9 set up unit testing workflow (#10)

Set up basic unit tests for copy number variant detection

.github/workflows/build-tests.yml

@@ -0,0 +1,37 @@
+name: build tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up conda environment
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: contextsv
+        environment-file: environment.yml
+        python-version: 3.9
+        auto-activate-base: false
+
+    - name: Install samtools and bcftools using sudo apt-get
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y samtools bcftools
+
+    - name: Build C++ code
+      shell: bash --login {0}  # --login enables PATH variable access
+      run: |
+        make
+
+    - name: Run unit tests
+      shell: bash --login {0}
+      run: |
+        mkdir -p tests/output
+        python -m pytest

.gitignore

@@ -7,6 +7,13 @@
 *.o
 *.obj
 
+# SWIG files
+src/swig_wrapper.cpp
+lib/contextsv.py
+
+# Pycache
+__pycache__/
+
 # Precompiled Headers
 *.gch
 *.pch

Makefile

@@ -0,0 +1,11 @@
+INCL_DIR := $(CURDIR)/include
+SRC_DIR := $(CURDIR)/src
+LIB_DIR := $(CURDIR)/lib
+
+
+all:
+	# Generate the SWIG wrapper (C++ -> Python)
+	swig -c++ -python -I$(INCL_DIR) -o $(SRC_DIR)/swig_wrapper.cpp -outdir $(LIB_DIR) $(SRC_DIR)/swig_wrapper.i
+
+	# Compile the SWIG wrapper using setuptools
+	python setup.py build_ext --build-lib $(LIB_DIR)

README.md

@@ -1,2 +1,5 @@
 # ContextSV
-An alignment-based, generalized structural variant caller for long-read sequencing/mapping data 
+An alignment-based, generalized structural variant caller for long-read
+sequencing/mapping data 
+
+[![build tests](https://github.com/WGLab/ContextSV/actions/workflows/build-tests.yml/badge.svg)](https://github.com/WGLab/ContextSV/actions/workflows/build-tests.yml)

__main__.py

@@ -0,0 +1,57 @@
+"""
+__main__.py: Run the program.
+"""
+
+import os
+import argparse
+from lib import contextsv
+
+def main():
+
+    # Grab the command line arguments using argparse.
+    parser = argparse.ArgumentParser(
+        description="ContextSV: A tool for integrative structural variant detection."
+    )
+    parser.add_argument(
+        "-b", "--bam",
+        help="The path to the BAM file.",
+        required=True
+    )
+    parser.add_argument(
+        "-s", "--snps",
+        help="The path to the SNPs file.",
+        required=True
+    )
+    parser.add_argument(
+        "-o", "--output",
+        help="The path to the output file.",
+        required=True
+    )
+    parser.add_argument(
+        "-r", "--region",
+        help="The region to analyze.",
+        required=True
+    )
+
+    # Get the command line arguments.
+    args = parser.parse_args()
+
+    # Run the program.
+    print("Running contextsv with the following arguments:")
+    print("BAM: {}".format(args.bam))
+    print("SNPs: {}".format(args.snps))
+    print("Output: {}".format(args.output))
+    print("Region: {}".format(args.region))
+
+    contextsv.run(
+        args.bam,
+        args.snps,
+        args.output,
+        args.region
+    )
+
+
+if __name__ == '__main__':
+
+    # Run the program.
+    main()

environment.yml

@@ -0,0 +1,12 @@
+name: contextsv
+channels:
+  - bioconda
+  - anaconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python
+  - numpy
+  - htslib
+  - swig
+  - pytest

include/cli.h

@@ -8,32 +8,8 @@
 
 #include "common.h"
 
-#include <htslib/sam.h>
 #include <string>
 
-class CLI {
-    private:
-        Common common;
-
-    public:
-        // Parse input arguments
-        int parse(int argc, char** argv);
-
-        // Run the CLI
-        int run();
-
-		// Get the command argument input
-		static std::string getCmdOption(char ** begin, char ** end, const std::string & option);
-
-        // Check if the input argument is provided
-		static bool cmdOptionExists(char** begin, char** end, const std::string& option);
-
-        // Check if the filepath exists
-        static bool fileExists(const std::string &name);
-
-        static void printHelpText();
-
-};
-
+int run(std::string bam, std::string snps, std::string outdir, std::string region);
 
 #endif //CONTEXTSV_CLI_H

include/common.h

@@ -8,6 +8,7 @@
 #include <string>
 #include <vector>
 #include <map>
+
 class Common {
     public:
         std::string get_bam_filepath();

include/contextsv.h

@@ -0,0 +1,15 @@
+//
+// contextsv.h
+// Main header file for the contextsv library.
+//
+
+#ifndef CONTEXTSV_H
+#define CONTEXTSV_H
+
+#include "khmm.h"
+#include "common.h"
+
+#include <string>
+#include <vector>
+
+#endif // CONTEXTSV_H

setup.py

@@ -0,0 +1,66 @@
+"""
+setup.py:
+    This file is used to install the package.
+"""
+
+print("Running setup.py...")
+
+import os
+import glob
+from setuptools import setup, find_packages, Extension
+
+
+# Set the project metadata
+name = "contextsv"
+version = "0.0.1"
+author = "WGLab"
+description = "ContextSV: A tool for integrative structural variant detection."
+
+# Get the conda environment's include path
+conda_prefix = os.environ.get("CONDA_PREFIX")
+if conda_prefix is None:
+    raise Exception("CONDA_PREFIX is not set.")
+conda_include_dir = os.path.join(conda_prefix, "include")
+
+print("CONDA_PREFIX: {}".format(conda_prefix))  # DEBUG
+print("include_dir: {}".format(conda_include_dir))  # DEBUG
+
+# Get the conda environment's lib path
+conda_lib_dir = os.path.join(conda_prefix, "lib")
+
+print("lib_dir: {}".format(conda_lib_dir))  # DEBUG
+
+# Set the project dependencies
+src_dir = "src"
+src_files = glob.glob(os.path.join(src_dir, "*.cpp"))
+include_dir = "include"
+include_files = glob.glob(os.path.join(include_dir, "*.h"))
+
+# Set up the extension
+ext = Extension(
+    name="_" + name,
+    sources=src_files,
+    include_dirs=[include_dir, conda_include_dir],
+    extra_compile_args=["-std=c++11"],
+    language="c++",
+    libraries=["hts"],
+    library_dirs=[conda_lib_dir]
+)
+
+# Set up the module
+setup(
+    name=name,
+    version=version,
+    author=author,
+    description=description,
+    ext_modules=[ext],
+    py_modules=[name],
+    packages=find_packages(),
+    test_suite="tests",
+    entry_points={
+        "console_scripts": [
+            "contextsv = contextsv:main"
+        ]
+    }
+)
+