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…query and target sequences
…sages for missing query and target metadata
…IGAR strings or tracepoints
…s, including validation for sequence data requirements and improved error messaging.
… name parameter, simplifying handling of output names.
…sequence index requirements for OneAln files.
…oved code organization and readability
…d efficiency and clarity
… enhancing logging in various functions
…nment calculations accordingly
…prove caching mechanism
… by skipping metadata loading
… update documentation to reflect no metadata loading.
…tracepoint scanning without CIGAR computation
…ate mode references from various files
…timization in output_results_bedpe and output_results_paf functions
…arget sequences and optimizing file reading with OneFile. Clean up code for clarity and maintainability.
…f using impg for genomic variation studies
…processing for improved accuracy and clarity
…duce code duplication
…d clarity and efficiency
…CIGAR reconstruction
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