genoray-cli 0.1.0__tar.gz → 0.1.1__tar.gz

genoray_cli-0.1.1/CHANGELOG.md

@@ -0,0 +1,11 @@
+## 0.1.1 (2025-11-13)
+
+### Fix
+
+- dosage field handling for SVAR writing
+
+## 0.1.0 (2025-10-09)
+
+### Feat
+
+- commit for bumping

{genoray_cli-0.1.0 → genoray_cli-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genoray-cli
-Version: 0.1.0
+Version: 0.1.1
 Summary: Command line interface for genoray
 Author-email: David Laub <dlaub@ucsd.edu>
 License: MIT License

{genoray_cli-0.1.0 → genoray_cli-0.1.1}/genoray_cli/__main__.py

@@ -1,8 +1,9 @@
 #! /usr/bin/env python
 
+from __future__ import annotations
+
 from importlib.metadata import version
 from pathlib import Path
-from typing import Optional, Union
 
 from cyclopts import App
 
@@ -36,42 +37,55 @@ def write(
     out: Path,
     max_mem: str = "1g",
     overwrite: bool = False,
-    dosages: Optional[Union[bool, Path]] = None,
+    dosages: bool | str | None = None,
 ) -> None:
     """
     Convert a VCF or PGEN file to a SVAR file.
 
     Parameters
     ----------
-    source : Path
+    source
         Path to the input VCF or PGEN file.
-    out : Path
+    out
         Path to the output SVAR file.
-    max_mem : str, optional
+    max_mem
         Maximum memory to use for conversion e.g. 1g, 250 MB, etc.
-    overwrite : bool, optional
+    overwrite
         Whether to overwrite the output file if it exists.
-    dosages : bool | Path | None, optional
+    dosages
         Whether to write dosages. If :code:`source` is a PGEN, this must be a path to a PGEN of dosages.
-        If :code:`source` is a VCF, this should be a boolean.
+        If :code:`source` is a VCF, this must be the name of the FORMAT field to use for dosages.
     """
     from genoray import PGEN, VCF, SparseVar
     from genoray._utils import variant_file_type
 
     file_type = variant_file_type(source)
+
+    if dosages is None:
+        with_dosages = False
+    else:
+        with_dosages = True
+
     if file_type == "vcf":
-        vcf = VCF(source)
-        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=dosages)
+        if isinstance(dosages, bool):
+            raise ValueError(
+                "Dosages must be provided as a string for a VCF FORMAT field if the source is a VCF."
+            )
+
+        if dosages is not None and Path(dosages).exists():
+            raise ValueError(
+                "The `dosages` argument appears to be a path to an existing file, but VCF requires a FORMAT field name."
+            )
+
+        vcf = VCF(source, dosage_field=dosages)
+        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=with_dosages)
     elif file_type == "pgen":
         if dosages is False:
             dosages = None
-            with_dosages = False
         elif dosages is True:
             raise ValueError(
                 "Dosages must be provided as a path to a PGEN if source is a PGEN."
             )
-        else:
-            with_dosages = True
 
         pgen = PGEN(source, dosage_path=dosages)
         SparseVar.from_pgen(out, pgen, max_mem, overwrite, with_dosages=with_dosages)

{genoray_cli-0.1.0 → genoray_cli-0.1.1}/pixi.lock

@@ -599,8 +599,8 @@ packages:
   requires_python: '>=3.9,<3.13'
 - pypi: ./
   name: genoray-cli
-  version: 0.0.0
-  sha256: b4c947d3fcdbe019bf00a19e26d110b11883b02b36f81b521ff8a1db816a9575
+  version: 0.1.0
+  sha256: d92e3195943936f36bb161a1469ef5615696138948fc81ba84bcfb8b116e31ee
   requires_dist:
   - genoray
   - cyclopts

{genoray_cli-0.1.0 → genoray_cli-0.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "genoray-cli"
-version = "0.1.0"
+version = "0.1.1"
 description = "Command line interface for genoray"
 authors = [{ name = "David Laub", email = "dlaub@ucsd.edu" }]
 readme = "README.md"

{genoray_cli-0.1.0 → genoray_cli-0.1.1}/uv.lock

@@ -286,7 +286,7 @@ wheels = [
 
 [[package]]
 name = "genoray-cli"
-version = "0.1.0"
+version = "0.1.1"
 source = { editable = "." }
 dependencies = [
     { name = "cyclopts" },

genoray_cli-0.1.0/CHANGELOG.md

@@ -1,5 +0,0 @@
-## 0.1.0 (2025-10-09)
-
-### Feat
-
-- commit for bumping