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Re: Help for next version of freebayes needed: libseqlib build error

On Fri, 2017-01-27 at 17:09 +0100, Andreas Tille wrote:
> On Fri, Jan 27, 2017 at 02:51:27PM +0000, Ghislain Vaillant wrote:
> > 
> > Looks like the system BWA and FML have conflicting bseq1_t
> > declaration. 
> > 
> > I noticed that upstream is using personal forks of BWA and FML, not the
> > upstream ones. If you look for bseq1_t in the SeqLib clones of BWA and
> > FML, no definition appears. However, they do appear in the respective
> > upstream repositories.
> > 
> > Looks like upstream had to patch the BWA and FML code bases to be able
> > to mix them without a multiple-definition error. I am not sure you can
> > get away from it.
> Upstream was very responsive[1] and seems to be willing to solve the
> issue.  Is there any suggestion whom to contact first BWA or FML?

Probably the newest of the two. Afterall, whoever was last should have
done their homework and check that the exported typedefs were not used
anywhere else. That being said, the SeqLib devs should have kickstarted
 this discussion instead of silently forking.

In practice, due to the lack of namespacing in C, it is strongly
encouraged to prefix anything publicly exported with a project specific
identifier (here bwa_ and fml_ for instance). This piece of advice
should apply to both projects anyway, so I believe it is worth
contacting both.


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