sai-pg 1.0.1__py3-none-any.whl → 1.1.0__py3-none-any.whl

sai_pg-1.1.0.dist-info/RECORD

@@ -0,0 +1,70 @@
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+sai/configs/pop_config.py,sha256=p_JUMN-UYSdIkaPLjoEQD620Y36JkmLVRX-_TeJaG7c,2659
+sai/configs/stat_config.py,sha256=WbHiGvDm6o1m6uEWXQ9sJfeqQUZiRFOgfNrcNeKO4H0,8037
+sai/generators/__init__.py,sha256=hpE4PUQIOZQXzdpSx7dEllecDoOfxIWXNu1-WHa_VcM,858
+sai/generators/chunk_generator.py,sha256=wL4ZX1yqFpCnQjQF4Wds5Gewo29VE4fG-UkSaGh8TUs,4313
+sai/generators/data_generator.py,sha256=bVz9KPjJSL4becTsVZ-zH4i40y5UDA0JJOtzbwf5n84,1635
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+sai/parsers/outlier_parser.py,sha256=tQomTsQ16Fqimuw97vbTX3_N2yl5lGRZRrBbF1hALV8,2403
+sai/parsers/score_parser.py,sha256=eAKqSluXJlLm5-k-7H6dU3bD-RUsubSjqD3I9NKl5AU,4429
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+sai/stats/danc_statistic.py,sha256=peMn4nUdek6sksyYJkzxusnsXdIYsYyx8IC2vJWya-s,2878
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+sai/stats/dplus_statistic.py,sha256=7WUm-h0MY2P-VhIxKaVfRRFEJmGNufAbjMEWkOpEdfo,3202
+sai/stats/fd_statistic.py,sha256=_uapDkTrpp4xXfOE_qNVTsludtYsk7wEYdHqZcFsC60,3360
+sai/stats/generic_statistic.py,sha256=YMG7P7fTgq6_fC8anziJHYZWgLvLvXSzGcP0SarWhz4,3409
+sai/stats/q_statistic.py,sha256=N1oLZxuu6TxdP_2RlnzfwXCNAhKV1woCVJYWBDOpxHA,4382
+sai/stats/stat_utils.py,sha256=NrukP7mZC3GUr6psSVdoK2Adc6U_7Eynv5BnRbNwWc0,9385
+sai/stats/u_statistic.py,sha256=ezMrUtD2KLej2nTCH4kI_IzH3Z3acNX9WoyUtAYRWgU,3956
+sai/utils/__init__.py,sha256=B3ZcC1ALSWieGHPiqXKBFQRTrnlTX4TaHc3tCx9fj0w,782
+sai/utils/genomic_dataclasses.py,sha256=HBYp2dehdW_y3Pd6Un8XFMnN1Odg1EiZb9ci1syIibU,1443
+sai/utils/utils.py,sha256=DggdghqERdK_bqb-dxX0kGvlqdS89QdOUwBWZxScxDk,25445
+sai_pg-1.1.0.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+tests/test___main__.py,sha256=b9-O8rzeYJSsnpO0pjxk8ftfshji0VMq7l34T2DdBw8,1913
+tests/test_sai.py,sha256=Q544XurG5wRZqVPlQ8EOKX05UceKl5EYPuV7i8RIHzA,3042
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+tests/configs/test_ploidy_config.py,sha256=KbWNYQUNYZdRsDgkpk-d2Fm3Ip8Zy57KBmE6_xWMgVQ,2609
+tests/configs/test_pop_config.py,sha256=pu7FXFE17x1uH9HLDScQ0XcztIS-tS7mcvm9tWTa3zc,2670
