[OT] Application case study comparing Java, Go, and C++

[Seb]

On Thursday, 28 February 2019 at 20:48:01 UTC, Jon Degenhardt 
wrote:
> This paper may be of interest to people here:
>
> "A comparison of three programming languages for a full-fledged 
> next-generation sequencing tool", P.Costanza, C.Herzeel, 
> W.Verachrert
> https://doi.org/10.1101/558056
>
> The paper compares implementations of a tool operating on 
> SAM/BAM files (bioinformatics) from a performance perspective. 
> Focus is on comparison of GC schemes used in Go and Java with 
> reference counting in C++. The GC schemes were materially 
> faster.
>
> I'm not familiar with the authors or the implementations, so 
> cannot say how well the implementations were done. However, it 
> appears to be a useful case study, and the authors go provide a 
> fair bit of analysis in the paper.
>
> There's a reddit thread also: 
> https://www.reddit.com/r/programming/comments/avsfc6/performance_comparison_of_go_c_and_java_for/

I wouldn't give much value to this paper. It hasn't been peer 
reviewed and I doubt it would pass any. A quick example:

"It [their tool] can be used as a drop-in replacement for many 
operations implemented by SAMtools [...]". Though no performance 
comparison was done against samtools (nor any other tools expect 
their own implementations). I find this pretty shocking, because 
their entire paper's purpose is about performance...

For reference, samtools is the de-facto standard for a reason 
(yes it's old and written in C).

Though, to be fair sambamba (written in D) is faster than the C 
"standard" implementation:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765878