py-gbcms 2.1.2__tar.gz → 2.2.0__tar.gz

{py_gbcms-2.1.2 → py_gbcms-2.2.0}/LICENSE

@@ -1,16 +1,11 @@
                     GNU AFFERO GENERAL PUBLIC LICENSE
                        Version 3, 19 November 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
-TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
-1. Definitions.
-
-   "License" shall mean the terms and conditions for use, reproduction,
-   and distribution as defined by Sections 1 through 9 of this document.
+                            Preamble
 
   The GNU Affero General Public License is a free, copyleft license for
 software and other kinds of works, specifically designed to ensure
@@ -18,15 +13,16 @@ cooperation with the community in the case of network server software.
 
   The licenses for most software and other practical works are designed
 to take away your freedom to share and change the works.  By contrast,
-the GNU Affero General Public License is intended to guarantee your
-freedom to share and change all versions of a program--to make sure it
-remains free software for all its users.  When we speak of free software,
-we are referring to freedom, not price.  Our General Public Licenses
-are designed to make sure that you have the freedom to distribute copies
-of free software (and charge for them if you wish), that you receive
-source code or can get it if you want it, that you can change the
-software or use pieces of it in new free programs, and that you know
-you can do these things.
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
 
   Developers that use our General Public Licenses protect your rights
 with two steps: (1) assert copyright on the software, and (2) offer
@@ -39,23 +35,39 @@ receive widespread use, become available for other developers to
 incorporate.  Many developers of free software are heartened and
 encouraged by the resulting cooperation.  However, in the case of
 software used on network servers, this result may fail to come about.
-The GNU Affero General Public License includes a provision that helps
-developers of such software achieve the same cooperation we expect
-from other free software.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+  The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community.  It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server.  Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+  An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals.  This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
 
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, and make the source code available to users so
-they can modify the program while keeping the network server running,
-you must offer the source code under the GNU Affero General Public
-License.
+                       TERMS AND CONDITIONS
 
-  The GNU Affero General Public License is based on the GNU General
-Public License, but includes an additional permission and a requirement
-regarding network server software that is different from the GNU GPL.
+  0. Definitions.
 
-  "The Program" here refers to any copyrightable work licensed under
-the GNU Affero General Public License.  Each licensee is addressed as
-"you".  "Licensees" and "recipients" may be individuals or organizations.
+  "This License" refers to version 3 of the GNU Affero General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
 
   To "modify" a work means to copy from or adapt all or part of the work
 in a fashion requiring copyright permission, other than the making of an
@@ -262,9 +274,9 @@ in one of these ways:
     available for as long as needed to satisfy these requirements.
 
     e) Convey the object code using peer-to-peer transmission, provided
-    you inform other peers where the object and its Corresponding Source
-    are being offered to the general public at no charge under
-    subsection 6d.
+    you inform other peers where the object code and Corresponding
+    Source of the work are being offered to the general public at no
+    charge under subsection 6d.
 
   A separable portion of the object code, whose source code is excluded
 from the Corresponding Source as a System Library, need not be
@@ -353,7 +365,7 @@ that material) supplement the terms of this License with terms:
     authors of the material; or
 
     e) Declining to grant rights under trademark law for use of some
-    trade names, marks, or slogans; or
+    trade names, trademarks, or service marks; or
 
     f) Requiring indemnification of licensors and authors of that
     material by anyone who conveys the material (or modified versions of
@@ -533,7 +545,7 @@ interacting with it remotely through a computer network (if your version
 supports such interaction) an opportunity to receive the Corresponding
 Source of your version by providing access to the Corresponding Source
 from a network server at no charge, through some standard or customary
-means of facilitating copying of software.  This corresponding source
+means of facilitating copying of software.  This Corresponding Source
 shall include the Corresponding Source for any work covered by version 3
 of the GNU General Public License that is incorporated pursuant to the
 following paragraph.
@@ -631,7 +643,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU Affero General Public License for more details.
 
     You should have received a copy of the GNU Affero General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -646,19 +658,4 @@ specific requirements.
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU AGPL, see
-<http://www.gnu.org/licenses/>.
-
-Copyright 2024 MSK-ACCESS Team
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero 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 Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.