+tests/configs/test_stat_config.py,sha256=BWBYGMjegC1bh83acmg5X3UpCiYI4dT_G9Z_OWzZL9Q,4868
+tests/generators/test_chunk_generator.py,sha256=V6cFufLcKmsAp9krTNPR3yaQWA6rM-G3HYY0O3wsTx4,1583
+tests/generators/test_window_generator.py,sha256=tp-OUc3ROi-wx6c6V39cXH3quneOZOekllzN-1xTMR0,5756
+tests/multiprocessing/test_mp_manager.py,sha256=KYd3MVDPw3egw_mQ2jy9s3_VuJ-uxHfHKoatkxKoi00,2706
+tests/multiprocessing/test_mp_pool.py,sha256=oCIC_BrKsgVpXevFyZ92sSU6SwVLa-jFEZZVg8nIMMk,2261
+tests/parsers/test_argument_validation.py,sha256=Q2WDGxDWjHM3-cJrtjzGGwm2qdI-kFHxU5f1_OFHGW0,4184
+tests/parsers/test_outlier_parser.py,sha256=0_wWIRMQ4qJRKuGfCNkukZrWg9sP6dqzAuMXMYyM6DM,1642
+tests/parsers/test_score_parser.py,sha256=-potixrJhMBm7pIf7R4WFQmdKv6s3wV_7rICO1sj6M4,1921
+tests/preprocessors/test_chunk_preprocessor.py,sha256=AAQBSN5KH3huXoSi-KvKouV839GbTjDfy29rIUz8qi0,2557
+tests/preprocessors/test_feature_preprocessor.py,sha256=nIncvpPJEr88iAPRhv0teL2mqirrZLgjeIA1LPSARmQ,6743
+tests/registries/test_registries.py,sha256=UPMj2tH435AprUBdFW767g77yj2kztchFHiVJvW8SUM,1710
+tests/stats/test_danc_statistic.py,sha256=WOA8GK3FvwWT9wD50v9BMLGc_gi7tGI1u5oRflW69i8,1643
+tests/stats/test_dd_statistic.py,sha256=yhBdTQyCdYcQse_DrAEaK-OPAitCG99KGDcyDSr4Xzs,1356
+tests/stats/test_df_statistic.py,sha256=kJi58bUs5QQGsS7Z2AmTv4ukrHjaGXHwXcjehOxFOqM,2246
+tests/stats/test_dplus_statistic.py,sha256=vIm7DjUZLZMsUWZj1qaV_AyRTnA7r5bjEtiHMoxLzXs,2476
+tests/stats/test_fd_statistic.py,sha256=jq7DGTlHbaIkCEA6KLrUV0vH4Th0gumoKUFWAM15vV8,2042
+tests/stats/test_q_statistic.py,sha256=b-YC66aA_NMNXOXlnot3vU_Lc9z0WGP19YJLp6MCcUc,7943
+tests/stats/test_stat_utils.py,sha256=n4nNCuiG79LOsk7mnpQPbivjgF9vnlWxEdzpJRjCZu0,10646
+tests/stats/test_u_statistic.py,sha256=V_vejLUCKIlFsVtOUEROwNoqNXO7x8rHaxJX0fyGssA,6659
+tests/utils/test_utils.py,sha256=yaoCuDYIqC4mFaJISZ8Juhze2NhUfRSQkGJBBlIJtxg,15673
+sai_pg-1.1.0.dist-info/METADATA,sha256=DG6BjlA--aZsetXCZVEZbny_vXCIoW7NtQrJLwgiMHI,1581
+sai_pg-1.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sai_pg-1.1.0.dist-info/entry_points.txt,sha256=uK34frE2UhEDNa5ISbGOtjF2HGAXF5uG_EgMocesEPs,42
+sai_pg-1.1.0.dist-info/top_level.txt,sha256=8-AsrbtORPvVD9w1Is6vyxKgJBuuYNrwii1UNi-8Lr4,10
+sai_pg-1.1.0.dist-info/RECORD,,

