Troubleshooting

• Conda Environment Activation Failed:
  • Ensure your_conda_env is installed and the environment exists.
• GNU Parallel Not Found:
  • The script attempts to install GNU Parallel via Conda. Ensure you have internet access and Conda is properly configured.
• No BAM Files Found:
  • Verify that BAM_DIR points to the correct directory containing .bam files.

License

This project is licensed under the MIT License.

Acknowledgements

• hmmcopy_utils: The readCounter tool is sourced from the hmmcopy_utils GitHub repository.

Future Improvements

• Dynamic Resource Allocation: Adjust CPU and memory usage based on the size of BAM files.
• Enhanced Logging: Implement more detailed logging for better monitoring and debugging.
• User Interface: Develop a simple GUI for easier configuration and execution of the script.

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