{py_gbcms-2.1.2 → py_gbcms-2.2.0}/PKG-INFO

@@ -1,38 +1,37 @@
 Metadata-Version: 2.4
 Name: py-gbcms
-Version: 2.1.2
-Summary: Python implementation of GetBaseCountsMultiSample (gbcms) for calculating base counts in BAM files
-Project-URL: Homepage, https://github.com/msk-access/py-gbcms
-Project-URL: Repository, https://github.com/msk-access/py-gbcms
-Project-URL: Documentation, https://github.com/msk-access/py-gbcms#readme
-Project-URL: Bug Tracker, https://github.com/msk-access/py-gbcms/issues
-Author-email: MSK-ACCESS <shahr2@mskcc.org>
-License: AGPL-3.0
-License-File: LICENSE
-Keywords: bam,base-counts,bioinformatics,gbcms,genomics,maf,vcf
+Version: 2.2.0
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU Affero General Public License v3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
-Requires-Dist: pydantic>=2.0.0
 Requires-Dist: pysam>=0.21.0
-Requires-Dist: rich>=13.0.0
 Requires-Dist: typer>=0.9.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: pytest>=7.4.0 ; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0 ; extra == 'dev'
+Requires-Dist: pytest-mock>=3.11.0 ; extra == 'dev'
+Requires-Dist: black>=23.0.0 ; extra == 'dev'
+Requires-Dist: ruff>=0.1.0 ; extra == 'dev'
+Requires-Dist: mypy>=1.5.0 ; extra == 'dev'
+Requires-Dist: types-pyyaml>=6.0.0 ; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.0.0 ; extra == 'dev'
 Provides-Extra: all
 Provides-Extra: dev
-Requires-Dist: black>=23.0.0; extra == 'dev'
-Requires-Dist: mkdocs-material>=9.0.0; extra == 'dev'
-Requires-Dist: mypy>=1.5.0; extra == 'dev'
-Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
-Requires-Dist: pytest-mock>=3.11.0; extra == 'dev'
-Requires-Dist: pytest>=7.4.0; extra == 'dev'
-Requires-Dist: ruff>=0.1.0; extra == 'dev'
-Requires-Dist: types-pyyaml>=6.0.0; extra == 'dev'
 Provides-Extra: fast
-Description-Content-Type: text/markdown
+License-File: LICENSE
+Summary: Python implementation of GetBaseCountsMultiSample (gbcms) for calculating base counts in BAM files
+Keywords: bioinformatics,genomics,bam,vcf,maf,base-counts,gbcms
+Author-email: MSK-ACCESS <shahr2@mskcc.org>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Bug Tracker, https://github.com/msk-access/py-gbcms/issues
+Project-URL: Documentation, https://github.com/msk-access/py-gbcms#readme
+Project-URL: Homepage, https://github.com/msk-access/py-gbcms
+Project-URL: Repository, https://github.com/msk-access/py-gbcms
 
 # py-gbcms
 
@@ -214,3 +213,4 @@ AGPL-3.0 - see [LICENSE](LICENSE) for details.
 
 - 🐛 **Issues:** https://github.com/msk-access/py-gbcms/issues
 - 💬 **Discussions:** https://github.com/msk-access/py-gbcms/discussions
+

{py_gbcms-2.1.2 → py_gbcms-2.2.0}/pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "py-gbcms"
-version = "2.1.2"
+version = "2.2.0"
 description = "Python implementation of GetBaseCountsMultiSample (gbcms) for calculating base counts in BAM files"
 authors = [
     {name = "MSK-ACCESS", email = "shahr2@mskcc.org"}
 ]
 readme = "README.md"
 requires-python = ">=3.10"
-license = {text = "AGPL-3.0"}
+license = {file = "LICENSE"}
 keywords = ["bioinformatics", "genomics", "bam", "vcf", "maf", "base-counts", "gbcms"]
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -51,29 +51,14 @@ Documentation = "https://github.com/msk-access/py-gbcms#readme"
 "Bug Tracker" = "https://github.com/msk-access/py-gbcms/issues"
 
 [build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/gbcms"]
-
-[tool.hatch.build.targets.sdist]
-exclude = [
-    "/.github",
-    "/docs",
-    "/tests",
-    "/nextflow",
-    "/examples",
-    "/.gitignore",
-    "/.gitbook.yaml",
-    "/mkdocs.yml",
-    "/docker-compose.yml",
-    "/Dockerfile",
-    "/Makefile",
-    "/test_real_data.sh",
-    "/git-flow-helper.sh",
-    "/scripts",
-]
+requires = ["maturin>=1.0,<2.0"]
+build-backend = "maturin"
+
+[tool.maturin]
+python-source = "src"
+manifest-path = "rust/Cargo.toml"
+module-name = "gbcms._rs"
+
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -96,7 +81,7 @@ include = '\.pyi?$'
 
