feat: Add VCF intersect and union tools

README.md

@@ -5,17 +5,28 @@
 WIP
 
 ## Table of contents<!-- omit in toc -->
+- [Getting started](#getting-started)
 - [Installation](#installation)
   - [Singularity](#singularity)
   - [Docker](#docker)
 - [Usage](#usage)
   - [Interface](#interface)
   - [Normalization](#normalization)
 - [Tools](#tools)
-  - [Pipeline designer](#pipeline-designer)
-  - [`vcf-ops`](#vcf-ops)
+  - [Pipeline Designer](#pipeline-designer)
+  - [VCF Intersect](#vcf-intersect)
+  - [VCF Union](#vcf-union)
 - [Modularity](#modularity)
 
+## Getting started
+
+WIP
+
+```
+git clone <TODO>
+```
+
+
 ## Installation
 
 It is highly recommended to use ONCOLINER with Docker or Singularity. However, you may also install it locally following the instructions in the [Dockerfile](/Dockerfile).
@@ -94,11 +105,15 @@ It is recommended to normalize indels and SNVs before executing ONCOLINER. For t
 
 Along with ONCOLINER, in this repository you can find some tools that may be useful.
 
-### Pipeline designer
+### Pipeline Designer
+
+WIP
+
+### VCF Intersect
 
 WIP
 
-### `vcf-ops`
+### VCF Union
 
 WIP
 

tools/pipeline_designer/README.md

@@ -7,26 +7,11 @@ The user just needs to provide the VCF files of the variant callers they want to
 Pipeline Designer is part of the [ONCOLINER suite](../../README.md) and is provided as a standalone command line tool. It is available as in the [Docker image](../../Dockerfile) and [Singularity image](../../singularity.def) of ONCOLINER.
 
 ## Table of contents<!-- omit in toc -->
-- [Dependencies](#dependencies)
 - [Usage](#usage)
   - [Interface](#interface)
   - [Output](#output)
 - [Use case example](#use-case-example)
 
-
-## Dependencies
-ONCOLINER's pipeline designer makes use of the following Python modules:
-* [`pandas`](https://pandas.pydata.org/)
-* [`pysam`](https://github.com/pysam-developers/pysam)
-* [`pysam`](https://github.com/pysam-developers/pysam)
-
-You may install them using pip:
-```
-pip3 install pandas pysam variant-extractor
-```
-
-However, we recommend using the provided [Dockerfile](../../Dockerfile)/[Singularity recipe](../../singularity.def) for building the whole ONCOLINER suite to avoid dependency issues.
-
 ## Usage
 
 **WARNING**: It is recommended to normalize indels and SNVs for each variant caller before executing the pipeline designer. For this purpose, we recommend using pre.py from [Illumina's Haplotype Comparison Tools (hap.py)](https://github.com/Illumina/hap.py). We provide an standalone and containerized **[EUCANCan's pre.py wrapper](https://github.com/EUCANCan/prepy-wrapper)** for this purpose.

tools/vcf_intersect/.gitignore

@@ -0,0 +1,160 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

tools/vcf_intersect/README.md

@@ -0,0 +1,14 @@
+# VCF Intersect<!-- omit in toc -->
+
+WIP
+
+## Table of contents<!-- omit in toc -->
+- [Usage](#usage)
+  - [Interface](#interface)
+  - [Output](#output)
+- [Use case example](#use-case-example)
+
+
+## Usage
+
+WIP

shared/vcf_ops/src/intersect_main.py → tools/vcf_intersect/src/intersect_main.py

@@ -1,7 +1,12 @@
 import argparse
-from vcf_ops.i_o import read_vcfs, write_masked_vcfs
-from vcf_ops.constants import DEFAULT_INDEL_THRESHOLD, DEFAULT_WINDOW_RADIUS
-from vcf_ops.intersect import intersect
+import os
+import sys
+
+# Add vcf-ops to the path
+sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(__file__)), '..', '..', '..', 'shared', 'vcf_ops', 'src'))
+from vcf_ops.i_o import read_vcfs, write_masked_vcfs  # noqa
+from vcf_ops.constants import DEFAULT_INDEL_THRESHOLD, DEFAULT_WINDOW_RADIUS  # noqa
+from vcf_ops.intersect import intersect  # noqa
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Intersect two sets of VCF/BCF/VCF.GZ files')