I saw that Li has another “mini” tool, so I though I’d look, as I did with minimap2. Also, it’s the literal last day of the month. Being on vacation does that to ya.
This month’s paper: Li H. Fast genomic read alignment with minibwa. arXiv
Original code
This paper’s code is on GitHub.
Critique
Standard disclaimer: issues with published code are not necessarily anyone’s fault, and often are due to nothing more nefarious than time constraints.
I have basically one main grip with this code, and it’s late, so I’m just going
to put it in a little center section. The filenames for this project are
incredibly inscrutable. What does mbpriv.h do? pe.c? If I’m trying to
navigate this to find the bit of algorithm that’s relevant to me, where do I
look? (Clicking in to the files doesn’t help either; things are over-briefly
named in general, and there aren’t good docstrings for anything
including the file in general.)
The README doesn’t provide pointers for what goes in what files. The files
themselves don’t provide help either. Usually I can at least go by names
(e.g. a file called readfilter.hpp is probably about filtering reads). But
abbreviations that only make sense to the maintainers? Those are inscrutable to
people trying to learn.
Brilliant tool and algorithms, I’m sure. I just can’t understand the code. And I can’t even navigate via filenames.
If there’s a recent paper you’d like me to look through, shoot me an email. Address in my CV.