 [tool.ruff]
 line-length = 100
-target-version = "py311"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = [
@@ -134,7 +119,7 @@ disable_error_code = ["call-arg"]
 [[tool.mypy.overrides]]
 module = [
     "pysam.*",
-    "gbcms_rs",
+    "gbcms._rs",
 ]
 ignore_missing_imports = true
 

{py_gbcms-2.1.2/src/gbcms_rs → py_gbcms-2.2.0/rust}/Cargo.lock

@@ -257,7 +257,7 @@ dependencies = [
 
 [[package]]
 name = "gbcms_rs"
-version = "2.0.0"
+version = "2.2.0"
 dependencies = [
  "anyhow",
  "bio-types",

{py_gbcms-2.1.2/src/gbcms_rs → py_gbcms-2.2.0/rust}/Cargo.toml

@@ -1,11 +1,11 @@
 [package]
 name = "gbcms_rs"
-version = "2.0.0"
-edition = "2024"
+version = "2.2.0"
+edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
-name = "gbcms_rs"
+name = "_rs"
 crate-type = ["cdylib"]
 
 [dependencies]

{py_gbcms-2.1.2/src/gbcms_rs → py_gbcms-2.2.0/rust}/src/lib.rs

@@ -5,9 +5,9 @@ mod counting;
 mod stats;
 mod types;
 
-/// A Python module implemented in Rust.
+/// A Python module implemented in Rust (bundled as gbcms._rs).
 #[pymodule]
-fn gbcms_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
+fn _rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
     pyo3_log::init();
     m.add_function(wrap_pyfunction!(counting::count_bam, m)?)?;
     m.add_class::<types::Variant>()?;

py_gbcms-2.2.0/src/gbcms/__init__.py

@@ -0,0 +1,23 @@
+"""
+gbcms (Get Base Counts Multi-Sample) - A tool for counting bases at variant positions.
+
+This package provides a command-line interface and Python API for genotyping
+variants in BAM files using a high-performance Rust counting engine.
+
+Example usage:
+    $ gbcms run -v variants.vcf -b sample.bam -f reference.fa -o output/
+"""
+
+__version__ = "2.2.0"
+
+from .models.core import GbcmsConfig, OutputFormat, Variant, VariantType
+from .pipeline import Pipeline
+
+__all__ = [
+    "__version__",
+    "GbcmsConfig",
+    "OutputFormat",
+    "Pipeline",
+    "Variant",
+    "VariantType",
+]

py_gbcms-2.2.0/src/gbcms/_rs.pyi

@@ -0,0 +1,49 @@
+# Type stubs for the Rust extension module (gbcms._rs)
+# This file tells mypy about the types in the native extension
+
+class Variant:
+    chrom: str
+    pos: int
+    ref_allele: str
+    alt_allele: str
+    variant_type: str
+
+    def __init__(
+        self,
+        chrom: str,
+        pos: int,
+        ref_allele: str,
+        alt_allele: str,
+        variant_type: str,
+    ) -> None: ...
+
+class BaseCounts:
+    chrom: str
+    pos: int
+    ref: str
+    alt: str
+    dp: int
+    rd: int
+    ad: int
+    rd_fwd: int
+    rd_rev: int
+    ad_fwd: int
+    ad_rev: int
+    dp_fragment: int
+    rd_fragment: int
+    ad_fragment: int
+    sb_pvalue: float
+
+def count_bam(
+    bam_path: str,
+    variants: list[Variant],
+    min_mapq: int = 20,
+    min_baseq: int = 0,
+    filter_duplicates: bool = True,
+    filter_secondary: bool = False,
+    filter_supplementary: bool = False,
+    filter_qc_failed: bool = False,
+    filter_improper_pair: bool = False,
+    filter_indel: bool = False,
+    threads: int = 1,
+) -> list[BaseCounts]: ...

