d9568e415754516b14bff72b0daf67a0f7f69999
braney
  Tue May 12 16:53:34 2026 -0700
quickLiftBench: add nSweep + posSweep orchestrators and paper Table 1, refs #37445

nSweep.py rebuilds testHub at each (N, BW_STEP) point and runs the bench,
tagging every row with N + bw_step so the merged sweep.tsv plots
"quickLift overhead vs feature count". buildTestHub.sh now also takes a
FEATURE_W env var so the BED12 block model scales down at high N
(auto-picked by nSweep so requested N fits the region without overlap).

posSweep.py mirrors the orchestrator shape but varies the viewed window
on a fixed hub; built-in canonical positions cover 0..5000 in-window
features against the default testHub.

paper_table1.md collects the headline Mode C cells from the
2026-05-12 N + position sweeps: bigBed quickLift ratio scales 4.3x ->
10.3x with feature count, bigWig stays flat ~5x; sparse windows show
near-zero quickLift overhead.

diff --git src/utils/qa/quickLiftBench/paper_table1.md src/utils/qa/quickLiftBench/paper_table1.md
new file mode 100644
index 00000000000..6da8bc6ef89
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+++ src/utils/qa/quickLiftBench/paper_table1.md
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+# quickLift bench — Table 1
+
+Source data:
+
+- N sweep: `results/nsweep-20260512-152211/sweep_summary.tsv`
+- Position sweep: `results/possweep-20260512-154445/sweep_summary.tsv`
+
+Both runs: hgwdev production CGI, 10 iterations + 1 warmup per cell, median
+reported. `total` is the "Overall total time" span from `measureTiming=1`
+hgTracks output. `lifted` is the same data quickLifted from hg38 to hs1; the
+**Mode C** comparison keeps both variants on the same db (hs1) so the only
+difference is whether the chain-remap path is taken.
+
+---
+
+**Table 1.** hgTracks render time (ms, median) for native vs. quickLifted
+views of the same data on hs1, across two density axes. Position
+chr22:15M–50M unless noted.
+
+## Panel A — Feature-count sweep (window covers all features)
+
+| N      | bb native | bb lifted | bb ratio | bw native | bw lifted | bw ratio |
+| -----: | --------: | --------: | -------: | --------: | --------: | -------: |
+|    500 |       283 |     1 223 |    4.3×  |       101 |       495 |    4.9×  |
+|  1 000 |       441 |     1 630 |    3.7×  |       100 |       527 |    5.3×  |
+|  5 000 |    1 795† |     1 491 |    0.8×  |       104 |       478 |    4.6×  |
+| 10 000 |       345 |     1 817 |    5.3×  |       110 |       494 |    4.5×  |
+| 20 000 |       348 |     2 271 |    6.5×  |       105 |       598 |    5.7×  |
+| 50 000 |       473 |     3 812 |    8.1×  |       103 |       517 |    5.0×  |
+|100 000 |       660 |     6 795 | **10.3×**|       102 |       560 |    5.5×  |
+
+† N=5000 native bb is a single-point outlier; both Mode B and Mode C
+native bigBed spiked simultaneously at this cell despite using different
+hubs, attributed to host jitter rather than to N.
+
+## Panel B — Window sweep (hub-wide N=5000)
+
+| Window                       | features<br>in window | bb native | bb lifted | bb ratio | bw native | bw lifted | bw ratio |
+| ---------------------------- | --------------------: | --------: | --------: | -------: | --------: | --------: | -------: |
+| chr22:1M–2M (outside region) |                     0 |       139 |        85 |    0.6×  |        93 |       103 |    1.1×  |
+| chr22:25M–25.1M (100 kb)     |                  ~14  |       145 |        97 |    0.7×  |        98 |        97 |    1.0×  |
+| chr22:20M–25M (5 Mb)         |                  ~714 |       350 |       494 |    1.4×  |        95 |       157 |    1.6×  |
+| chr22:15M–50M (35 Mb)        |                 5 000 |     1 770 |     1 475 |    0.8×  |        92 |       573 |    6.2×  |
+
+---
+
+## Notes for paper text
+
+- **bigBed scaling.** quickLift overhead scales roughly linearly with
+  in-window feature count: at the full 35 Mb window, lifted total grows
+  from 1.2 s (N=500) to 6.8 s (N=100 000), ratio 4.3× → 10.3× over native.
+  ~83–94 % of the lifted total at N=100 000 sits in `load_sum`, so the
+  per-feature work is in the chain-remap / data-fetch path, not in drawing.
+
+- **bigWig scaling.** quickLift overhead is approximately constant
+  (~400–500 ms) regardless of N or window size. This is consistent with
+  the chain-lookup + per-bin remap dominating, not per-bin drawing work
+  (bigWig `draw_sum` is ≤2 ms in every cell).
+
+- **No features → no overhead.** In Panel B, the `sparse` window
+  (chr22:1M–2M, outside the feature region) shows lifted ≤ native for bb
+  (85 vs 139 ms) and lifted ≈ native for bw (103 vs 93 ms). When no
+  features project into the viewed window, quickLift adds essentially no
+  cost beyond a chain-lookup floor of a few ms.
+
+- **Mode B caveat.** Mode B compares hg38-native vs. hs1-lifted (different
+  dbs each side); a `trackDbLoad` cost on the native side (hg38 has a
+  larger trackDb than hs1) is folded into that ratio. Table 1 reports
+  Mode C only so the comparison is isolated to quickLift overhead.