Fix #152: handle mixed alleles gracefully instead of crashing#157
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Previously raised ValueError if reads had different alleles. Now uses the most common allele and filters to only matching reads, with a warning. Return signature changed to (allele, filtered_reads) tuple. This handles edge cases from indel representation ambiguity or subclonal mixtures without crashing. Callers using the old single-return-value signature are updated (variant_sequence_creator.py). Fixes #152
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coverage: 93.174% (+0.1%) from 93.077% — fix-152-subclonal-allele-crash into master |
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Summary
get_single_allele_from_readsnow returns(allele, filtered_reads)instead of justallele.variant_sequence_creator.py.Fixes #152
Test plan
./test.shpasses (169 tests)./lint.shpasses