Re: Mugsy (Was: Seqan knowledge needed (Was: Help needed in C++ / seqan issue))
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
>
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