Feat/cached screen#4
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- Introduced `cut_cache_test.go` with comprehensive tests for cut functions. - Enhanced `Cuts` and `CutsEach` methods for improved enzyme cut handling. - Added error handling for nil emit callbacks in digest functions.
- Introduced the `screen` package for cached cut-index helpers. - Implemented `BuildCutIndex` to store enzyme cut positions. - Added functions to score enzyme pairs and generate summaries. - Created tests for the new functionality to ensure correctness.
- Introduced a new command `radigest-screen-pairs-cached` for enzyme pair screening. - Added support for outputting results in JSON format. - Implemented parallel processing for scoring enzyme pairs. - Enhanced the Makefile to include the new command in build and install processes. - Added unit tests to validate the new functionality.
- Introduced BuildCutIndexFromFASTA for efficient cut index creation. - Added BuildCutIndexFromRecords to handle streaming records. - Updated main CLI to utilize new cut index methods for performance. - Enhanced error handling in cut index functions. - Added tests for new cut index methods to ensure correctness.
- Updates the version number in main.go to v0.3.1.
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