py-gbcms 2.0.0__tar.gz → 2.2.0__tar.gz

{py_gbcms-2.0.0 → 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-2.2.0/PKG-INFO

@@ -0,0 +1,216 @@
+Metadata-Version: 2.4
+Name: py-gbcms
+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-Dist: pysam>=0.21.0
+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
+Provides-Extra: fast
+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
+
+**Complete orientation-aware counting system for genomic variants**
+
+[![Tests](https://github.com/msk-access/py-gbcms/workflows/Tests/badge.svg)](https://github.com/msk-access/py-gbcms/actions)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+## Features
+
+- 🚀 **High Performance**: Rust-powered core engine with multi-threading
+- 🧬 **Complete Variant Support**: SNP, MNP, insertion, deletion, and complex variants (DelIns, SNP+Indel)
+- 📊 **Orientation-Aware**: Forward and reverse strand analysis with fragment counting
+- 🔬 **Statistical Analysis**: Fisher's exact test for strand bias
+- 📁 **Flexible I/O**: VCF and MAF input/output formats
+- 🎯 **Quality Filters**: 7 configurable read filtering options
+
+## Installation
+
+**Quick install:**
+```bash
+pip install py-gbcms
+```
+
+**From source (requires Rust):**
+```bash
+git clone https://github.com/msk-access/py-gbcms.git
+cd py-gbcms
+pip install .
+```
+
+**Docker:**
+```bash
+docker pull ghcr.io/msk-access/py-gbcms:2.1.0
+```
+
+📖 **Full documentation:** https://msk-access.github.io/py-gbcms/
+
+---
+
+## Usage
+
+`py-gbcms` can be used in two ways:
+
+### 🔧 Option 1: Standalone CLI (1-10 samples)
+
+**Best for:** Quick analysis, local processing, direct control
+
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam sample1.bam \
+    --fasta reference.fa \
+    --output-dir results/
+```
+
+**Output:** `results/sample1.vcf`
+
+**Learn more:**
+- 📘 [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)
+- 📖 [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)
+
+---
+
+### 🔄 Option 2: Nextflow Workflow (10+ samples, HPC)
+
+**Best for:** Many samples, HPC clusters (SLURM), reproducible pipelines
+
+```bash
+nextflow run nextflow/main.nf \
+    --input samplesheet.csv \
+    --variants variants.vcf \
+    --fasta reference.fa \
+    -profile slurm
+```
+
+**Features:**
+- ✅ Automatic parallelization across samples
+- ✅ SLURM/HPC integration
+- ✅ Container support (Docker/Singularity)
+- ✅ Resume failed runs
+
+**Learn more:**
+- 🔄 [Nextflow Workflow Guide](https://cmo-ci.gitbook.io/py-gbcms/nextflow)
+- 📋 [Usage Patterns Comparison](https://cmo-ci.gitbook.io/py-gbcms/workflows)
+
+---
+
+## Which Should I Use?
+
+| Scenario | Recommendation |
+|----------|----------------|
+| 1-10 samples, local machine | **CLI** |
+| 10+ samples, HPC cluster | **Nextflow** |
+| Quick ad-hoc analysis | **CLI** |
+| Production pipeline | **Nextflow** |
+| Need auto-parallelization | **Nextflow** |
+| Full manual control | **CLI** |
+
+---
+
+## Quick Examples
+
+### CLI: Single Sample
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam tumor.bam \
+    --fasta hg19.fa \
+    --output-dir results/ \
+    --threads 4
+```
+
+### CLI: Multiple Samples (Sequential)
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam-list samples.txt \
+    --fasta hg19.fa \
+    --output-dir results/
+```
+
+### Nextflow: Many Samples (Parallel)
+```bash
+# samplesheet.csv:
+# sample,bam,bai
+# tumor1,/path/to/tumor1.bam,
+# tumor2,/path/to/tumor2.bam,
+
+nextflow run nextflow/main.nf \
+    --input samplesheet.csv \
+    --variants variants.vcf \
+    --fasta hg19.fa \
+    --outdir results \
+    -profile slurm
+```
+
+---
+
+## Documentation
+
+📚 **Full Documentation:** https://cmo-ci.gitbook.io/py-gbcms/
+
+**Quick Links:**
+- [Installation](https://cmo-ci.gitbook.io/py-gbcms/installation)
+- [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)
+- [Nextflow Workflow](https://cmo-ci.gitbook.io/py-gbcms/nextflow)
+- [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)
+- [Input & Output Formats](https://cmo-ci.gitbook.io/py-gbcms/input_output)
+- [Architecture](https://cmo-ci.gitbook.io/py-gbcms/architecture)
+
+---
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development guidelines.
+
+To contribute to documentation, see the [`gh-pages` branch](https://github.com/msk-access/py-gbcms/tree/gh-pages).
+
+---
+
+## Citation
+
+If you use `py-gbcms` in your research, please cite:
+
+```
+[Citation to be added]
+```
+
+---
+
+## License
+
+AGPL-3.0 - see [LICENSE](LICENSE) for details.
+
+---
+
+## Support
+
+- 🐛 **Issues:** https://github.com/msk-access/py-gbcms/issues
+- 💬 **Discussions:** https://github.com/msk-access/py-gbcms/discussions
+

