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

[John Marshall]

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.

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 You will also want to remove the existing use_private_htslib_headers.patch as it is superseded by this.

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.

    John

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