Error during make

[rule-110]

Hi At [ 45%] Building CXX object I got this error:

pwd/popscle-master/popscle-master/filter.cpp:3149:86: error: 'VCF_OVERLAP' was not declared in this scope else if ( !strcasecmp(out[ival].key,"overlap") ) { out[ival].threshold = VCF_OVERLAP<<1; out[ival].is_str = 0; }

It seems that VCF_OVERLAP value is missing. Do you know how to fix that?

Thanks a lot Nicolas

[caleblareau]

I'm getting the same error... was this ever addressed or does a workaround exist?

[caleblareau]

Perhaps relevant: https://github.com/samtools/bcftools/issues/1166

[caleblareau]

I can get past the 45% build error by upfrading hts-lib to v1.11 but run into a different error if anyone has any ideas:

[ 56%] Building CXX object CMakeFiles/popscle.dir/hts_utils.cpp.o
In file included from /home/groups/satpathy/software/popscle/hts_utils.h:42:0,
                 from /home/groups/satpathy/software/popscle/hts_utils.cpp:24:
/home/groups/satpathy/software/popscle/hts_utils.cpp: In function ‘char* faidx_fetch_uc_seq(const faidx_t*, const char*, int, int, int*)’:
/home/groups/satpathy/software/popscle/hts_utils.cpp:63:25: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
     iter = kh_get(s, fai->hash, c_name);
                         ^
/home/groups/satpathy/software/htslib-1.11/include/htslib/khash.h:511:42: note: in definition of macro ‘kh_get’
 #define kh_get(name, h, k) kh_get_##name(h, k)
                                          ^
In file included from /home/groups/satpathy/software/popscle/hts_utils.h:47:0,
                 from /home/groups/satpathy/software/popscle/hts_utils.cpp:24:
/home/groups/satpathy/software/htslib-1.11/include/htslib/faidx.h:69:8: error: forward declaration of ‘const faidx_t {aka const struct faidx_t}’
 struct faidx_t;
        ^
In file included from /home/groups/satpathy/software/popscle/hts_utils.h:42:0,
                 from /home/groups/satpathy/software/popscle/hts_utils.cpp:24:

[Gvaihir]

@caleblareau htslib 1.11 breaks the compilation of popscle - use 1.10.2 or earlier.

[romain-lopez]

Ran into a similar error a few years later, it'd be great to have a more precise install procedure :) this thread helped a lot!