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
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
📝 Documentation
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_deletionto 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 DetailAdded
report.insertion_refractor.pyto 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 Detailrandom.sample()for subsetting reads.call_consensus_insertion_sequence.extract_score_and_sequenceto ensure correct appending of scores for the insertions_merged_subset.Changed the function name of
reportto be more explicit. Commit DetailUpdated
utils.report_report_generatorCommit DetailUpdated
utils.io.read_xlsxto 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 annin inversion. Commit DetailModified 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
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