Compilation fails with samtools v.1.3 and htslib v.1.3

[magicDGS]

When configure with pre-compiled samtools-1.3 and htslib-1.3, make produce the following error:

In file included from bam_md_ext.c:38:0:
samtools-1.3/bam.h:189:28: error: conflicting types for ‘seq_nt16_int’
 #define bam_nt16_nt4_table seq_nt16_int
                            ^
bam_md_ext.c:54:12: note: in expansion of macro ‘bam_nt16_nt4_table’
 const char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
            ^
In file included from htslib-1.3/htslib/sam.h:30:0,
                 from bam_md_ext.c:37:
htslib-1.3/htslib/hts.h:255:18: note: previous declaration of ‘seq_nt16_int’ was here
 extern const int seq_nt16_int[];
                  ^
In file included from bam_md_ext.c:43:0:
samutils.h:47:14: warning: ‘op_cat_str’ defined but not used [-Wunused-variable]
 static char *op_cat_str[] = {
              ^
make[1]: *** [bam_md_ext.o] Error 1
make: *** [all-recursive] Error 1

[andreas-wilm]

Yep. The Debian team suggested to remove the samtools dependency altogether and only rely on htslib. Will need to look into it

[jmarshall]

👍 to the suggestion to modify lofreq to use only HTSlib. HTSlib is maintained as a coherent and usable library, but the legacy samtools API is not.

In the meantime, you can work around this particular problem and compile successfully by adding the following to e.g. src/lofreq/bam_md_ext.h:

#undef bam_nt16_nt4_table

I have not tested whether the resulting executable is fully functional.

[andreas-wilm]

That's definitely the best way to go forward. Might take some time to implement though.

[mmterpstra]

hints for creating a decent version with fixed dependencies (aka patch out includedir path for both HTSlib and SAMtools and fix compile error):

https://github.com/easybuilders/easybuild-easyconfigs/blob/44dc94e901cd40c3044e2fad2e0f0b5590c61b8f/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.2_SAMtools-HTSlib.patch

the $EBROOT[SAMTOOLS|HTSLIB] variables are (easy)build system defaults. These can be replaced with SAMTOOLS|HTSLIB parameters pointing to the installation dirs of SAMTOOLS|HTSLIB instead of the sourcedirs.