0.3988	0.7242
+chr11	4284110	0.7068	0.7058	0.7059	0.6075	0.7065
+chr11	4285090	0.7035	0.7028	0.7026	0.6985	0.7024
+chr11	4286016	0.6996	0.6997	0.6992	0.698	0.6996
+chr11	4288936	0.7039	0.704	0.7031	0.7012	0.7032
+chr11	4301371	0.6994	0.6997	0.699	0.6981	0.6996
+chr11	4310171	0.6997	0.6996	0.6991	0.6988	0.6995
+chr11	4330042	0.7035	0.7036	0.7021	0.7013	0.703
+chr11	4908477	-0.2937	3.3684	-0.2934	-0.2937	-0.2934
+chr11	4941705	-0.2991	3.3273	-0.3012	-0.2917	-0.3011
+chr11	4944016	-0.2945	3.3274	-0.2946	-0.2944	-0.2946
+chr11	4945582	-0.2945	3.3273	-0.2946	-0.2944	-0.2946
+chr11	4949541	-0.2934	3.3271	-0.2941	-0.295	-0.294
+chr11	4971995	-0.2948	3.3243	-0.295	-0.2959	-0.295
diff --git a/test-data/genotype3-without-reference.tsv b/test-data/genotype3-without-reference.tsv
new file mode 100644
index 0000000..177a626
--- /dev/null
+++ b/test-data/genotype3-without-reference.tsv
@@ -0,0 +1,101 @@
+chromosome	position	Q_CFW-SW/100.0r	Q_CFW-SW/10.0b	Q_CFW-SW/10.0c	Q_CFW-SW/10.0d	Q_CFW-SW/10.0f
+chr11	3200246	0.2733	0.408	0.388	-3.6091	0.381
+chr11	3205355	0.2807	0.3991	0.384	-3.5452	0.3728
+chr11	3218908	0.3071	0.3728	0.3672	-3.5468	0.3528
+chr11	3414044	-0.3538	-0.3239	-0.3452	3.6101	-0.3177
+chr11	3460427	-0.3419	-0.33	-0.3332	3.664	-0.3154
+chr11	3462290	-0.3514	-0.323	-0.343	3.6699	-0.3101
+chr11	3462323	-0.3495	-0.3244	-0.3411	3.6675	-0.3111
+chr11	3462325	-0.3501	-0.324	-0.3417	3.6682	-0.3108
+chr11	3462348	-0.3551	-0.32	-0.3469	3.6751	-0.3079
+chr11	3464016	-0.3455	-0.3279	-0.3369	3.6601	-0.3138
+chr11	3554197	0.3492	0.3396	0.3289	-3.5317	0.3086
+chr11	3558414	-0.3686	-0.3297	-0.3505	3.5287	-0.2993
+chr11	3619052	-0.3453	-0.3142	-0.3346	2.9131	-0.2884
+chr11	3883306	-0.3016	-0.2836	-0.2786	-0.2529	-0.3149
+chr11	4017210	-0.3643	-0.2958	-0.3026	-0.4183	-0.3808
+chr11	4017211	-0.3673	-0.2987	-0.3055	-0.4064	-0.3776
+chr11	4017223	-0.3812	-0.3125	-0.3194	-0.3509	-0.3623
+chr11	4017385	-0.3665	-0.2982	-0.3048	-0.3998	-0.3746
+chr11	4022004	-0.3692	-0.3	-0.307	-0.4045	-0.3774
+chr11	4024616	-0.7502	-0.7397	-0.7496	2.9891	0.8355
+chr11	4110988	0.7916	0.781	0.7821	-2.8836	-1.038
+chr11	4124677	0.7882	0.78	0.7807	-2.7205	-0.9568
+chr11	4139413	-0.721	-0.7207	-0.7207	2.8905	1.084
+chr11	4139426	-0.7171	-0.7171	-0.7171	2.8898	1.0862
+chr11	4140742	-0.7174	-0.7174	-0.7174	2.8883	1.0853
+chr11	4141532	-0.7187	-0.7187	-0.7187	2.8742	1.0776
+chr11	4141701	-0.7173	-0.7173	-0.7173	2.8892	1.0858
+chr11	4141949	-0.7188	-0.7188	-0.7188	2.8726	1.0768
+chr11	4142088	-0.7178	-0.7178	-0.7178	2.8783	1.0802
+chr11	4142629	-0.7175	-0.7174	-0.7174	2.8877	1.085
+chr11	4142987	-0.7216	-0.7215	-0.7216	2.7988	1.0386
+chr11	4143502	-0.7177	-0.7177	-0.7177	2.8869	1.0845
+chr11	4143779	-0.7171	-0.7171	-0.7171	2.8887	1.0858
+chr11	4143838	-0.717	-0.717	-0.717	2.889	1.086
+chr11	4143850	-0.7174	-0.7174	-0.7174	2.888	1.0853
+chr11	4144873	-0.7174	-0.7174	-0.7174	2.8838	1.0832
+chr11	4146736	-0.719	-0.719	-0.7191	2.863	1.072
+chr11	4147532	-0.7188	-0.7187	-0.7187	2.8714	1.0763
+chr11	4147579	-0.7182	-0.7182	-0.7182	2.8763	1.0791
+chr11	4148004	-0.717	-0.717	-0.717	2.8874	1.0853
+chr11	4148006	-0.717	-0.717	-0.717	2.8883	1.0857
+chr11	4149618	-0.7172	-0.7172	-0.7172	2.8868	1.0848
+chr11	4151366	-0.712	-0.7119	-0.712	2.5804	0.9343
+chr11	4151391	-0.7121	-0.712	-0.7121	2.5826	0.9353
+chr11	4151936	-0.7173	-0.7173	-0.7173	2.8854	1.0841
+chr11	4156606	-0.7124	-0.7123	-0.7123	2.5788	0.9332
