[Debian-med-packaging] Bug#946924: Patch to remove any need for libhts-private-dev

[Andreas Tille]

Hi John,

thanks a lot for your very helpful contribution.

On Tue, Dec 17, 2019 at 11:24:35PM +0000, John Marshall wrote:
> Source: libseqlib
> Version: 1.1.2+dfsg-4
> 
> SeqLib uses private HTSlib headers that HTSlib would prefer were not installed, and at last count SeqLib was the only package desiring these private HTSlib cram/*.h headers. The attached patch recodes to avoid the need for these headers. See bug #881170 for background; this patch is option (B) from the initial message on that bug, and it turns out that the changes required are trivial.

Yes, that's actually trivial.  Thanks again.
 
> This has also been proposed upstream as <https://github.com/walaj/SeqLib/pull/53>. However as upstream releases are infrequent and the problem was caused by Debian's desire to build against a non-bundled HTSlib, it would be appropriate for Debian to apply this patch now rather than wait for upstream to incorporate it and make a new release.
> 
> Please apply the attached patch, which is also available at <https://github.com/walaj/SeqLib/commit/3fc64616a64adfcaf5271ae24f35e443ce822faf.patch>. You will also want to remove the existing use_private_htslib_headers.patch as it is superseded by this.

Done and uploaded.
 
> Once this has been done, if libseqlib was still the only Debian package using libhts-private-dev then it will be appropriate to remove that bodge from htslib -- for which I am happy to submit another bug as appropriate.

The headers are now only used in htslib-test package - thus these can be
merged into this package easily.  I'd be happy if you might file a bug
report about this to document the issue properly.

BTW, there is bug #922860 remaining where you suggest to rename the
package tabix to libhts-utils.  Did I understood this correctly?  If yes
this is probably the right moment to do this once we are fiddling around
with the package layout.

Kind regards

      Andreas.

-- 
http://fam-tille.de