Build fails due to htslib code

[caldodge]

Building popscle with gcc 9.4. It fails with the following messages:

In file included from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:42:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp: In function ‘char* faidx_fetch_uc_seq(const faidx_t*, const char*, int, int, int*)’:
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:51:25: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
iter = kh_get(s, fai->hash, c_name);
^
/hpc/apps/htslib/1.18/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/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:47:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/hpc/apps/htslib/1.18/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/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:42:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:52:26: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
if(iter == kh_end(fai->hash)) return 0;
^
/hpc/apps/htslib/1.18/include/htslib/khash.h:563:21: note: in definition of macro ‘kh_end’
#define kh_end(h) ((h)->n_buckets)
^
In file included from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:47:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/hpc/apps/htslib/1.18/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/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:42:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:53:23: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
val = kh_value(fai->hash, iter);
^
/hpc/apps/htslib/1.18/include/htslib/khash.h:549:26: note: in definition of macro ‘kh_value’
#define kh_value(h, x) ((h)->vals[x])
^
In file included from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:47:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/hpc/apps/htslib/1.18/include/htslib/faidx.h:69:8: error: forward declaration of ‘const faidx_t {aka const struct faidx_t}’
struct faidx_t;
^
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:61:29: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
^
In file included from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:47:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/hpc/apps/htslib/1.18/include/htslib/faidx.h:69:8: error: forward declaration of ‘const faidx_t {aka const struct faidx_t}’
struct faidx_t;
^
/home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:70:29: error: invalid use of incomplete type ‘const faidx_t {aka const struct faidx_t}’
while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
^
In file included from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.h:47:0,
from /home/dodgec/xiss-64708/popscle-0.1-beta/hts_utils.cpp:24:
/hpc/apps/htslib/1.18/include/htslib/faidx.h:69:8: error: forward declaration of ‘const faidx_t {aka const struct faidx_t}’
struct faidx_t;
^
make[2]: *** [CMakeFiles/popscle.dir/hts_utils.cpp.o] Error 1
make[1]: *** [CMakeFiles/popscle.dir/all] Error 2
make: *** [all] Error 2

This also happened with htslib 1.17. Does this mean htslib needed some special flags during build?

[caldodge]

This seems to be version-related. I installed htslib and htslib-devel from EPEL, specified the include directory and library file locations, and Popscle built without a problem.