On a system with an installation of htslib 1.10.2 system wide, in /usr/local/lib and /bin. I suspected cortex was linking against that installation not the bundled htslib. Indeed if you remove
-L /usr/local/lib from the top-level Makefile it then compiles fine. I think if we just put that at the end of
# Add -L/usr/local/lib/ to satisfy some systems that struggle to link libz
LIBINCS = -L/usr/local/lib -I$(IDIR_BAM) \
-I$(IDIR_SEQ) -I$(IDIR_STRS) \
-L$(IDIR_BAM) -L$(IDIR_SEQ) -L$(IDIR_STRS)
in the Makefile, instead of beginning, it should be fine.
When running
make NUM_COLS=1 cortex_var
I got the following:On a system with an installation of htslib 1.10.2 system wide, in
/usr/local/lib
and /bin. I suspected cortex was linking against that installation not the bundled htslib. Indeed if you remove-L /usr/local/lib
from the top-levelMakefile
it then compiles fine. I think if we just put that at the end ofin the Makefile, instead of beginning, it should be fine.