test: A/B bench harness that drops rounds it could not measure honestly

[BenjaminDEMAILLE]

test/bench_ab.sh: interleaved A/B of two binaries, which drops the rounds it could not measure honestly instead of averaging over them.

Why

Four traps, each of which I fell into at least once while measuring this aligner over one session. Three are now enforced by the script; the fourth is documented in its header because no script can enforce it.

Idle was checked once, at the start. A previous harness sampled CPU idle before the first run and never again. Three separate measurements then drifted below the threshold mid-series and it kept going, leaving the contaminated rounds to be spotted by eye. This samples idle before and after every run, drops the round if any of the four samples falls short, and prints the count:

round1  binA=3.33s binB=3.42s  idle>=84.92%
round3  binA=3.25s binB=3.22s  DROPPED (idle fell to 71.4%)

kept 4 of 6 rounds (2 dropped)

A median over four surviving rounds now cannot be read as a median over six. No silent truncation.

Load average is the wrong signal. It is an exponential average over minutes, so it stays high long after the offending job has gone. An earlier guard refused to measure at 2.24 on a machine whose sixteen cores were all free. The check is on CPU idle percentage, which answers the question actually being asked.

A median can be smaller than the noise. The script prints the spread within each side next to the difference between the medians, and when the difference is smaller it says so:

median  binA=3.305s  binB=3.25s  delta=-1.7%
spread  binA=0.08s   binB=0.20s

the difference between the medians is smaller than the spread within a side.
that is not a result: report it as unmeasured rather than as a speedup.

That message is not hypothetical. Two changes I measured this week looked like wins on medians alone and were inside the spread; both are now described as unmeasured in their PRs (#169, #170).

Both sides must see identical argv. @PG CL: records the command line verbatim, so running ./old against ./new, or writing to differently-named output directories, makes the BAM differ in the header and in its compressed size. That cost me two false "output is not neutral" alarms. Each side is copied to rustar-aligner inside its own directory and run with --outFileNamePrefix ./.

Timing a total hides the part that changed. Only in the header, since it is a judgement the script cannot make: BAM writing is 1-4% of a yeast run, so a total dominated by alignment cannot resolve a change to the writer at any reachable scale. Run one configuration with --outSAMtype None alongside and read the difference. #164 was closed because that difference, once isolated, showed the change was a regression rather than the improvement its description claimed.

Usage

test/bench_ab.sh <binA> <binB> <genomeDir> <reads.fastq> [threads] [rounds]

BENCH_MIN_IDLE=88   percent CPU idle a round must hold to count
BENCH_MODE="None"   --outSAMtype words (quote the two-word forms)
BENCH_ARGS=""       extra flags passed to both sides

It exits non-zero if every round was dropped, rather than printing a median over nothing.

Scope

Test tooling only: no source change, no dependency, nothing user-facing, so no CHANGELOG entry. The numbers in #167 and #170 were produced with the same method; this makes the method reproducible rather than living in my shell history.

Happy to add a pointer to it from CONTRIBUTING.md's verification section if you want one there, but I did not want to edit that file uninvited.

Related: #168 has the allocation measurements taken with this method, including the result that removing 7.6% of the allocations moved nothing.