Last week (week 23 – May 12th) I was on vacation.
This week I didn’t do much to complete my Ph.D application. I started looking at BWA to create a timed version, to compare bwa and bwa-gasal2 on equal basis.
This implies to integrate the timing structures in bwa the same way they are in bwa-gasal2. Of course, some fields won’t be used (like data transfert hostdevice, GPU mallocs/frees times, etc.) but I’ll make it comparable somehow.
It is currently implemented as a global structure, accessed with extern keywords, so I guess I’ll do the same.
I notice that bwa-gasal2 was writing a file, which might slowed it down, so I made that part easily disabled, just in case.
I’ll write more when I’ll have more.