{sai_pg-1.0.1.dist-info → sai_pg-1.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

sai_pg-1.1.0.dist-info/top_level.txt

@@ -0,0 +1,2 @@
+sai
+tests

tests/configs/test_global_config.py

@@ -0,0 +1,163 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import pytest
+from sai.configs.global_config import GlobalConfig
+from sai.configs.stat_config import StatConfig
+from sai.configs.ploidy_config import PloidyConfig
+from sai.configs.pop_config import PopConfig
+
+
+def test_global_config_valid(tmp_path):
+    ref_file = tmp_path / "ref.txt"
+    tgt_file = tmp_path / "tgt.txt"
+    src_file = tmp_path / "src.txt"
+
+    ref_file.write_text("popA sample1\npopA sample2")
+    tgt_file.write_text("popB sample3\npopB sample4")
+    src_file.write_text("popC sample5\npopC sample6")
+
+    stat_cfg = StatConfig.model_validate(
+        {
+            "Q": {
+                "ref": {"popA": 0.3},
+                "tgt": {"popB": 0.95},
+                "src": {"popC": "=1"},
+            }
+        }
+    )
+
+    ploidy_cfg = PloidyConfig.model_validate(
+        {
+            "ref": {"popA": 2},
+            "tgt": {"popB": 2},
+            "src": {"popC": 2},
+        }
+    )
+
+    pop_cfg = PopConfig.model_validate(
+        {
+            "ref": str(ref_file),
+            "tgt": str(tgt_file),
+            "src": str(src_file),
+        }
+    )
+
+    global_cfg = GlobalConfig(
+        statistics=stat_cfg,
+        ploidies=ploidy_cfg,
+        populations=pop_cfg,
+    )
+
+    assert global_cfg.statistics.get_parameters("Q")["ref"]["popA"] == 0.3
+    assert global_cfg.ploidies.get_ploidy("ref", "popA") == 2
+    assert global_cfg.populations.get_population("ref") == str(ref_file)
+
+
+def test_global_config_invalid_ploidy(tmp_path):
+    ref_file = tmp_path / "ref.txt"
+    tgt_file = tmp_path / "tgt.txt"
+    src_file = tmp_path / "src.txt"
+
+    ref_file.write_text("popA sample1\npopA sample2")
+    tgt_file.write_text("popB sample3\npopB sample4")
+    src_file.write_text("popC sample5\npopC sample6")
+
+    stat_cfg = StatConfig.model_validate(
+        {
+            "Q": {
+                "ref": {"popA": 0.3},
+                "tgt": {"popB": 0.95},
+                "src": {"popC": "=1"},
+            }
+        }
+    )
+
+    ploidy_cfg = PloidyConfig.model_validate(
+        {
+            "ref": {"popA": 2},
+            "tgt": {"popD": 2},
+            "src": {"popC": 2},
+        }
+    )
+
+    pop_cfg = PopConfig.model_validate(
+        {
+            "ref": str(ref_file),
+            "tgt": str(tgt_file),
+            "src": str(src_file),
+        }
+    )
+
+    with pytest.raises(
+        ValueError,
+        match=r"Population 'popB' used in statistics\[Q\]\[tgt\] is not defined in ploidies\[tgt\]",
+    ):
+        GlobalConfig(
+            statistics=stat_cfg,
+            ploidies=ploidy_cfg,
+            populations=pop_cfg,
+        )
+
+
+def test_global_config_invalid_population(tmp_path):
+    ref_file = tmp_path / "ref.txt"
+    tgt_file = tmp_path / "tgt.txt"
+    src_file = tmp_path / "src.txt"
+
+    ref_file.write_text("popA sample1\npopA sample2")
+    tgt_file.write_text("popD sample3\npopD sample4")
+    src_file.write_text("popC sample5\npopC sample6")
+
+    stat_cfg = StatConfig.model_validate(
+        {
+            "Q": {
+                "ref": {"popA": 0.3},
+                "tgt": {"popB": 0.95},
+                "src": {"popC": "=1"},
+            }
+        }
+    )
+
+    ploidy_cfg = PloidyConfig.model_validate(
+        {
+            "ref": {"popA": 2},
+            "tgt": {"popB": 2},
+            "src": {"popC": 2},
+        }
+    )
+
+    pop_cfg = PopConfig.model_validate(
+        {
+            "ref": str(ref_file),
+            "tgt": str(tgt_file),
+            "src": str(src_file),
+        }
+    )
+
+    with pytest.raises(
+        ValueError,
+        match=r"Population 'popB' used in statistics\[Q\]\[tgt\] is not found in the population file for group 'tgt'",
+    ):
+        GlobalConfig(
+            statistics=stat_cfg,
+            ploidies=ploidy_cfg,
+            populations=pop_cfg,
+        )

