e4b101c93789880b099cdd781ef75ea32002707e braney Tue May 12 12:13:39 2026 -0700 quickLiftBench: Mode B cases + split hub.txt into per-genome files, refs #37445 Adds mode_b_bb and mode_b_bw cases: native render on the source assembly (hg38) vs the same source data quickLifted to a different assembly (hs1). Different db per variant; positions chosen to cover approximately the same biological region on chr22. buildTestHub.sh now emits two single-genome useOneFile hubs (hub_hs1.txt + hub_hg38.txt). A single useOneFile hub cannot host multiple genomes -- trackHubGenomeReadRa() in trackHub.c:679 breaks out of the genome-parsing loop at the first `track` line, so any 2nd `genome` block after a track stanza is silently dropped. The Mode C cases are updated to point at hub_hs1.txt. First numbers (n=10, hgwdev, chr22:15M-50M): case native lifted ratio notes mode_b_bb 2746 ms 1682 ms 0.61 hg38 trackDb load dominates native; lifted on hs1 is faster despite the chain remap. mode_b_bw 786 ms 639 ms 0.81 same effect. mode_c_hs1_bb 1830 ms 2071 ms 1.13 ~240 ms remap cost. mode_c_hs1_bw 111 ms 623 ms 5.61 ~510 ms remap cost (cold chain cache). Mode B captures the full cross-assembly cost a user sees; Mode C is the controlled isolation of pure quickLift overhead. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/utils/qa/quickLiftBench/cases.yaml src/utils/qa/quickLiftBench/cases.yaml index 89ff48c1083..5232bdc1f50 100644 --- src/utils/qa/quickLiftBench/cases.yaml +++ src/utils/qa/quickLiftBench/cases.yaml @@ -50,70 +50,115 @@ lifted: Brianraney/benchQuickList1 compare: - [native, lifted] # -------- Bench pair 1: same sessions on the public RR -------- - id: bench1_rr description: | Same session pair as bench1_hgwdev, run against genome.ucsc.edu. server: rr variants: native: Brianraney/benchQuickNative1 lifted: Brianraney/benchQuickList1 compare: - [native, lifted] + # -------- Mode B: native on source assembly vs lifted to a different one -------- + # Same hub, but the native variant views the source bigBed/bigWig on its + # own assembly (hg38) while the lifted variant views the same data quickLifted + # to a different assembly (hs1). Different db per variant. Positions chosen + # so the two windows cover approximately the same biological region. + - id: mode_b_bb + description: | + Mode B bigBed: hg38-native render (modeB_bb_native) vs the same + hg38-coord bigBed quickLifted to hs1 (modeC_bb_lifted). Measures + the cost of remap + cross-assembly rendering relative to a clean + native render. + server: hgwdev + variants: + native: + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hg38.txt + db: hg38 + position: chr22:15000000-50000000 + tracks: {modeB_bb_native: pack, modeB_bw_native: hide} + lifted: + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt + db: hs1 + position: chr22:15000000-50000000 + tracks: {modeC_bb_native: hide, modeC_bb_lifted: pack, modeC_bw_native: hide, modeC_bw_lifted: hide} + compare: + - [native, lifted] + + - id: mode_b_bw + description: | + Mode B bigWig: hg38-native render (modeB_bw_native) vs the same + hg38-coord bigWig quickLifted to hs1 (modeC_bw_lifted). + server: hgwdev + variants: + native: + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hg38.txt + db: hg38 + position: chr22:15000000-50000000 + tracks: {modeB_bb_native: hide, modeB_bw_native: full} + lifted: + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt + db: hs1 + position: chr22:15000000-50000000 + tracks: {modeC_bb_native: hide, modeC_bb_lifted: hide, modeC_bw_native: hide, modeC_bw_lifted: full} + compare: + - [native, lifted] + # -------- Mode C: lift on/off, same hub on hs1 (refs #37445) -------- # Reference hub at utils/qa/quickLiftBench/testHub/ (built by buildTestHub.sh). # Both stanzas render the same conceptual features at the same hs1 coords; # the only difference is whether the lifted variant goes through the # quickLift chain-remap path. This isolates pure quickLift overhead from # track-content differences -- the cleanest measurement for the paper. - id: mode_c_hs1_bb description: | Mode C bigBed: same hub, same position on hs1; native (hs1-coord bigBed) vs lifted (hg38-coord bigBed + quickLiftUrl chain). Isolates the chain-remap overhead from track-content differences. server: hgwdev variants: native: - hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub.txt + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt db: hs1 position: chr22:15000000-50000000 tracks: {modeC_bb_native: pack, modeC_bb_lifted: hide, modeC_bw_native: hide, modeC_bw_lifted: hide} lifted: - hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub.txt + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt db: hs1 position: chr22:15000000-50000000 tracks: {modeC_bb_native: hide, modeC_bb_lifted: pack, modeC_bw_native: hide, modeC_bw_lifted: hide} compare: - [native, lifted] - id: mode_c_hs1_bw description: | Mode C bigWig: same hub + position; native (hs1-coord bigWig) vs lifted (hg38-coord bigWig + quickLiftUrl chain). Same isolation as mode_c_hs1_bb but for the bigWig track type. server: hgwdev variants: native: - hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub.txt + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt db: hs1 position: chr22:15000000-50000000 tracks: {modeC_bb_native: hide, modeC_bb_lifted: hide, modeC_bw_native: full, modeC_bw_lifted: hide} lifted: - hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub.txt + hubUrl: https://hgwdev.gi.ucsc.edu/~braney/quickLiftBench/testHub/hub_hs1.txt db: hs1 position: chr22:15000000-50000000 tracks: {modeC_bb_native: hide, modeC_bb_lifted: hide, modeC_bw_native: hide, modeC_bw_lifted: full} compare: - [native, lifted] # -------- Regression: parallel-fetch tripwire (refs #37488, #37470) -------- # phase_asserts make this case fail-fast if the parallel pool stops # firing for quickLift tracks (e.g. a regression in isTrackForParallelLoad # or customFactoryParallelLoad). - id: regress_quickLift_parallel description: | Regression tripwire: a quickLifted multi-track session must spawn the parallel-fetch worker pool. Asserts the "Waiting for parallel..." span is emitted in every iteration.