openvax / isovar / 24485183893

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Fix: collapse_substrings no longer re-appends absorbed short sequences (#139)

The inner loop over candidate superstrings reassigned `found_superstring` on
every iteration, so its final value only reflected whether the LAST candidate
contained the short sequence — not whether any of them did. When a shorter
VariantSequence was contained in an earlier (longer) result but not in a
later one, the short sequence's reads were both absorbed into the earlier
result AND the short sequence itself was appended to result_list, causing
the same reads to be counted twice in downstream assembly.

Add a `break` after the first superstring match so short sequences are
absorbed into exactly one superstring and not reappended.

Add two regression tests covering (a) the original scenario and (b) the
case where the short sequence has multiple valid superstrings.

Fixes #130

4 of 4 new or added lines in 2 files covered. (100.0%)

2022 of 2176 relevant lines covered (92.92%)

2.79 hits per line