+chr11	4156658	-0.7125	-0.7124	-0.7124	2.5786	0.9331
+chr11	4156678	-0.7124	-0.7123	-0.7124	2.5787	0.9332
+chr11	4157061	-0.7162	-0.7163	-0.7163	2.8866	1.0854
+chr11	4157575	-0.7172	-0.7172	-0.7172	2.6516	0.9672
+chr11	4157625	-0.7124	-0.7124	-0.7124	2.5796	0.9336
+chr11	4157692	-0.7124	-0.7123	-0.7123	2.5782	0.9329
+chr11	4157786	-0.7124	-0.7123	-0.7124	2.5793	0.9334
+chr11	4157829	-0.7126	-0.7125	-0.7125	2.5807	0.9341
+chr11	4157846	-0.712	-0.7119	-0.712	2.5736	0.9308
+chr11	4158681	-0.7117	-0.7116	-0.7117	2.5688	0.9285
+chr11	4159249	-0.7176	-0.7176	-0.7176	2.883	1.0827
+chr11	4159512	-0.7124	-0.7123	-0.7124	2.5774	0.9325
+chr11	4159576	-0.7181	-0.7181	-0.7181	2.6659	0.9739
+chr11	4160767	-0.7173	-0.7173	-0.7173	2.8852	1.0839
+chr11	4161449	-0.7209	-0.7208	-0.7209	2.7387	1.0089
+chr11	4163009	-0.7123	-0.7122	-0.7122	2.5713	0.9295
+chr11	4164110	-0.7171	-0.7171	-0.7171	2.885	1.084
+chr11	4165583	-0.7191	-0.719	-0.719	2.6835	0.9822
+chr11	4166188	-0.7173	-0.7173	-0.7173	2.884	1.0833
+chr11	4169047	-0.7173	-0.7174	-0.7174	2.8676	1.0753
+chr11	4169344	-0.7172	-0.7172	-0.7172	2.8844	1.0836
+chr11	4173901	-0.7187	-0.7186	-0.7186	2.8749	1.078
+chr11	4174384	-0.7174	-0.7174	-0.7174	2.8822	1.0824
+chr11	4177048	-0.7174	-0.7174	-0.7174	2.881	1.0818
+chr11	4178320	-0.7127	-0.7127	-0.7127	2.5766	0.9319
+chr11	4178518	-0.7173	-0.7173	-0.7173	2.8834	1.083
+chr11	4183635	-0.7211	-0.7211	-0.7211	2.8293	1.0541
+chr11	4185242	-0.7173	-0.7174	-0.7174	2.8825	1.0826
+chr11	4209116	-0.7169	-0.7169	-0.7169	2.8809	1.0821
+chr11	4211694	-0.7214	-0.7214	-0.7213	2.8188	1.0487
+chr11	4228604	-0.718	-0.718	-0.718	2.8746	1.0783
+chr11	4229176	-0.7174	-0.7174	-0.7174	2.8822	1.0824
+chr11	4229195	-0.7173	-0.7173	-0.7173	2.882	1.0824
+chr11	4230918	-0.7175	-0.7175	-0.7175	2.8804	1.0815
+chr11	4237235	-0.7217	-0.7217	-0.7217	2.8039	1.0411
+chr11	4238100	-0.7218	-0.7218	-0.7217	2.8051	1.0417
+chr11	4246351	-0.7193	-0.7193	-0.7193	2.847	1.064
+chr11	4246985	-0.7218	-0.7218	-0.7217	2.8009	1.0395
+chr11	4261375	-0.7176	-0.7176	-0.7176	2.8823	1.0823
+chr11	4273327	-0.7175	-0.7175	-0.7175	2.8839	1.0832
+chr11	4283717	0.7249	0.7253	0.7249	-2.9836	-1.1298
+chr11	4284110	0.7067	0.7068	0.7067	-2.9807	-1.1376
+chr11	4285090	0.7034	0.703	0.703	-2.8865	-1.0925
+chr11	4286016	0.6996	0.6997	0.6997	-2.9627	-1.1315
+chr11	4288936	0.704	0.704	0.7041	-2.8247	-1.061
+chr11	4301371	0.6994	0.6996	0.6996	-2.964	-1.1323
+chr11	4310171	0.6997	0.6996	0.6996	-2.9604	-1.1308
+chr11	4330042	0.7035	0.7036	0.7037	-2.8725	-1.0853
+chr11	4908477	3.3681	-0.2937	-0.2934	-0.2938	-0.2937
+chr11	4941705	3.3298	-0.2983	-0.2982	-0.2917	-0.2924
+chr11	4944016	3.3274	-0.2945	-0.2945	-0.2944	-0.2944
+chr11	4945582	3.3273	-0.2945	-0.2945	-0.2944	-0.2944
+chr11	4949541	3.3267	-0.2941	-0.2944	-0.2948	-0.2948
+chr11	4971995	3.3241	-0.2952	-0.2954	-0.2958	-0.2958
diff --git a/test-data/pool-test-summary1-without-reference b/test-data/pool-test-summary1-without-reference
new file mode 100644
index 0000000..5ea4287
--- /dev/null
+++ b/test-data/pool-test-summary1-without-reference
@@ -0,0 +1,5 @@
+# pyhegp summary file version 1
+# number-of-samples 10
+chromosome	position	mean	standard-deviation
+chr1	1	0	1
+chr2	19	2	3
diff --git a/test-data/pool-test-summary2-without-reference b/test-data/pool-test-summary2-without-reference
new file mode 100644
index 0000000..e0aede0
--- /dev/null
+++ b/test-data/pool-test-summary2-without-reference
@@ -0,0 +1,7 @@