py_gbcms-2.2.0/README.md

@@ -0,0 +1,180 @@
+# py-gbcms
+
+**Complete orientation-aware counting system for genomic variants**
+
+[![Tests](https://github.com/msk-access/py-gbcms/workflows/Tests/badge.svg)](https://github.com/msk-access/py-gbcms/actions)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+## Features
+
+- 🚀 **High Performance**: Rust-powered core engine with multi-threading
+- 🧬 **Complete Variant Support**: SNP, MNP, insertion, deletion, and complex variants (DelIns, SNP+Indel)
+- 📊 **Orientation-Aware**: Forward and reverse strand analysis with fragment counting
+- 🔬 **Statistical Analysis**: Fisher's exact test for strand bias
+- 📁 **Flexible I/O**: VCF and MAF input/output formats
+- 🎯 **Quality Filters**: 7 configurable read filtering options
+
+## Installation
+
+**Quick install:**
+```bash
+pip install py-gbcms
+```
+
+**From source (requires Rust):**
+```bash
+git clone https://github.com/msk-access/py-gbcms.git
+cd py-gbcms
+pip install .
+```
+
+**Docker:**
+```bash
+docker pull ghcr.io/msk-access/py-gbcms:2.1.0
+```
+
+📖 **Full documentation:** https://msk-access.github.io/py-gbcms/
+
+---
+
+## Usage
+
+`py-gbcms` can be used in two ways:
+
+### 🔧 Option 1: Standalone CLI (1-10 samples)
+
+**Best for:** Quick analysis, local processing, direct control
+
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam sample1.bam \
+    --fasta reference.fa \
+    --output-dir results/
+```
+
+**Output:** `results/sample1.vcf`
+
+**Learn more:**
+- 📘 [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)
+- 📖 [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)
+
+---
+
+### 🔄 Option 2: Nextflow Workflow (10+ samples, HPC)
+
+**Best for:** Many samples, HPC clusters (SLURM), reproducible pipelines
+
+```bash
+nextflow run nextflow/main.nf \
+    --input samplesheet.csv \
+    --variants variants.vcf \
+    --fasta reference.fa \
+    -profile slurm
+```
+
+**Features:**
+- ✅ Automatic parallelization across samples
+- ✅ SLURM/HPC integration
+- ✅ Container support (Docker/Singularity)
+- ✅ Resume failed runs
+
+**Learn more:**
+- 🔄 [Nextflow Workflow Guide](https://cmo-ci.gitbook.io/py-gbcms/nextflow)
+- 📋 [Usage Patterns Comparison](https://cmo-ci.gitbook.io/py-gbcms/workflows)
+
+---
+
+## Which Should I Use?
+
+| Scenario | Recommendation |
+|----------|----------------|
+| 1-10 samples, local machine | **CLI** |
+| 10+ samples, HPC cluster | **Nextflow** |
+| Quick ad-hoc analysis | **CLI** |
+| Production pipeline | **Nextflow** |
+| Need auto-parallelization | **Nextflow** |
+| Full manual control | **CLI** |
+
+---
+
+## Quick Examples
+
+### CLI: Single Sample
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam tumor.bam \
+    --fasta hg19.fa \
+    --output-dir results/ \
+    --threads 4
+```
+
+### CLI: Multiple Samples (Sequential)
+```bash
+gbcms run \
+    --variants variants.vcf \
+    --bam-list samples.txt \
+    --fasta hg19.fa \
+    --output-dir results/
+```
+
+### Nextflow: Many Samples (Parallel)
+```bash
+# samplesheet.csv:
+# sample,bam,bai
+# tumor1,/path/to/tumor1.bam,
+# tumor2,/path/to/tumor2.bam,
+
+nextflow run nextflow/main.nf \
+    --input samplesheet.csv \
+    --variants variants.vcf \
+    --fasta hg19.fa \
+    --outdir results \
+    -profile slurm
+```
+
+---
+
+## Documentation
+
+📚 **Full Documentation:** https://cmo-ci.gitbook.io/py-gbcms/
+
+**Quick Links:**
+- [Installation](https://cmo-ci.gitbook.io/py-gbcms/installation)
+- [CLI Quick Start](https://cmo-ci.gitbook.io/py-gbcms/quick-start)
+- [Nextflow Workflow](https://cmo-ci.gitbook.io/py-gbcms/nextflow)
+- [CLI Reference](https://cmo-ci.gitbook.io/py-gbcms/cli_features)
+- [Input & Output Formats](https://cmo-ci.gitbook.io/py-gbcms/input_output)
+- [Architecture](https://cmo-ci.gitbook.io/py-gbcms/architecture)
+
+---
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md) for development guidelines.
+
+To contribute to documentation, see the [`gh-pages` branch](https://github.com/msk-access/py-gbcms/tree/gh-pages).
+
+---
+
+## Citation
+
+If you use `py-gbcms` in your research, please cite:
+
+```
+[Citation to be added]
+```
+
+---
+
+## License
+
+AGPL-3.0 - see [LICENSE](LICENSE) for details.
+
+---
+
+## Support
+
+- 🐛 **Issues:** https://github.com/msk-access/py-gbcms/issues
+- 💬 **Discussions:** https://github.com/msk-access/py-gbcms/discussions

