Change: Method of counting indels modified to use only matches as the denominator, instead of matches + indels.
Reason: To specifically focus on the occurrence rate of particular mutations.
find_dissimilar_indices:
Change: Mutation detection modified. If the p-value remains < 0.05 after removing the target base sequence, the area is not detected as a mutation, assuming the significance is due to other parts.
Implication: Increases mutation detection accuracy by excluding irrelevant base sequences.
merge_index_of_consecutive_indel:
Change: Merged merge_surrounding_index and merge_index_of_consecutive_insertions into a single function.
Benefit: Streamlines the process and enhances efficiency in handling consecutive indels.
Addressed a precision issue in floating-point calculations where N equals 100%, leading to 100 != 100.000002. Changed the condition to "having only one key and that key being N". Commit details
Update mutation_extractor.py:
Switched to the Wilcoxon signed-rank test due to false negatives in the t-test for data with peak-like shapes. Commit details
Others
Modified batch processing to run on a single CPU thread per process.
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preprocess.mutation_extractor.pycount_indels:find_dissimilar_indices:merge_index_of_consecutive_indel:merge_surrounding_indexandmerge_index_of_consecutive_insertionsinto a single function.Commit details
Update
consensus.consensus.py:100 != 100.000002. Changed the condition to "having only one key and that key beingN". Commit detailsUpdate
mutation_extractor.py:Others
clust_formatter.cache_mutation_loci.mutation_extractor.merge_locito use union instead of intersection.insertions_to_fasta.py.insertion_to_fasta.save_fastatoutils.io.save_fasta.