Hi, On 19.04.2016 14:03, Andreas Tille wrote: > On Tue, Apr 19, 2016 at 12:29:59PM +0200, Fabian Klötzl wrote: >> Hi Andreas, >> >> I spent the last few weeks meandering in the murky marshes of the mugsy >> source code; It is a monstrosity. >> >> [ … lots of whining … ] > > Thanks a lot for the energy you have put into this code.
Yeah, I was lucky that “improving mugsy” was supposed to be my next big project at work. Little did we know I had to get past “compiling” first. >>> The current status is: >>> >>> 0. The code seems to be orphaned / unmaintained since 2011. >>> 1. Mugsy contains a *patched* version of MUMmer 3.20. I took over >>> those changes to the Debian MUMmer 3.23 package that sounded >>> sensible >> >> I have some extra patches for those tools, making them up to ten times >> faster. Will commit in due course. > > Cool. Just ping me for sponsering. I guess it makes sense, to move the packaging to git, first. >> It has to be patched first, to provide the same functionality as the >> upstream build (see above). > > Once there were patches posted to this list[2] - are you aware of these? Yes, I had seen them; But the rest of the code still is abysmal. The patches are a drop in the ocean, basically. >>> 2. Find some modern replacement that is better regarding code >>> maintenance as well as functionality / speed. >>> I can not really imagine that the last 5 years did not brought >>> up something better. >> >> My advise: drop mugsy entirely. It is just not worth it, waisting any >> more time on it. Also, according to the study [1], mugsy has inferior >> quality to other tools. > > Thanks for the summary I'll foreward for further discussion. Cheers, Fabian >> [1]: http://www.ncbi.nlm.nih.gov/pubmed/25273068 > > [2] https://lists.debian.org/debian-med/2015/04/msg00036.html >