+# pyhegp summary file version 1
+# number-of-samples 5
+chromosome	position	mean	standard-deviation
+chr1	1	0	1
+chr2	19	2	3
+chrX	21	4	5
+chrX	21	4	5
diff --git a/tests/test_pyhegp.py b/tests/test_pyhegp.py
index d119858..cdf3a7f 100644
--- a/tests/test_pyhegp.py
+++ b/tests/test_pyhegp.py
@@ -26,6 +26,7 @@ from hypothesis import given, strategies as st
 from hypothesis.extra.numpy import arrays, array_shapes
 import numpy as np
 import pandas as pd
+import pytest
 from pytest import approx
 
 from pyhegp.pyhegp import Stats, main, hegp_encrypt, hegp_decrypt, random_key, pool_stats, standardize, unstandardize, genotype_summary, encrypt_genotype, encrypt_phenotype, cat_genotype, cat_phenotype
@@ -52,12 +53,17 @@ def test_pool_stats(pools):
             and pooled_stats.std == approx(np.std(combined_pool, axis=0, ddof=1),
                                            rel=1e-6))
 
-def test_encrypt_command(tmp_path):
-    shutil.copy("test-data/encrypt-test-genotype.tsv", tmp_path)
-    ciphertext = tmp_path / "encrypt-test-genotype.tsv.hegp"
+@pytest.mark.parametrize("genotype_file,summary_file",
+                         [(Path("test-data/encrypt-test-genotype.tsv"),
+                           Path("test-data/encrypt-test-summary")),
+                          (Path("test-data/encrypt-test-genotype-without-reference.tsv"),
+                           Path("test-data/encrypt-test-summary-without-reference"))])
+def test_encrypt_command(tmp_path, genotype_file, summary_file):
+    shutil.copy(genotype_file, tmp_path)
+    ciphertext = tmp_path / f"{genotype_file.name}.hegp"
     result = CliRunner().invoke(main, ["encrypt",
-                                       "-s", "test-data/encrypt-test-summary",
-                                       str(tmp_path / "encrypt-test-genotype.tsv")])
+                                       "-s", summary_file,
+                                       str(tmp_path / genotype_file.name)])
     assert result.exit_code == 0
     assert ciphertext.exists()
     assert "Dropped 1 SNP(s)" in result.output
@@ -143,13 +149,17 @@ def test_encrypt_genotype_does_not_produce_na(genotype, key):
 def test_encrypt_phenotype_does_not_produce_na(phenotype, key):
     assert not encrypt_phenotype(phenotype, key).isna().any(axis=None)
 
-def test_pool_command(tmp_path):
+@pytest.mark.parametrize("summary_files",
+                         [[Path("test-data/pool-test-summary1"),
+                           Path("test-data/pool-test-summary2")],
+                          [Path("test-data/pool-test-summary1-without-reference"),
+                           Path("test-data/pool-test-summary2-without-reference")]])
+def test_pool_command(tmp_path, summary_files):
     columns = ["chromosome", "position", "reference", "mean", "std"]
     complete_summary = tmp_path / "complete-summary"
     result = CliRunner().invoke(main, ["pool",
                                        "-o", complete_summary,
-                                       "test-data/pool-test-summary1",
-                                       "test-data/pool-test-summary2"],
+                                       *(str(summary_file) for summary_file in summary_files)],
                                 catch_exceptions=True)
     assert result.exit_code == 0
     assert complete_summary.exists()
@@ -203,21 +213,33 @@ def test_cat_phenotype(phenotypes):
     pd.testing.assert_frame_equal(complete_phenotype,