{py_gbcms-2.1.2 → py_gbcms-2.2.0}/src/gbcms/cli.py

@@ -2,12 +2,24 @@
 CLI Entry Point: Exposes the gbcms functionality via command line.
 """
 
+import logging
 from pathlib import Path
 
 import typer
 
-from .models.core import GbcmsConfig, OutputFormat
+from .models.core import (
+    GbcmsConfig,
+    OutputConfig,
+    OutputFormat,
+    QualityThresholds,
+    ReadFilters,
+)
 from .pipeline import Pipeline
+from .utils import setup_logging
+
+__all__ = ["app", "run"]
+
+logger = logging.getLogger(__name__)
 
 app = typer.Typer(help="gbcms: Get Base Counts Multi-Sample")
 
@@ -22,6 +34,7 @@ def main():
 
 @app.command()
 def run(
+    # Input options
     variant_file: Path = typer.Option(
         ..., "--variants", "-v", help="Path to VCF or MAF file containing variants"
     ),
@@ -32,6 +45,7 @@ def run(
         None, "--bam-list", "-L", help="File containing list of BAM paths (one per line)"
     ),
     reference: Path = typer.Option(..., "--fasta", "-f", help="Path to reference FASTA file"),
+    # Output options
     output_dir: Path = typer.Option(
         ..., "--output-dir", "-o", help="Directory to write output files"
     ),
@@ -41,65 +55,106 @@ def run(
     output_suffix: str = typer.Option(
         "", "--suffix", "-S", help="Suffix to append to output filename (e.g. '.genotyped')"
     ),
+    # Quality thresholds
     min_mapq: int = typer.Option(20, "--min-mapq", help="Minimum mapping quality"),
     min_baseq: int = typer.Option(0, "--min-baseq", help="Minimum base quality"),
+    # Read filters
     filter_duplicates: bool = typer.Option(True, help="Filter duplicate reads"),
     filter_secondary: bool = typer.Option(False, help="Filter secondary alignments"),
     filter_supplementary: bool = typer.Option(False, help="Filter supplementary alignments"),
     filter_qc_failed: bool = typer.Option(False, help="Filter reads failing QC"),
     filter_improper_pair: bool = typer.Option(False, help="Filter improperly paired reads"),
     filter_indel: bool = typer.Option(False, help="Filter reads containing indels"),
+    # Performance
     threads: int = typer.Option(
-        1, "--threads", "-t", help="Number of threads (not yet implemented in v2 python layer)"
+        1, "--threads", "-t", help="Number of threads for parallel processing"
     ),
     verbose: bool = typer.Option(False, "--verbose", "-V", help="Enable verbose debug logging"),
 ):
     """
     Run gbcms on one or more BAM files.
     """
-    import logging
+    # Configure logging
+    setup_logging(verbose=verbose)
 
-    from rich.console import Console
-    from rich.logging import RichHandler
+    # Parse BAM inputs
+    bams_dict = _parse_bam_inputs(bam_files, bam_list)
 
-    # Configure logging
-    log_level = logging.DEBUG if verbose else logging.INFO
-    logging.basicConfig(
-        level=log_level,
-        format="%(message)s",
-        datefmt="[%X]",
-        handlers=[RichHandler(rich_tracebacks=True, markup=True)],
-    )
+    if not bams_dict:
+        logger.error("No valid BAM files provided via --bam or --bam-list")
+        raise typer.Exit(code=1)
+
+    logger.info("Found %d BAM file(s) to process", len(bams_dict))
+
+    try:
+        # Build nested config objects
+        output_config = OutputConfig(
+            directory=output_dir,
+            format=output_format,
+            suffix=output_suffix,
+        )
+
+        quality_config = QualityThresholds(
+            min_mapping_quality=min_mapq,
+            min_base_quality=min_baseq,
+        )
 
-    console = Console()
+        filter_config = ReadFilters(
+            duplicates=filter_duplicates,
+            secondary=filter_secondary,
+            supplementary=filter_supplementary,
+            qc_failed=filter_qc_failed,
+            improper_pair=filter_improper_pair,
+            indel=filter_indel,
+        )
+
+        config = GbcmsConfig(
+            variant_file=variant_file,
+            bam_files=bams_dict,
+            reference_fasta=reference,
+            output=output_config,
+            quality=quality_config,
+            filters=filter_config,
+            threads=threads,
+        )
+
+        pipeline = Pipeline(config)
+        pipeline.run()
+
+    except Exception as e:
+        logger.exception("Pipeline failed: %s", e)
+        raise typer.Exit(code=1) from e
 
