Develop 0.3.6 #19
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Develop 0.3.6 #19
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…ith less than 10 reads back to the previous labels.
…i` because it is no longer being used.
…en an error occurs. In such cases, "Very Early Error" is indicated in the Title. Therefore, we have made it so that it returns False in those situations.
Due to alignment errors, there can be instances where a true match is mistakenly replaced with "insertion following a deletion". For example, although it should be "=C,=T", it gets replaced by "-C,+C|=T". In such cases, a process is performed to revert it back to "=C,=T".
…d in mutation_loci as mutations by replacing them with "@". For example, if there are no mutations in mutation_loci, "=G,=C,-C" and "~G,=G,=C" become "@,@,@" and "@,@,@" respectively, making them the same and ensuring they do not affect clustering.
…uence as a coverage
…ally returns True if the 'sample' shows more than 5% variation compared to the 'control'.
…d in mutation_loci as mutations by replacing them with "@". For example, if there are no mutations in mutation_loci, "=G,=C,-C" and "~G,=G,=C" become "@,@,@" and "@,@,@" respectively, making them the same and ensuring they do not affect clustering.
…rence between sample and control is more than 20%, it is unconditionally considered a mutation.
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v0.3.6 (2024-01-10)
📝 Documentation
🚀 Update
Preprocess
Updated
input_validator.py: The UCSC Blat server sometimes returns a 200 HTTP status code even when an error occurs. In such cases, "Very Early Error" is indicated in the title. Therefore, we have made it so that it returns False in those situations. Commit DetailSimplified
homopolymer_handler.pyfor error detection using cosine similarity. Commit DetailUpdated
mutation_extractor.pyto use cosine similarity to filter dissimilar loci. Commit DetailUpdated the
mutation_extractor.identify_dissimilar_lociso that it unconditionally returns True if the 'sample' shows more than 5% variation compared to the 'control'. Commit DetailAdded
preprocess.midsv_caller.convert_consecutive_indels_to_match: Due to alignment errors, instances where a true match is mistakenly replaced with "insertion following a deletion" are corrected. For example, "=C,=T" mistakenly replaced by "-C,+C|=T" is reverted back to "=C,=T". Commit DetailClassification
allele_merger.merge_minor_allelesto reclassify alleles with fewer than 10 reads to suppress excessive subdivision of alleles. Commit DetailClustering
Added the function
merge_minor_clusterto revert labels clustered with fewer than 10 reads back to the previous labels to suppress excessive subdivision of alleles. Commit DetailUpdated
generate_mutation_kmersto consider indices not registered in mutation_loci as mutations by replacing them with "@". For example, "=G,=C,-C" and "=G,=G,=C" become "@,@,@" in both cases, making them the same and ensuring they do not affect clustering. Commit DetailConsensus
LocalOutlierFactorto filter abnormal control reads. Commit Detail