feat: Ingestion of CSI-indexed VCF files

pixy/core.py

@@ -1004,9 +1004,9 @@ def check_and_validate_args(
             '[pixy] ERROR: The vcf is not compressed with bgzip (or has no .gz extension). To fix this, run "bgzip [filename].vcf" first (and then index with "tabix [filename].vcf.gz" if necessary)'
         )
 
-    if not os.path.exists(args.vcf + ".tbi"):
+    if not (os.path.exists(args.vcf + ".tbi") or os.path.exists(args.vcf + ".csi")):
         raise Exception(
-            '[pixy] ERROR: The vcf is not indexed with tabix. To fix this, run "tabix [filename].vcf.gz" first'
+            '[pixy] ERROR: The vcf is not indexed. Please either use `tabix` or `bcftools` to produce a `.tbi` or `.csi` index.'
         )
 
     if os.path.exists(args.populations) is not True:

tests/conftest.py

@@ -58,6 +58,12 @@ def ag1000_vcf_path(datadir: Path) -> Path:
     return datadir / "ag1000_pixy_test.vcf.gz"
 
 
+@pytest.fixture()
+def ag1000_csi_path(datadir: Path) -> Path:
+    """Path to ag1000 VCF CSI index."""
+    return datadir / "ag1000_pixy_test.vcf.gz.csi"
+
+
 @pytest.fixture()
 def missing50_vcf_path(datadir: Path) -> Path:
     """Path to a simulated VCF that is known to be missing a small number of genotypes."""

tests/main/test_main.py

@@ -94,7 +94,7 @@ def test_vcf_missing_index(
     """Assert that we raise an exception when missing .tbi index."""
     missing_index_vcf_path: Path = tmp_path / "ag1000_pixy_test.vcf.gz"
     shutil.copy(ag1000_vcf_path, missing_index_vcf_path)
-    with pytest.raises(Exception, match="ERROR: The vcf is not indexed with tabix"):
+    with pytest.raises(Exception, match="ERROR: The vcf is not indexed."):
         run_pixy_helper(
             pixy_out_dir=pixy_out_dir,
             stats=["pi", "fst", "dxy"],
@@ -351,6 +351,59 @@ def test_bypass_invariant_check_warns(
 # Tests for pixy.main(): valid inputs and expected results
 ################################################################################
 
+#############################
+# Tests for VCF file indexes
+#############################
+
+
+def test_pixy_csi_index(
+    tmp_path: Path,
+    ag1000_pop_path: Path,
+    ag1000_vcf_path: Path,
+    ag1000_csi_path: Path,
+    pixy_out_dir: Path,
+    expected_outputs: Path,
+) -> None:
+    """
+    Assert that a VCF can have either a `.tbi` or a `.csi` index with valid inputs.
+
+    The outputs with a `.csi` index should match the outputs of the `.tbi` index.
+
+    NB, we copy `ag1000_pixy_test.vcf.gz` and `ag1000_pixy_test.vcf.gz.csi` into a clean directory
+    so that we can be confident there is no interference from the pre-existing `.tbi` file.
+    """
+    vcf_path: Path = tmp_path / "ag1000_pixy_test.vcf.gz"
+    csi_path: Path = tmp_path / "ag1000_pixy_test.vcf.gz.csi"
+    shutil.copy(ag1000_vcf_path, vcf_path)
+    shutil.copy(ag1000_csi_path, csi_path)
+
+    run_pixy_helper(
+        pixy_out_dir=pixy_out_dir,
+        window_size=10000,
+        vcf_path=vcf_path,
+        populations_path=ag1000_pop_path,
+        stats=["pi", "dxy", "fst"],
+        output_prefix="pixy",
+    )
+
+    expected_out_files: List[Path] = [
+        Path("pixy_dxy.txt"),
+        Path("pixy_fst.txt"),
+        Path("pixy_pi.txt"),
+    ]
+    # this run of `pixy` should match the run using the same inputs and a `.tbi` index
+    for file in expected_out_files:
+        generated_data_path: Path = pixy_out_dir / file
+        exp_data_path: Path = expected_outputs / "baseline" / file
+        assert generated_data_path.exists()
+
+        assert filecmp.cmp(generated_data_path, exp_data_path)
+
+
+#######################################
+# Tests for output formatting/creation
+#######################################
+
 
 @pytest.mark.parametrize(
     "output_prefix, stats_requested, expected_files",