Migrate to mappy - #63
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- Implemented a test suite for validating the migration from minimap2 executable to mappy, ensuring compatibility and performance. - Added tests for basic alignment, output format, and edge cases in the minimap2 compatibility tests. - Created unit tests for SAM format conversion utilities, including CIGAR string conversion and SAM line construction. - Included tests for calculating SAM flags and generating SAM headers. - Established helper functions for converting mappy's internal format to SAM format, ensuring proper integration with the existing codebase.
…th complex sequences
…ions and ensuring backward compatibility. Update documentation and migration checklist.
…for mappy installation in migration checklist.
…lation assumptions to rely solely on mappy.
…se mappy exclusively
…ove Docker/Singularity testing steps
… verify no minimap2 dependency
…ve deprecated parameters, and complete code cleanup.
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Closes #29