openvax / isovar / 24490768466

93%

master: 94%

Pull #156

github

Add max_assembly_sequences circuit breaker to iterative_overlap_assembly

When the number of variant sequences after substring collapse exceeds
max_assembly_sequences (default 1000), skip the O(n^2)-per-round greedy
merge and return sequences sorted by read support. This prevents silent
hangs on high-coverage loci.

Three new tests: breaker triggers above threshold, disabled with None,
normal merge below threshold.

Fixes #151

5 of 5 new or added lines in 2 files covered. (100.0%)

2057 of 2210 relevant lines covered (93.08%)

2.79 hits per line