                                   cat_phenotype(split_phenotypes))
 
-def test_simple_workflow(tmp_path):
-    shutil.copy(f"test-data/genotype.tsv", tmp_path)
-    ciphertext = tmp_path / "genotype.tsv.hegp"
+@pytest.mark.parametrize("genotype_file",
+                         [Path("test-data/genotype.tsv"),
+                          Path("test-data/genotype-without-reference.tsv")])
+def test_simple_workflow(tmp_path, genotype_file):
+    shutil.copy(genotype_file, tmp_path)
+    ciphertext = tmp_path / f"{genotype_file.name}.hegp"
     result = CliRunner().invoke(main,
-                                ["encrypt", str(tmp_path / "genotype.tsv")])
+                                ["encrypt", str(tmp_path / genotype_file.name)])
     assert result.exit_code == 0
     assert ciphertext.exists()
 
-def test_joint_workflow(tmp_path):
+@pytest.mark.parametrize("genotype_files",
+                         [[Path("test-data/genotype0.tsv"),
+                           Path("test-data/genotype1.tsv"),
+                           Path("test-data/genotype2.tsv"),
+                           Path("test-data/genotype3.tsv")],
+                          [Path("test-data/genotype0-without-reference.tsv"),
+                           Path("test-data/genotype1-without-reference.tsv"),
+                           Path("test-data/genotype2-without-reference.tsv"),
+                           Path("test-data/genotype3-without-reference.tsv")]])
+def test_joint_workflow(tmp_path, genotype_files):
     runner = CliRunner()
-    for i in range(4):
-        shutil.copy(f"test-data/genotype{i}.tsv", tmp_path)
-        summary = tmp_path / f"summary{i}"
+    for genotype_file in genotype_files:
+        shutil.copy(genotype_file, tmp_path)
+        summary = tmp_path / f"{genotype_file.name}.summary"
         result = runner.invoke(
-            main, ["summary", str(tmp_path / f"genotype{i}.tsv"),
+            main, ["summary", str(tmp_path / genotype_file.name),
                    "-o", summary])
         assert result.exit_code == 0
         assert summary.exists()
@@ -225,21 +247,23 @@ def test_joint_workflow(tmp_path):
     result = runner.invoke(
         main, ["pool",
                "-o", complete_summary,
-               *(str(tmp_path / f"summary{i}") for i in range(4))])
+               *(str(tmp_path / f"{genotype_file.name}.summary")
+                 for genotype_file in genotype_files)])
     assert result.exit_code == 0
     assert complete_summary.exists()
-    for i in range(4):
-        ciphertext = tmp_path / f"genotype{i}.tsv.hegp"
+    for genotype_file in genotype_files:
+        ciphertext = tmp_path / f"{genotype_file.name}.hegp"
         result = runner.invoke(
             main, ["encrypt",
                    "-s", complete_summary,
-                   str(tmp_path / f"genotype{i}.tsv")])
+                   str(tmp_path / f"{genotype_file.name}")])
         assert result.exit_code == 0
         assert ciphertext.exists()
     complete_ciphertext = tmp_path / "complete-genotype.tsv.hegp"
     result = runner.invoke(
         main, ["cat-genotype",
                "-o", complete_ciphertext,
-               *(str(tmp_path / f"genotype{i}.tsv.hegp") for i in range(4))])
+               *(str(tmp_path / f"{genotype_file.name}.hegp")
+                 for genotype_file in genotype_files)])
     assert result.exit_code == 0
     assert complete_ciphertext.exists()