[Debian-med-packaging] Bug#938431: Fixing sambamba 0.8.6

[Andreas Tille]

Hi Pjotr,

On Thu, Nov 28, 2019 at 07:50:34AM -0600, Pjotr Prins wrote:
> Dear Andreas and Matthias,
> 
> Good news, I think I have fixed the Sambamba bug! After a 3 day bug
> hunt. Thanks Andreas for pushing me again. Let me ping you when I have
> a new release. I need to do some performance testing still. But no
> more segfaults using the Debian ldc 1.17 compiler.

Very cool!  Just waiting for your ping. :-)
 
> With regard to BioD I suggest the following:
> 
> 1. We create libraries libbiod.so and libbiod.a which ship with D
>    source code - they act like header files in C.
> 2. sambamba uses these header files to build (not linking against the 
>    shared lib)
> 
> The reason is simply performance. The ldc compiler is capable of heavy
> optimizations (mostly unrolling loops and inlining code) when it has
> all code available. Point I am making that code is available anyway.
> 
> You can choose to change that compile time behaviour by linking
> against a shared lib, but just realise you'll end with a much slower
> sambamba. The BioD source code shoud be included because you can't
> build anything without it.

As we discussed at BioHackathon: I just got your point but I have no
idea how to implement that source code shipping model for the
libbiod-dev package.  I'm fine with whatever is done with D packaging
in Debian.

To get some numbers:  Do you think rinning test/test_suite.sh could
give some impression about the performance gain / loss?

Kind regards

       Andreas.

-- 
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