Allow building against htslib?

[rekado]

Currently anno bundles a copy of the libtabix sources. Would it be possible to optionally allow linking with an installed upstream library, such as htslib? htslib includes an interface to the tabix library at include/htslib/tbx.h.

[zhanxw]

That should be possible. Let me look into the htslib codes.

Are there certain advantages to link with the installed upstream library? Is htslib faster?

[rekado]

The issue is mostly about packaging. Packaging guidelines of most distributions do not permit bundling of third-party libraries as this makes it harder to apply patches, and it wastes memory at runtime.

When I package anno for GNU Guix I'll try to patch the build system anyway so that an existing version of htslib (or another source of tabix) can be linked with, in order to comply with packaging guidelines. It would be better, though, if these changes were implemented upstream.

If I should find a way to do this, I'll send a patch / pull request.

Thanks for your consideration!

[zhanxw]

I plan to benchmark with htslib and see if there is speed advantages. Thanks.