Test/updating testing - #26
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Changes across all source files: - Remove dead code: delete unused src/read_parser.rs (old duplicate of file_parser.rs) and src/test.sh (unrelated rainbow ASCII script) - Pin bio dependency from "*" to "2.2.0" bloom_filter.rs: - Remove unnecessary std::ops::Drop import and extra blank lines - Merge duplicate std::io imports - Use field shorthand and implicit returns - Optimize distance() to avoid cloning entire BitVec (zero-allocation iterator) bloom_filter/hash_iter.rs: - Use BuildHasher::hash_one() instead of manual hash construction - Remove unused Hasher import, use field shorthand, clean up blank lines bloom_tree.rs: - Remove redundant 'static lifetime on constant - Remove unnecessary -> () return type and .clone() calls - Replace explicit returns with implicit returns - Simplify prune_tree conditional guards file_parser.rs: - Change get_kmers(&Vec<u8>) to idiomatic &[u8] - Fix kmer_size <= 0 (always false for usize) to kmer_size == 0 - Remove commented-out code blocks - Deduplicate FASTA/FASTQ branches in next_read() - Increase BufReader capacity from 100 bytes to 8192 query.rs: - Remove explicit returns and unused kmer_size parameter - Use .copied() instead of .map(|&x| x) - Replace .write() with .write_all() for correctness - Reduce unnecessary cloning in leaf node mapping result_map.rs: - Change &String parameters to idiomatic &str - Use entry().or_default() API instead of get_mut/else/insert - Remove commented-out debug println cache.rs: - Change &PathBuf to &Path in trait and impl signatures - Replace println! cache-miss message with log::warn! main.rs: - Remove unused 'use log' import - Fix 'cuttoff' typo to 'cutoff' - Use if-let for search_depth instead of double unwrap() - Change &PathBuf to &Path in helper function - Remove unnecessary &mut on read_block Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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This PR updates existing tests, removes dead code, and performs several optimizations.