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@akikuno akikuno released this 13 Feb 05:40
· 301 commits to main since this release
0.4.1
777bb74
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Learn about vigilant mode.

📝 Documentation

  • Added documentation for a new feature in README.md: DAJIN2 can now detect complex mutations characteristic of genome editing, such as insertions occurring in regions where deletions have occurred.

🚀 New Features

  • Introduced cssplits_handler.detect_insertion_within_deletion to extract insertion sequences within deletions. This addresses cases where minimap2 may align bases that partially match the reference through local alignment, potentially failing to detect them as insertions. This enhancement ensures the proper detection of insertion sequences. Commit Detail

  • Added report.insertion_refractor.py to include original insertion information in the consensus for mappings made by insertion. This addition enables the listing of both insertions and deletions within the insertion allele on a single HTML file. Commit Detail

🔧 Maintenance

  • Updated insertions_to_fasta.py. Commit Detail

    • Modified the approach to reduce randomness by replacing set or frozenset with list or tuple, and using random.sample() for subsetting reads.
    • Refactored call_consensus_insertion_sequence.
    • Fixed a bug in extract_score_and_sequence to ensure correct appending of scores for the insertions_merged_subset.

  • Changed the function name of report to be more explicit. Commit Detail

  • Updated utils.report_report_generator Commit Detail

    • Capitalized "Allele" (e.g., control) and "Allele type" (e.g., intact).
    • Changed the output format of read_all and read_summary from CSV to XLSX.
    • Corrected the order of the Legend to follow a logical sequence from control to sample, and then to specific insertions.

  • Updated utils.io.read_xlsx to switch from using pandas to openpyxl due to the DeprecationWarning in Pandas being cumbersome. Commit Detail

🐛 Bug Fixes

  • Added = to the prefix for valid cstag recognition when there is an n in inversion. Commit Detail

  • Modified the io.load_from_csv function to trim spaces before and after each field, addressing an error caused by spaces in batch.csv. Commit Detail

⛔️ Deprecated

  • Removed reads_all.csv. This CSV file, which showed the allele for each read, is no longer reported due to its limited usefulness and because the same information can be obtained from the BAM file. Commit Detail
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