-    # Map BAMs to sample names (filename stem for now)
-    bams_dict = {}
+
+def _parse_bam_inputs(bam_files: list[Path] | None, bam_list: Path | None) -> dict[str, Path]:
+    """
+    Parse BAM inputs from direct arguments and/or BAM list file.
+
+    Args:
+        bam_files: List of BAM paths (optionally with sample_id:path format).
+        bam_list: Path to file containing BAM paths (one per line).
+
+    Returns:
+        Dictionary mapping sample names to BAM paths.
+    """
+    bams_dict: dict[str, Path] = {}
 
     # 1. Process direct BAM arguments
     if bam_files:
         for bam_arg in bam_files:
-            # Check for sample_id:path format
-            bam_str = str(bam_arg)
-            if ":" in bam_str:
-                parts = bam_str.split(":", 1)
-                sample_name = parts[0]
-                bam_path = Path(parts[1])
-            else:
-                bam_path = bam_arg
-                sample_name = bam_path.stem
+            sample_name, bam_path = _parse_bam_arg(bam_arg)
 
             if not bam_path.exists():
-                console.print(f"[bold red]Error: BAM file not found: {bam_path}[/bold red]")
-                raise typer.Exit(code=1)
+                logger.error("BAM file not found: %s", bam_path)
+                continue
 
             bams_dict[sample_name] = bam_path
 
     # 2. Process BAM list file
     if bam_list:
         if not bam_list.exists():
-            console.print(f"[bold red]Error: BAM list file not found: {bam_list}[/bold red]")
-            raise typer.Exit(code=1)
+            logger.error("BAM list file not found: %s", bam_list)
+            return bams_dict
 
         try:
             with open(bam_list) as f:
@@ -107,7 +162,7 @@ def run(
                     line = line.strip()
                     if not line or line.startswith("#"):
                         continue
-                    # Check for 2 columns (sample_id path)
+
                     parts = line.split()
                     if len(parts) >= 2:
                         sample_name = parts[0]
@@ -117,46 +172,32 @@ def run(
                         sample_name = bam_path.stem
 
                     if not bam_path.exists():
-                        console.print(
-                            f"[yellow]Warning: BAM file from list not found: {bam_path}[/yellow]"
-                        )
+                        logger.warning("BAM file from list not found: %s", bam_path)
                         continue
+
                     bams_dict[sample_name] = bam_path
+
         except Exception as e:
-            console.print(f"[bold red]Error reading BAM list file {bam_list}: {e}[/bold red]")
-            raise typer.Exit(code=1) from e
+            logger.error("Error reading BAM list file %s: %s", bam_list, e)
 
-    if not bams_dict:
-        console.print(
-            "[bold red]Error: No valid BAM files provided via --bam or --bam-list[/bold red]"
-        )
-        raise typer.Exit(code=1)
+    return bams_dict
 
-    try:
-        config = GbcmsConfig(
-            variant_file=variant_file,
-            bam_files=bams_dict,
-            reference_fasta=reference,
-            output_dir=output_dir,
-            output_format=output_format,
-            output_suffix=output_suffix,
-            min_mapping_quality=min_mapq,
-            min_base_quality=min_baseq,
-            filter_duplicates=filter_duplicates,
-            filter_secondary=filter_secondary,
-            filter_supplementary=filter_supplementary,
-            filter_qc_failed=filter_qc_failed,
-            filter_improper_pair=filter_improper_pair,
-            filter_indel=filter_indel,
-            threads=threads,
-        )
 
-        pipeline = Pipeline(config)
-        pipeline.run()
+def _parse_bam_arg(bam_arg: Path) -> tuple[str, Path]:
+    """
+    Parse a BAM argument that may be in sample_id:path format.
 
-    except Exception as e:
-        console.print(f"[bold red]Error: {e}[/bold red]")
-        raise typer.Exit(code=1) from e
+    Args:
+        bam_arg: Path object (may contain sample_id:path as string).
+
+    Returns:
+        Tuple of (sample_name, bam_path).
+    """
+    bam_str = str(bam_arg)
+    if ":" in bam_str:
+        parts = bam_str.split(":", 1)
+        return parts[0], Path(parts[1])
+    return bam_arg.stem, bam_arg
 
 
 if __name__ == "__main__":

py_gbcms-2.2.0/src/gbcms/core/__init__.py

@@ -0,0 +1,9 @@
+"""
+Core module for gbcms.
+
+Provides the coordinate transformation kernel for handling VCF/MAF coordinates.
+"""
+
+from .kernel import CoordinateKernel
+
+__all__ = ["CoordinateKernel"]