New Features
- Add comprehensive README documentation
- Implement factor ordering for TYPE column in manifest processing
- Add LSF submission example to usage message
- Create makeIntegrateProjectFile script for data integration
- Add results documentation for split and spanning reads
Improvements
- Update regex for forteFusionFile search in reports
- Update output directory for LSF job logs
- Improve usage message clarity
Bug Fixes
- Fix typo in usage message in bicMapToSTARMap.R
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