System-wide htslib can fail linkage #26
Description
When running make NUM_COLS=1 cortex_var I got the following:
mkdir -p bin; gcc -Iinclude/cortex_var/core -Iinclude/basic -Iinclude/hash_table -Iinclude/cortex_var/many_colours -Iinclude/basic/event_encoding/base_encoding -L/usr/local/lib -Ilibs/htslib/htslib -Ilibs/seq_file -Ilibs/string_buffer -Llibs/htslib/htslib -Llibs/seq_file -Llibs/string_buffer -O3 -m64 -Wall -DVERSION_STR='""' -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=1 -DNUMBER_OF_COLOURS=1 -o bin/cortex_var_""31"_c"1 src/obj/cortex_var/many_colours/genotyping_element.o src/obj/cortex_var/many_colours/little_hash_for_genotyping.o src/obj/cortex_var/many_colours/model_info.o src/obj/cortex_var/many_colours/genome_complexity.o src/obj/cortex_var/many_colours/global.o src/obj/cortex_var/many_colours/db_complex_genotyping.o src/obj/cortex_var/many_colours/cortex_var.o src/obj/cortex_var/many_colours/binary_kmer.o src/obj/cortex_var/many_colours/element.o src/obj/cortex_var/many_colours/seq.o src/obj/cortex_var/many_colours/hash_value.o src/obj/cortex_var/many_colours/hash_table.o src/obj/cortex_var/many_colours/dB_graph.o src/obj/cortex_var/many_colours/dB_graph_population.o src/obj/cortex_var/many_colours/dB_graph_supernode.o src/obj/cortex_var/many_colours/db_variants.o src/obj/cortex_var/many_colours/cmd_line.o src/obj/cortex_var/many_colours/event_encoding.o src/obj/cortex_var/many_colours/graph_info.o src/obj/cortex_var/many_colours/db_differentiation.o src/obj/cortex_var/many_colours/model_selection.o src/obj/cortex_var/many_colours/maths.o src/obj/cortex_var/many_colours/seq_error_rate_estimation.o src/obj/cortex_var/many_colours/file_reader.o src/obj/cortex_var/many_colours/error_correction.o -lseqfile -lstrbuf -lhts -lpthread -lz -lm
libs/seq_file/libseqfile.a(seq_file.o): In function `seq_file_close':
seq_file.c:(.text+0xeae): undefined reference to `bam_hdr_destroy'
collect2: error: ld returned 1 exit status
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.