[x] Added ROADMAP.md to track the progress of the project Commit Detail
[x] Added Prerequisites section to README.md Commit Detail
🚀 Features
Preprocessing
[x] Updated homopolymer_handler.get_counts_homopolymer to change to count mutations in homopolymer regions considering only the control Commit Detail
Clustering
[x] Changed clustering algorithm from KMeans to BisectingKMeans to handle larger dataset Commit Detail
Consensus
[x] Added convert_consecutive_indels_to_match to offset the effect when the same base insertion/deletion occurs consecutively Commit Detail
[x] Added similarity_searcher.py to extract control reads resembling the consensus sequence, thereby enhancing the accuracy of detecting sample-specific mutations. Commit Detail
[x] Changed the method in `clust_formatter.get_thresholds`` to dynamically define the thresholds for ignoring mutations, instead of using fixed values.Commit Detail
[x] Removed code that was previously commented out Commit Detail
🐛 Bug Fixes
None
🔧 Maintenance
[x] Modified batch processing to run on a single CPU thread per process Commit Detail
v0.3.5
Last update: 2023-12-23
📝 Documentation
ROADMAP.mdto track the progress of the project Commit Detail🚀 Features
Preprocessing
homopolymer_handler.get_counts_homopolymerto change to count mutations in homopolymer regions considering only the control Commit DetailClustering
Consensus
[x] Added
convert_consecutive_indels_to_matchto offset the effect when the same base insertion/deletion occurs consecutively Commit Detail[x] Added
similarity_searcher.pyto extract control reads resembling the consensus sequence, thereby enhancing the accuracy of detecting sample-specific mutations. Commit Detail[x] Changed the method in `clust_formatter.get_thresholds`` to dynamically define the thresholds for ignoring mutations, instead of using fixed values.Commit Detail
[x] Removed code that was previously commented out Commit Detail
🐛 Bug Fixes
🔧 Maintenance
[x] Modified batch processing to run on a single CPU thread per process Commit Detail
[x] Simplifed import path Commit Detail
preprocess.midsv_caller.executetopreprocess.generate_midsvpreprocess.mapping.generate_samtopreprocess.generate_sam[x] Added tests to
consensus.convert_consecutive_indels_to_matchCommit Detail⛔️ Deprecated