tests/configs/test_ploidy_config.py

@@ -0,0 +1,93 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import pytest
+from pydantic import ValidationError
+from sai.configs import PloidyConfig
+
+
+def test_valid_config():
+    config = PloidyConfig(
+        {
+            "ref": {"popA": 2},
+            "tgt": {"popB": 2},
+            "src": {"popC": 2, "popD": 4},
+            "outgroup": {"popE": 1},
+        }
+    )
+    assert config.get_ploidy("ref", "popA") == 2
+    assert config.get_ploidy("src", "popD") == 4
+
+
+def test_missing_required_keys():
+    with pytest.raises(ValidationError, match="Missing required ploidy keys"):
+        PloidyConfig(
+            {
+                "ref": {"popA": 2},
+                "src": {"popC": 2},
+            }
+        )
+
+
+def test_extra_keys():
+    with pytest.raises(ValidationError, match="Unsupported ploidy keys"):
+        PloidyConfig(
+            {
+                "ref": {"popA": 2},
+                "tgt": {"popB": 2},
+                "src": {"popC": 2},
+                "badkey": {"popD": 3},
+            }
+        )
+
+
+def test_invalid_ploidy_values():
+    with pytest.raises(ValidationError, match="must be a positive integer"):
+        PloidyConfig(
+            {
+                "ref": {"popA": 2},
+                "tgt": {"popB": 0},
+                "src": {"popC": 1},
+                "outgroup": {"popD": 1},
+            }
+        )
+
+    with pytest.raises(ValidationError, match="must be a positive integer"):
+        PloidyConfig(
+            {
+                "ref": {"popA": 2},
+                "tgt": {"popB": 2},
+                "src": {"popC": -2, "popD": -3},
+                "outgroup": {"popE": 1},
+            }
+        )
+
+
+def test_get_ploidy_key_error():
+    config = PloidyConfig(
+        {
+            "ref": {"popA": 2},
+            "tgt": {"popB": 2},
+            "src": {"popC": 2},
+            "outgroup": {"popD": 1},
+        }
+    )
+    with pytest.raises(KeyError):
+        config.get_ploidy("ghost", "popE")

tests/configs/test_pop_config.py

@@ -0,0 +1,90 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import tempfile
+import os
+import pytest
+from sai.configs import PopConfig
+
+
+@pytest.fixture
+def temp_files():
+    files = {}
+    for key in ["ref", "tgt", "src", "outgroup"]:
+        f = tempfile.NamedTemporaryFile(delete=False)
+        f.write(b"sample1\nsample2\n")
+        f.close()
+        files[key] = f.name
+    yield files
+    for path in files.values():
+        os.unlink(path)
+
+
+def test_valid_pop_config_with_outgroup(temp_files):
+    config = PopConfig(
+        {
+            "ref": temp_files["ref"],
+            "tgt": temp_files["tgt"],
+            "src": temp_files["src"],
+            "outgroup": temp_files["outgroup"],
+        }
+    )
+    assert config.get_population("ref") == temp_files["ref"]
+    assert config.get_population("outgroup") == temp_files["outgroup"]
+
+
+def test_valid_pop_config_without_outgroup(temp_files):
+    config = PopConfig(
+        {
+            "ref": temp_files["ref"],
+            "tgt": temp_files["tgt"],
+            "src": temp_files["src"],
+        }
+    )
+    assert config.get_population("tgt") == temp_files["tgt"]
+    assert config.get_population("outgroup") is None
+
+
+def test_missing_required_key(temp_files):
+    with pytest.raises(ValueError, match="Missing required population keys"):
+        PopConfig({"ref": temp_files["ref"], "src": temp_files["src"]})
+
+
+def test_invalid_extra_key(temp_files):
+    with pytest.raises(ValueError, match="Unsupported population keys"):
+        PopConfig(
+            {
+                "ref": temp_files["ref"],
+                "tgt": temp_files["tgt"],
+                "src": temp_files["src"],
+                "ghost": temp_files["outgroup"],
+            }
+        )
+
+
+def test_file_not_exist():
+    with pytest.raises(ValueError, match="does not exist"):
+        PopConfig(
+            {
+                "ref": "/non/existent/path",
+                "tgt": "/non/existent/path",
+                "src": "/non/existent/path",
+            }
+        )

