fix(alignments): pileup soft-clip layout cap and sort order (#3471, #4671)#5526
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fix(alignments): pileup soft-clip layout cap and sort order (#3471, #4671)#5526
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Layout used full mismatch soft-clip lengths for collision intervals while region fetch only expands by maxClippingSize (PileupRenderer.getExpandedRegion). Cap left/right expansion per side to match config and reduce pathological layout width with show soft clipping (GMOD#3471). Tests: layoutFeature.test.ts Made-with: Cursor
…lipping (GMOD#4671) PileupLayout relies on processing reads in left-to-right order of the collision interval. Sorting only by genomic start disagrees with expanded left coordinates from soft clips, breaking row hints and spacing. Export getPileupLayoutSpan and use it for the default sort when not using sortedBy. Made-with: Cursor
Abdeltoto
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Summary
#3471 — cap layout span
Pileup layout expanded soft-clipped reads using the full
mismatchesclip lengths, while feature fetching only expands the visible block bymaxClippingSize(PileupRenderer.getExpandedRegion). That mismatch could make layout intervals far wider than the data region and stress the pileup layout.Change: cap left and right soft-clip expansion per side to
maxClippingSize, summing clips on each side first then applying the cap. Shared helper:getPileupLayoutSpan.#4671 — sort order vs layout interval
PileupLayoutassumes features are processed in left-to-right order of the collision interval. Sorting only by genomicstartdisagrees with expanded left coordinates when soft clipping is on, which breaks row hints and can produce poor vertical spacing.Change: when not using
sortedBy, sort by layout left edgesfromgetPileupLayoutSpan(tie-break: genomicstart).Testing
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