Consolidate dot_prep into uniq_anchor; add regression tests#71
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dot_prep previously re-read the delta file twice and re-ran the full planesweep filtering already done by uniq_anchor. Now uniq_anchor builds and returns (reference_lengths, fields_by_query) during its existing second pass, which cli.py threads directly into index_for_dot(). This removes ~300 lines of duplicate code and shaves ~3-4s off every run. Also fixed a latent bug in index_for_dot() where all_references_by_query used a stale `ref` variable for repetitive alignments; now uses fields[6]. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Runs the full pipeline on the ecoli example (fast, ~5s) and compares key text outputs against checked-in fixtures. Covers structural variants BED, coords files, dot visualization coords/index, and assembly stats. GitHub Actions runs these on every push and PR. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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From Maria
Remove a duplicate step that Dot and Assemblytics had in common. They both did unique anchor filtering, so now that's only done once.
Also add pytest with a github action to ensure basic regression testing runs automatically on all new PRs.
From Claude
dot_prep.pypreviously re-read the delta file twice and re-ran the full planesweep filtering thatuniq_anchor.pyhad already done. Nowuniq_anchor.run()builds and returns(reference_lengths, fields_by_query)during its existing second pass, whichcli.pythreads directly intoindex_for_dot().dot_prep.py(duplicatesummarize_planesweep,binary_search,getQueryRefCombinations,calculateUniqueness,writeFilteredDeltaFile).index_for_dot()whereall_references_by_queryused a stalerefvariable for repetitive alignments instead offields[6].tests/test_pipeline.pyruns the full pipeline on the ecoli example (~5s) and does exact-match comparison against checked-in fixture files for all key text outputs..github/workflows/test.ymlrunspyteston every push and PR.Test plan
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