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No, they are not at all the same thing. An archive is just that. A collection of object files that can be statically linked to your executable. Shared objects are dynamically linked at runtime. They...

If you link to a shared library intead of the archive it's a little more complicted. If the shared library isn't installed in a directory know to the loader then you need to tell it where to find it....

rpath is actually a linker option rather then a compiler option. gcc passes it to ld.



Well, th estandard way to use shared objects (.so) is to install them in the system directories used for...

No. Each folder requires a -L entry.






I presumed htslib-1.10-2 was your library. The -l option is for the library itself. If the library is libhts.so then use -lhts





I'll have a...

Undefined references means the compiler can't find compiled code for functions being called. If you want to use a subset of the library then you'll have to compile and link all the files used by the...

You have several replies and I don't kow if your problem is solved but I'll mention that includes in <> are supposed to be for files in system directories i.e. /usr/include

Files in other...