funannotate train: operator-precedence bug in bamthreads calculation (aux_scripts/trinity.py)

[hyphaltip]

Describe the bug

In runTrinityGG(), the number of samtools sort compression threads is
computed as:

https://github.com/nextgenusfs/funannotate/blob/target_1.9/rust_EVM_trinity_PASA/funannotate/aux_scripts/trinity.py#L54

bamthreads = (args.cpus + 2 // 2) // 2

Python operator precedence evaluates 2 // 2 first (= 1), so this is
actually (args.cpus + 1) // 2, not (args.cpus + 2) // 2 as the spacing
implies was intended (a "use half the CPUs, rounded up" comment would fit
(args.cpus + 1) // 2 for round-up-of-half, but the + 2 visually suggests
a different rounding intent that isn't what's executed).

Concretely:

• args.cpus=2: intended-looking (2+2)//2=2, actual (2+1)//2=1 — happens
  to be harmless here since 1 is a reasonable thread count at cpus=2, which
  is likely why this has gone unnoticed.
• args.cpus=8: (8+2)//2=5 vs actual (8+1)//2=4 — diverges once CPU
  counts increase (e.g. as part of fixing funannotate train: Trinity-GG Butterfly assembly pool sized cpus-1, wastes requested parallelism (serial at --cpus 2) #1178, which will make higher
  --cpus values more effective for this stage and more likely to be used
  in practice).

Not a functional break either way, just not computing what the code visually
appears to intend, and worth fixing while touching nearby throughput-tuning
code.

Suggested fix

Either add explicit parens to compute the evidently-intended
(args.cpus + 2) // 2, or simplify to the clearer max(1, args.cpus // 2)
if that's the actual intent (leave headroom for the hisat2/pipe side of the
hisat2 | samtools sort pipeline). Whichever is chosen should be a
deliberate one-line fix, not a silent behavior change disguised as a
formatting cleanup.

What command did you issue?

funannotate train -i genome.fa --left_norm R1 --right_norm R2 --cpus N ...
(any invocation that reaches runTrinityGG()'s hisat2/samtools alignment
step)

OS/Install Information

Found via static code review; not tied to a specific OS.