tests/configs/test_stat_config.py

@@ -0,0 +1,171 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import pytest
+import yaml
+from sai.configs import StatConfig
+
+
+def test_stat_config_valid():
+    config = StatConfig(
+        {
+            "U": {
+                "ref": {"popA": 0.01},
+                "tgt": {"popB": 0.5},
+                "src": {"Nea": "=1", "Den": ">0.8"},
+            },
+            "Q": {
+                "ref": {"popA": 0.01},
+                "tgt": {"popB": 0.95},
+                "src": {"Nea": ">0.2", "Den": "<0.8"},
+            },
+            "fd": {},  # No parameters
+            "df": {},  # No parameters
+        }
+    )
+
+    # Test valid configuration
+    assert config.get_parameters("U") == {
+        "ref": {"popA": 0.01},
+        "tgt": {"popB": 0.5},
+        "src": {"Nea": ("=", 1.0), "Den": (">", 0.8)},
+    }
+
+    assert config.get_parameters("Q") == {
+        "ref": {"popA": 0.01},
+        "tgt": {"popB": 0.95},
+        "src": {"Nea": (">", 0.2), "Den": ("<", 0.8)},
+    }
+    assert config.get_parameters("fd") == {}
+    assert config.get_parameters("df") == {}
+
+
+def test_stat_config_invalid():
+    # Test unsupported statistics
+    with pytest.raises(ValueError):
+        StatConfig({"qq": {}})
+
+    # Test invalid src format (not a list)
+    with pytest.raises(ValueError):
+        StatConfig(
+            {"U": {"ref": "0.01", "tgt": "0.5", "src": "=1"}}  # src should be a list
+        )
+
+    # Test out-of-range numeric values for 'ref'
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": -0.1, "tgt": 0.5, "src": ["=1", ">0.8"]},
+            }
+        )
+
+    # Test out-of-range numeric values for 'tgt'
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": 0.01, "tgt": -100, "src": ["=1", ">0.8"]},
+            }
+        )
+
+    # Test out-of-range numeric values for 'src'
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": 0.01, "tgt": 0.5, "src": ["=-1", ">0.8"]},
+            }
+        )
+
+    # Test non-numeric string values for 'ref'
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": "foo", "tgt": 0.5, "src": ["=1", ">0.8"]},
+            }
+        )
+
+    # Test non-numeric string values for 'tgt'
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": 0.01, "tgt": "foo", "src": ["=1", ">0.8"]},
+            }
+        )
+
+    # Test non-numeric string values after comparator
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "U": {"ref": 0.01, "tgt": 0.5, "src": ["=invalid", ">0.8"]},
+            }
+        )
+
+    # Test missing ref, tgt, src in U and Q statistics
+    with pytest.raises(ValueError):
+        StatConfig({"U": {"ref": "0.01", "tgt": "0.5"}})  # src is missing
+
+    with pytest.raises(ValueError):
+        StatConfig({"Q": {}})
+
+    # Test invalid src comparator (invalid value)
+    with pytest.raises(ValueError):
+        StatConfig(
+            {
+                "Q": {
+                    "ref": "0.01",
+                    "tgt": "0.95",
+                    "src": ["invalid_value"],
+                }
+            }
+        )
+
+
+def test_stat_config_from_file():
+    with open("tests/data/test_config.yaml", "r") as f:
+        data = yaml.safe_load(f)
+
+    stat_config = StatConfig(data["statistics"])
+
+    stat_names = list(stat_config.root.keys())
+    assert "U" in stat_names
+    assert "Q" in stat_names
+
+    u_params = stat_config.get_parameters("U")
+    assert u_params == {
+        "ref": {"popA": 0.01},
+        "tgt": {"popB": 0.5},
+        "src": {"Nea": ("=", 1), "Den": (">=", 0.8)},
+    }
+
+    q_params = stat_config.get_parameters("Q")
+    assert q_params == {
+        "ref": {"popA": 0.01},
+        "tgt": {"popB": 0.95},
+        "src": {"Nea": (">", 0.2), "Den": ("<=", 0.8)},
+    }
+
+    assert "ref" in u_params
+    assert "tgt" in u_params
+    assert "src" in u_params
+
+    with open("tests/data/test_invalid_stat_config.yaml", "r") as f:
+        invalid_data = yaml.safe_load(f)
+
+    with pytest.raises(ValueError):
+        StatConfig(statistics=invalid_data["statistics"])

tests/generators/test_chunk_generator.py

@@ -0,0 +1,51 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import pytest
+from sai.generators import ChunkGenerator
+
+
+def test_chunk_generator():
+    # Initialize
+    generator = ChunkGenerator(
+        vcf_file="tests/data/test.data.vcf",
+        chr_name="21",
+        step_size=5000,
+        window_size=10000,
+        num_chunks=2,
+    )
+
+    # Check that length is calculated properly (mocked to 3 records)
+    assert len(generator) == 2  # num_workers
+
+    # Check that chunks were split correctly
+    expected_chunks = [(1, 30000), (25001, 55000)]
+    assert generator.chunks == expected_chunks
+
+
+def test_chunk_generator_chr_not_found():
+    with pytest.raises(ValueError, match="Chromosome 1 not found in VCF."):
+        ChunkGenerator(
+            vcf_file="tests/data/test.data.vcf",
+            chr_name="1",
+            step_size=10000,
+            window_size=10000,
+            num_chunks=2,
+        )