genoray-cli 0.1.2__tar.gz → 0.2.0__tar.gz

{genoray_cli-0.1.2 → genoray_cli-0.2.0}/CHANGELOG.md

@@ -1,3 +1,9 @@
+## 0.2.0 (2026-02-04)
+
+### Feat
+
+- specifying number of threads. fix(perf): write PGEN index without loading it entirely
+
 ## 0.1.2 (2025-11-18)
 
 ### Fix

{genoray_cli-0.1.2 → genoray_cli-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genoray-cli
-Version: 0.1.2
+Version: 0.2.0
 Summary: Command line interface for genoray
 Author-email: David Laub <dlaub@ucsd.edu>
 License: MIT License
@@ -25,9 +25,9 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Requires-Python: <3.13,>=3.9
+Requires-Python: <3.14,>=3.10
 Requires-Dist: cyclopts
-Requires-Dist: genoray
+Requires-Dist: genoray>=2.1.0
 Description-Content-Type: text/markdown
 
 # genoray-cli

{genoray_cli-0.1.2 → genoray_cli-0.2.0}/genoray_cli/__main__.py

@@ -19,7 +19,8 @@ app = App(
 @app.command
 def index(source: Path):
     """Create a genoray index for a VCF or PGEN file."""
-    from genoray import PGEN, VCF
+    from genoray import VCF
+    from genoray._pgen import _write_index
     from genoray._utils import variant_file_type
 
     file_type = variant_file_type(source)
@@ -27,7 +28,16 @@ def index(source: Path):
         vcf = VCF(source)
         vcf._write_gvi_index()
     elif file_type == "pgen":
-        _ = PGEN(source)
+        index = source.with_suffix(".pvar")
+
+        if not index.exists():
+            index = source.with_suffix(".pvar.zst")
+
+        if not index.exists():
+            raise FileNotFoundError("No index file found.")
+
+        index = index.with_suffix(f"{index.suffix}.gvi")
+        _write_index(index)
     else:
         raise ValueError(f"Unsupported file type: {source}")
 
@@ -39,6 +49,7 @@ def write(
     max_mem: str = "1g",
     overwrite: bool = False,
     dosages: Union[str, None] = None,
+    threads: int | None = None,
 ) -> None:
     """
     Convert a VCF or PGEN file to a SVAR file.
@@ -58,6 +69,8 @@ def write(
         If `source` is a PGEN, this must be a path to a PGEN of dosages.
         If `source` is a VCF, this must be the name of the FORMAT field to use for dosages.
         If not provided, dosages will not be written.
+    threads
+        Number of threads to use for conversion. Defaults to the number of available CPU cores.
     """
     from genoray import PGEN, VCF, SparseVar
     from genoray._utils import variant_file_type
@@ -69,6 +82,9 @@ def write(
     else:
         with_dosages = True
 
+    if threads is None:
+        threads = -1
+
     if file_type == "vcf":
         if dosages is not None and Path(dosages).exists():
             raise ValueError(
@@ -76,10 +92,14 @@ def write(
             )
 
         vcf = VCF(source, dosage_field=dosages)
-        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=with_dosages)
+        SparseVar.from_vcf(
+            out, vcf, max_mem, overwrite, with_dosages=with_dosages, n_jobs=threads
+        )
     elif file_type == "pgen":
         pgen = PGEN(source, dosage_path=dosages)
-        SparseVar.from_pgen(out, pgen, max_mem, overwrite, with_dosages=with_dosages)
+        SparseVar.from_pgen(
+            out, pgen, max_mem, overwrite, with_dosages=with_dosages, n_jobs=threads
+        )
     else:
         raise ValueError(f"Unsupported file type: {source}")