Add tests: bamCoverage RPKM/scaleFactor, alignmentSieve fragment/strand filters#1434
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…t/strand filtering Fills coverage gaps identified while triaging the stalled #1369 tests: - bamCoverage: --normalizeUsing RPKM (RPKM was untested; suite only had CPM/RPGC) and --scaleFactor. - alignmentSieve: --minFragmentLength/--maxFragmentLength and --filterRNAstrand (neither was tested anywhere). Expected values derived by running the current tools; all pass under `pixi run pytest`. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Fills coverage gaps surfaced while triaging the stalled #1369 tests (the direct-Rust-binding versions couldn't be salvaged, but two of their ideas covered untested paths).
bamCoverage (
test_bamCoverage_and_bamCompare.py)--normalizeUsing RPKM— RPKM was untested; the suite only covered CPM and RPGC.--scaleFactor— manual scale factor (also documents that it takes precedence over--normalizeUsing).alignmentSieve (
test_alignmentseive.py)--minFragmentLength/--maxFragmentLength— fragment-size selection was untested.--filterRNAstrand forward— not exercised anywhere in the suite.Expected values were derived by running the current tools; assertions use the existing filterMetrics/bedgraph style. Verified locally:
pixi run pyteston both files → 26 passed (22 existing + 4 new).🤖 Generated with Claude Code