Add parasail alignment backend to pileup tile functions#167
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- Add cigar_to_subs() to convert parasail extended-CIGAR to HiGlass subs format
- Add tile_functions_parasail() that pre-builds one scoring profile per
reference sequence and aligns all queries against it, ~9x faster than
the BioPython PairwiseAligner path for large batches
- Update get_pileup_alignment_data() with a method parameter
("biopython" default, or "parasail") and fix the tile ID from "0.0"
to "x.0.0"; return key renamed from "type" to "tileset_info"
- Make the csv_sequence_tileset_functions import lazy to avoid pulling
in smart_open on every module import
- Add examples/sequence_pileup.py benchmark script
- Restructure test file so mappy-dependent tests skip individually (via autouse fixture) rather than skipping the whole module, allowing parasail and BioPython tests to run without mappy installed - Add TestCigarToSubs: covers all-match, single mismatch, insertion, deletion, and multiple-mismatch CIGAR patterns - Add TestGetPileupAlignmentDataParasail: covers result structure, identical sequence, substitution detection, multiple sequences, tileset_info fields, and read IDs
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Summary
tile_functions_parasail()which pre-builds a parasail scoring profile from the reference once and aligns all query sequences against it using NW global alignment with CIGAR traceback — approximately 9× faster than the existing BioPythonPairwiseAlignerpath on large batches (benchmarked at 50k × 250 nt sequences)cigar_to_subs()to convert parasail's extended-CIGAR (=/X/I/D) to the HiGlass pileup subs format, matching the coordinate convention ofalignment_to_subs()get_pileup_alignment_data()with amethodparameter ("biopython"default,"parasail")"0.0"(which would raiseIndexError) to"x.0.0"; renames the return key"type"→"tileset_info"for consistencycsv_sequence_tileset_functionsimport lazy to avoid pulling insmart_open(and its transitive deps) on everyimport clodius.tiles.pileupexamples/sequence_pileup.pybenchmark scriptTest plan
pytest test/tiles/pileup_test.pyexamples/sequence_pileup.pyand verify parasail output is produced without errorfrom clodius.tiles.pileup import get_pileup_alignment_datadoes not raiseModuleNotFoundErrorforsmart_openin a minimal environment