openvax / isovar / 24491093336

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Handle mixed alleles in get_single_allele_from_reads instead of crashing (#157)

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

9 of 9 new or added lines in 3 files covered. (100.0%)

2061 of 2212 relevant lines covered (93.17%)

2.8 hits per line