0.3.5

Last update: 2023-12-23

📝 Documentation

• Added ROADMAP.md to track the progress of the project Commit Detail
• Added Prerequisites section to README.md Commit Detail

🚀 Features

Preprocessing

• Updated homopolymer_handler.get_counts_homopolymer to change to count mutations in homopolymer regions considering only the control Commit Detail

Clustering

• Changed clustering algorithm from KMeans to BisectingKMeans to handle larger dataset Commit Detail

Consensus

• Added convert_consecutive_indels_to_match to offset the effect when the same base insertion/deletion occurs consecutively Commit Detail

• Added similarity_searcher.py to extract control reads resembling the consensus sequence, thereby enhancing the accuracy of detecting sample-specific mutations. Commit Detail

• Changed the method in `clust_formatter.get_thresholds`` to dynamically define the thresholds for ignoring mutations, instead of using fixed values.Commit Detail

• Removed code that was previously commented out Commit Detail

🐛 Bug Fixes

• None

🔧 Maintenance

• Modified batch processing to run on a single CPU thread per process Commit Detail

• Simplifed import path Commit Detail

  • preprocess.midsv_caller.execute to preprocess.generate_midsv
  • preprocess.mapping.generate_sam to preprocess.generate_sam

• Added tests to consensus.convert_consecutive_indels_to_match Commit Detail

⛔️ Deprecated

• None