Releases: JSBarrington/ez-phase
Releases · JSBarrington/ez-phase
1.1.2
Full Changelog: v1.1.1...1.1.2
EZ-PHASE v1.10.0 - Enhanced File Management & Process Control
EZ-PHASE v1.10.0 - Enhanced File Management & Process Control
This major release transforms EZ-PHASE into a professional-grade bioinformatics tool with robust file management, enhanced process control, and advanced parameter support.
What's New?
Enhanced File Management System
- Visual Status Tracking: Real-time indicators show file progress (📄 pending → ⚙️ processing → ✅ completed → ❌ error)
- Smart File Controls: Remove files with status-aware buttons (can't remove files currently being processed)
- File Information: Display file sizes and detailed metadata
- Batch Processing: Handle multiple .inp files with individual progress tracking
Advanced Process Control
- Stop/Cancel Functionality: Safely terminate PHASE processes with proper cleanup
- Process Group Management: Handles child processes and prevents zombies
- Force-Kill Protection: Automatic cleanup if processes don't respond gracefully
- Recovery Mechanisms: Reset file states and UI after interruptions
Auto-Detection Features
- Parallel Processing: Automatically detect optimal CPU core count
- Smart Defaults: Intelligent parameter suggestions based on system capabilities
- Resource Optimization: Better memory and CPU usage for large datasets
Advanced PHASE Parameters
- Full MR Model Support: Complete implementation of MR1, MR2, MR4 recombination models
- Hotspot Analysis: Specify custom hotspot intervals with visual controls
- Mutation Models: Support for delta-files and parent-independent mutation (PIM)
- Parameter Validation: Real-time validation with helpful error messages
Real-Time Progress Tracking
- Live Updates: Watch files progress through processing stages
- Output Streaming: Real-time PHASE output and error messages
- Progress Bars: Visual indication of overall completion status
- Execution Logs: Detailed logging for troubleshooting and analysis
🔧 Technical Improvements
Performance & Stability
- Reduced memory usage for large datasets (>500 individuals)
- Better cross-platform process management (Windows/macOS/Linux)
- Enhanced error recovery and cleanup mechanisms
- Improved file system operations with proper locking
User Experience
- More intuitive parameter organization and tooltips
- Better visual feedback for all user actions
- Enhanced error messaging with actionable suggestions
- Responsive design improvements for different screen sizes
Who Should Upgrade?
Essential for users who:
- Process multiple files regularly (batch workflows)
- Work with large datasets requiring reliable process control
- Need advanced PHASE parameters (hotspots, custom priors)
- Want professional-grade progress tracking and logging
Especially valuable for:
- Population geneticists analyzing multiple populations
- Researchers working with recombination hotspots
- Labs processing high-throughput genotyping data
- Anyone who has experienced crashes or hangs with previous versions
Download & Install
| Platform | File | Size | Instructions |
|---|---|---|---|
| macOS | EZ-PHASE-1.10.0.dmg | ~120MB | Download, mount, drag to Applications |
| Windows | EZ-PHASE Setup 1.10.0.exe | ~140MB | Download and run installer |
| Linux | EZ-PHASE-1.10.0.AppImage | ~130MB | Download, chmod +x, and execute |
Quick Start
- Download PHASE 2.1.1 from Stephens Lab
- Launch EZ-PHASE and browse to your PHASE binary
- Select your .inp files and watch the enhanced status tracking
- Configure parameters with the improved advanced options
- Run with real-time progress monitoring and robust process control
Changelog Summary
- Enhanced file management with visual status tracking
- Robust stop/cancel functionality with proper cleanup
- Auto-detect parallel processing optimization
- Complete advanced parameter UI (MR1/MR2/MR4 models)
- Real-time progress tracking and output streaming
- Improved cross-platform stability and performance
- Better error handling and recovery mechanisms
Bug Fixes
- Fixed process zombie prevention on all platforms
- Resolved file locking issues during batch processing
- Eliminated memory leaks in long-running operations
- Corrected cross-platform path handling inconsistencies
Full documentation: See the updated README.md for comprehensive usage instructions and parameter explanations.
Need help? Open an issue or discussion on this repository.
Citation: If you use EZ-PHASE in your research, please cite both this software and the original PHASE paper (Stephens et al. 2001)
EZ-PHASE 1.1.1.
Fixed a critical bug where the stop button was not functional.
Resolved an issue preventing the application icon from displaying correctly on macOS.
Corrected a syntax error in the analysis script that caused runs to fail immediately.
General stability improvements.
Happy phashing!