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DEVELOPER.md: Onboarding New Contributors

Welcome to the Decoding-Us Navigator project! This document aims to provide new contributors with an overview of the project's technology stack and identify areas where your contributions can make a significant impact.

Project Overview

Decoding-Us Navigator is an Edge-computing companion to decoding.us.com. It enables local, privacy-preserving analysis of BAM/CRAM files for citizen scientists, leveraging GATK and providing a user-friendly interface. The application is built on the JVM for cross-platform compatibility.

Technology Stack

Language

  • Scala 3: The primary programming language, chosen for its conciseness, strong type system, and functional programming capabilities, running on the JVM.

Build Tool

  • SBT (Scala Build Tool): Used for compiling, testing, and packaging the application.

Core Libraries & Frameworks

  • GATK (Genome Analysis Toolkit): The core bioinformatics library used for various genomic analyses, such as CallableLoci.
  • HTSJDK: A Java API for accessing high-throughput sequencing data (BAM, CRAM, VCF, etc.). Used for reading and manipulating genomic files.
  • FS2 (Functional Streams for Scala): A functional streaming library used for asynchronous and efficient processing of large files and data streams.
  • ScalaFX: A Scala wrapper for JavaFX, used for building the graphical user interface (GUI) of the application.

Configuration

  • HOCON (Human-Optimized Config Object Notation): Used for application configuration, including feature toggles (feature_toggles.conf).

Data Formats

  • JSON: Used for data serialization, especially for summary statistics uploaded to the PDS.
  • BED: Output format for genomic regions from tools like GATK CallableLoci.
  • BAM/CRAM: Input formats for high-throughput sequencing data.

Project Structure

The project follows a standard Scala/SBT directory structure:

  • src/main/scala/com/decodingus/: Contains the main Scala source code, organized by domain (e.g., analysis, haplogroup, ui).
  • src/main/resources/: Stores application resources, such as configuration files (feature_toggles.conf) and CSS (style.css).
  • project/: SBT build definitions.

Areas for Contribution

We welcome contributions in various areas, from core bioinformatics logic to UI/UX improvements and testing.

1. Performance Improvements

  • GATK Integration Optimization: Explore ways to optimize GATK tool invocations, potentially through better parameter tuning or parallel execution strategies.
  • Large File Processing: Enhance the efficiency of reading and processing large BAM/CRAM files, especially for memory management and I/O operations.
  • Parallelization: Identify and implement further parallelization opportunities within the analysis pipelines to leverage multi-core processors more effectively.

2. Maintainability & Code Quality

  • Code Refactoring: Refactor existing code to improve clarity, reduce complexity, and adhere to functional programming principles where appropriate.
  • Modularity: Enhance the modularity of components to make them more independent and easier to test and maintain.
  • Documentation: Improve in-code documentation (Scaladoc) for complex functions, classes, and modules.

3. Test Coverage

  • Unit Tests: Expand unit test coverage for core logic components, especially in the analysis and haplogroup packages.
  • Integration Tests: Develop integration tests to ensure that different modules and external tool integrations (like GATK) work together seamlessly.
  • UI Tests: Implement tests for the ScalaFX user interface to ensure consistent behavior and responsiveness.

4. New Features & Enhancements

  • Federation Integration: Implement the "autosomal DNA matches with other researchers in the Federation" feature.
  • Improved UI/UX: Enhance the user interface with new visualizations, better feedback mechanisms, and more intuitive workflows.
  • Additional Bioinformatics Tools: Integrate other useful bioinformatics tools or analyses as identified by the community.
  • Error Handling & Reporting: Improve robust error handling and user-friendly error reporting.

Getting Started

  1. Clone the repository: git clone [repository-url]
  2. Install SBT: Follow the instructions on the SBT website.
  3. Open in IDE: Import the project into your favorite Scala IDE (e.g., IntelliJ IDEA with Scala plugin).
  4. Run the application: sbt run
  5. Run tests: sbt test

We look forward to your contributions! If you have any questions, please don't hesitate to reach out.