NEWS

baseq 0.2.0 (2026-03-11)

Replaced slow loops with highly optimized, vectorized functions for sequence translation, cleaning, and file reading.
Introduced universal wrappers (clean_seq, read_seq, write_seq, rev_comp) to simplify workflows, along with snake_case aliases (clean_dna_seq, clean_rna_seq) while maintaining backward compatibility.
Added find_longest_orf, find_cpg_islands, search_motif, shuffle_sequence, and robust sequence simulators (simulate_sequence, simulate_fasta, simulate_fastq).
Added calculate_tm, calculate_mw, calculate_pi, calculate_charge, and simulate_pcr, simulate_digestion.
Added publication-ready ggplot2 functions (plot_gc_skew, plot_hydrophobicity, plot_aa_composition, plot_dotplot).
Added baseq_dna and baseq_rna object classes and translate() S3 method. Added as_Biostrings bridge.
Added a comprehensive testthat suite with 30+ passing categories handling edge cases (NA/NULL handling, blank inputs, malformed files).