{py_gbcms-2.0.0 → py_gbcms-2.2.0}/pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "py-gbcms"
-version = "2.0.0"
+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 = ">=3.11"
-license = {text = "AGPL-3.0"}
+requires-python = ">=3.10"
+license = {file = "LICENSE"}
 keywords = ["bioinformatics", "genomics", "bam", "vcf", "maf", "base-counts", "gbcms"]
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -19,27 +19,16 @@ classifiers = [
 ]
 
 dependencies = [
-    "pysam>=0.22.0",
-    "numpy>=1.24.0",
+    "pysam>=0.21.0",
     "typer>=0.9.0",
     "rich>=13.0.0",
-    "pandas>=2.0.0",
     "pydantic>=2.0.0",
-    "pydantic-settings>=2.0.0",
-    "numba>=0.58.0",
-    "joblib>=1.3.0",
-    "scipy>=1.11.0",
 ]
 
 [project.optional-dependencies]
-fast = [
-    "cyvcf2>=0.30.0",
-]
-
+fast = []
 
-all = [
-    "cyvcf2>=0.30.0",
-]
+all = []
 
 dev = [
     "pytest>=7.4.0",
@@ -48,25 +37,28 @@ dev = [
     "black>=23.0.0",
     "ruff>=0.1.0",
     "mypy>=1.5.0",
-    "pre-commit>=3.3.0",
     "types-pyyaml>=6.0.0",
+    "mkdocs-material>=9.0.0",
 ]
 
 [project.scripts]
 gbcms = "gbcms.cli:app"
 
 [project.urls]
-Homepage = "https://github.com/msk-access/getbasecounts"
-Repository = "https://github.com/msk-access/getbasecounts"
-Documentation = "https://github.com/msk-access/getbasecounts#readme"
-"Bug Tracker" = "https://github.com/msk-access/getbasecounts/issues"
+Homepage = "https://github.com/msk-access/py-gbcms"
+Repository = "https://github.com/msk-access/py-gbcms"
+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"
+requires = ["maturin>=1.0,<2.0"]
+build-backend = "maturin"
+
+[tool.maturin]
+python-source = "src"
+manifest-path = "rust/Cargo.toml"
+module-name = "gbcms._rs"
 
-[tool.hatch.build.targets.wheel]
-packages = ["src/gbcms"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -89,7 +81,7 @@ include = '\.pyi?$'
 
 [tool.ruff]
 line-length = 100
-target-version = "py311"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = [
@@ -127,9 +119,7 @@ disable_error_code = ["call-arg"]
 [[tool.mypy.overrides]]
 module = [
     "pysam.*",
-    "numba.*",
-    "joblib.*",
-    "cyvcf2.*",
+    "gbcms._rs",
 ]
 ignore_missing_imports = true
 
@@ -152,7 +142,6 @@ exclude_lines = [
 dev = [
     "black>=25.9.0",
     "mypy>=1.18.2",
-    "pre-commit>=4.3.0",
     "pytest>=8.4.2",
     "pytest-cov>=4.1.0",
     "pytest-benchmark>=5.1.0",