Changes in version 0.99.12 (2026-03-31) Pre-release version on Bioconductor devel. Changes in version 0.99.11 (2026-03-10) OTHER CHANGES - Bioconductor compliance: run_fRagmentomics() now returns a S4Vectors::DataFrame instead of a base data.frame. - VCF import: Replaced the custom VCF parser with VariantAnnotation::readVcf() for standard-compliant VCF reading. Compressed files (.vcf.gz) must now be bgzip-compressed and tabix-indexed. Added VariantAnnotation as an explicit dependency. - Performance: Replaced incremental rbind()/rbindlist() patterns in run_fRagmentomics(), normalize_mut(), and remove_bad_mut() with list-based collection followed by a single bind. - Pipe cleanup: Replaced all magrittr pipes (%>%) with the native R base pipe (|>) across all plotting functions. magrittr is no longer a dependency. Changes in version 0.99.10 (2026-02-22) OTHER CHANGES - Windows Compatibility: Enforced strict LF line endings for FASTA files via .gitattributes to prevent Rsamtools indexing errors (.fai) on Windows environments. - Compatibility: Replaced native R pipes (|>) with magrittr pipes (%>%) to ensure broader backward compatibility and avoid R (>= 4.1.0) dependency warnings. Changes in version 0.99.9 (2026-02-18) OTHER CHANGES - Preparing pre-release version. - Test: Add test to the package. Changes in version 0.99.4 (2026-02-17) NEW FEATURES - Example Dataset: Added a benchmark case study featuring a 15-bp in-frame deletion in EGFR exon 19 (lung cancer cfDNA) to demonstrate indel-specific fragment sizing and genotyping. - Reproducibility Scripts: Included data generation and anonymization scripts for the test dataset in inst/scripts/. - Developer Tools: Added a pre-commit configuration to standardize the development workflow. OTHER CHANGES - Documentation: - Updated README and vignette to incorporate the new case study and illustrative figures. - Testing: Updated the test suite to include coverage for the new EGFR case study. Changes in version 0.99.3 (2026-02-16) OTHER CHANGES - QC Logic: Improved process_fragment_reads_QC with updated default parameters and enhanced messaging for failed fragments. - Code Refactoring: Factorized internal code and replaced stop() calls in extract_fragment_features to improve robustness. Changes in version 0.99.2 (2025-10-28) OTHER CHANGES - Improved future.apply::future_lapply parallelization by setting properly the chunk parameter and reduced exported objects per worker. Changes in version 0.99.1 (2025-10-22) NEW FEATURES - Added flag_bam_list instead of TLEN (default: FALSE). Parameter to include all BAM fields in the output. - Added Position_3p to the output. Position_3p represents the last aligned position of the 3′ read of the fragment. - Replaced rbind in the main function with data.table::rbindlist to make it more consistent and faster. OTHER CHANGES - Change future.apply::future_lapply parameter to remove a warning. Changes in version 0.99.0 (2025-10-09) NEW FEATURES - Added verbose (default FALSE) parameter to remove messages. Changes in version 0.2.9 (2025-10-07) NEW FEATURES - Change fragment if DIS with potentially compatible with DIS. OTHER CHANGES - Update vignette. - Fix some display errors on graph functions. Changes in version 0.2.8 (2025-08-27) NEW FEATURES - Added new plotting functions for in-depth fragment analysis: - plot_size_distribution() to visualize fragment size distributions. - plot_freq_barplot() to display nucleotide frequencies in end motifs. - plot_ggseqlogo_meme() for generating sequence logo plots of end motifs using ggseqlogo. - plot_motif_barplot() for generating end motifs in barplot. OTHER CHANGES - The package has been updated to meet all Bioconductor submission requirements. Changes in version 0.2.7 (2025-08-15) IMPROVEMENTS - Improved fragment size calculation to more accurately account for insertions and deletions within the overlapping section of read pairs. - Added the remove_softclip parameter to trim soft-clipped bases from the ends of fragments. Changes in version 0.2.6 (2025-07-30) IMPROVEMENTS - Upgraded BAM flag selection for more precise read filtering. - Fragments with reads aligned in the same orientation are now automatically removed. - The definition of 5' and 3' reads is now based on strand information rather than genomic position for greater accuracy. Changes in version 0.2.5 (2025-07-10) NEW FEATURES - Introduced parallel processing (future) and a progress bar (progressr) to significantly speed up analysis on multi-core systems. IMPROVEMENTS - Improved mutation classification for reads with soft-clipping at their ends, preventing potential false negatives. Cases previously classified as WT are now correctly labeled AMB. - Added an Input_Mutation column to the output to retain the original mutation information before normalization. Changes in version 0.2.4 (2025-06-25) BUG FIXES - Fixed a critical bug related to incorrect fetching of the reference sequence. - Improved handling of ambiguous cases and multi-nucleotide variants (MNVs). - Optimized the SNV detection algorithm. Changes in version 0.2.3 (2025-06-12) IMPROVEMENTS - Improved performance by replacing per-fragment FASTA requests with a single, larger request per mutation, resulting in a 1.5x to 2x speed increase. Changes in version 0.2.2 (2025-05-20) IMPROVEMENTS - Introduced more descriptive mutation statuses (e.g., "MUT but potentially larger MNV", "OTH (DEL)"). - Updated the reporting of BASE_5p and BASE_3p to be more comprehensive around the variant position. - Finalized the definitions for Fragment_Status_Simple and Fragment_Status_Detail columns. BUG FIXES - Corrected mutation status assignment for reads with hard or soft-clipping near the variant. - The get_index_aligning_with_pos() function now correctly handles deletions at the position of interest. OTHER CHANGES - Renamed parameter cigar_free_mode to cigar_free_indel_match for clarity. Changes in version 0.2.1 (2025-05-01) BUG FIXES - Corrected the Variant Allele Frequency (VAF) calculation. OTHER CHANGES - Harmonized all output column names to use "Upper_Snake_Case" for consistency. Changes in version 0.2.0 (2025-04-15) NEW FEATURES - Implemented a new, alternative algorithm for determining mutation status that is independent of the CIGAR string. This significantly improves INDEL detection and is controllable via the cigar_free_indel_match parameter. OTHER CHANGES - Major code refactoring for clearer function names and better maintainability. Changes in version 0.1.0 (2025-03-01) NEW FEATURES - Initial beta version of the package. - Core functionality for extracting key fragmentomic features, including end motifs and fragment size. - Initial implementation of fragment mutational status classification (e.g., WT, MUT, AMB, and more complex states)