nahmedraja / gase Goto Github PK
View Code? Open in Web Editor NEWA generic DNA read aligner that allows to use different combinations of seeding and extension algorithms.
License: MIT License
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sdwfrostgase's Issues
Build issues
I have run into some build issues - tried both GCC v7.5.0 and v4.6 - neither works.
Log:
make
If you donot see anything below this line then there is nothing to "make"
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/bwamem.c -o ./obj/bwamem.o
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/mmintrin.h:45:89: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef int __m64_u __attribute__ ((__vector_size__ (8), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:72:93: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef float __m128_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:57:98: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef long long __m128i_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:58:95: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef double __m128d_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
src/bwamem.c: In function ‘mem_collect_intv’:
src/bwamem.c:162:21: warning: unused variable ‘w’ [-Wunused-variable]
bwt_mem_width_t *w;
^
src/bwamem.c:161:8: warning: unused variable ‘min_miss_match’ [-Wunused-variable]
int min_miss_match = 0;
^~~~~~~~~~~~~~
src/bwamem.c:158:33: warning: unused variable ‘max_i’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~~~
src/bwamem.c:158:28: warning: unused variable ‘max’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~
src/bwamem.c: In function ‘mem_shd_flt_chained_seeds’:
src/bwamem.c:880:18: warning: variable ‘ref_display’ set but not used [-Wunused-but-set-variable]
char ref_display[320] __aligned__;
^~~~~~~~~~~
src/bwamem.c:851:18: warning: variable ‘read_display’ set but not used [-Wunused-but-set-variable]
char read_display[320] __aligned__;
^~~~~~~~~~~~
src/bwamem.c:947:18: warning: variable ‘ref_display’ set but not used [-Wunused-but-set-variable]
char ref_display[320] __aligned__;
^~~~~~~~~~~
src/bwamem.c:919:18: warning: variable ‘read_display’ set but not used [-Wunused-but-set-variable]
char read_display[320] __aligned__;
^~~~~~~~~~~~
src/bwamem.c:840:15: warning: variable ‘seed’ set but not used [-Wunused-but-set-variable]
char seed[s->len+1];
^~~~
src/bwamem.c:833:74: warning: variable ‘left_len’ set but not used [-Wunused-but-set-variable]
int qb, qe, is_right_pass = 1, is_left_pass = 1, right_len = 0, left_len = 0;
^~~~~~~~
src/bwamem.c:833:59: warning: variable ‘right_len’ set but not used [-Wunused-but-set-variable]
int qb, qe, is_right_pass = 1, is_left_pass = 1, right_len = 0, left_len = 0;
^~~~~~~~~
Makefile:36: recipe for target 'bwamem.o' failed
make: *** [bwamem.o] Error 1
frankyc@congo:/fml/chones/local/GASE 10:08 PM : vi Makefile
frankyc@congo:/fml/chones/local/GASE 10:09 PM : make clean
rm -f -r gmon.out ./obj/ a.out gase *~ ./lib/
#make -C ./src/shd_filter/ clean
frankyc@congo:/fml/chones/local/GASE 10:09 PM : make
If you donot see anything below this line then there is nothing to "make"
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/utils.c -o ./obj/utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/kthread.c -o ./obj/kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/kstring.c -o ./obj/kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/ksw.c -o ./obj/ksw.o
src/ksw.c: In function ‘ksw_u8’:
src/ksw.c:219:22: warning: statement with no effect [-Wunused-value]
gmax = imax;100930;
^~~~~~
src/ksw.c: In function ‘ksw_local_ext’:
src/ksw.c:424:128: warning: unused variable ‘max_off’ [-Wunused-variable]
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
^~~~~~~
src/ksw.c:424:120: warning: unused variable ‘gscore’ [-Wunused-variable]
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
^~~~~~
src/ksw.c:424:112: warning: unused variable ‘max_ie’ [-Wunused-variable]
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
^~~~~~
src/ksw.c:424:103: warning: unused variable ‘max_del’ [-Wunused-variable]
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
^~~~~~~
src/ksw.c:424:94: warning: unused variable ‘max_ins’ [-Wunused-variable]
int i, j, k, oe_del = o_del + e_del, oe_ins = o_ins + e_ins, beg, end, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
^~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/bwt.c -o ./obj/bwt.o
src/bwt.c: In function ‘bwt_bowtie_seed_inexact’:
src/bwt.c:474:30: warning: unused variable ‘new_intv’ [-Wunused-variable]
bwtintv_t ik, ok[4], tmp, new_intv;
^~~~~~~~
src/bwt.c: In function ‘bwt_fwd_mem’:
src/bwt.c:575:6: warning: unused variable ‘seed_i’ [-Wunused-variable]
int seed_i = 0;
^~~~~~
src/bwt.c: In function ‘bwt_fwd_mem_inexact’:
src/bwt.c:658:11: warning: unused variable ‘k’ [-Wunused-variable]
int k;
^
src/bwt.c:668:11: warning: unused variable ‘k’ [-Wunused-variable]
int k;
^
src/bwt.c:600:6: warning: variable ‘last_miss_pos’ set but not used [-Wunused-but-set-variable]
int last_miss_pos = -len;
^~~~~~~~~~~~~
src/bwt.c:657:28: warning: ‘miss_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ik.info = miss_start + max_extend;
~~~~~~~~~~~^~~~~~~~~~~~
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/bntseq.c -o ./obj/bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/bwa.c -o ./obj/bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -msse4.2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS src/bwamem.c -o ./obj/bwamem.o
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/mmintrin.h:45:89: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef int __m64_u __attribute__ ((__vector_size__ (8), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:72:93: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef float __m128_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:57:98: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef long long __m128i_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:21: error: expected ‘)’ before ‘__attribute__’
#define __aligned__ __attribute__((aligned(16)))
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:31:0,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/7/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:58:95: error: expected ‘,’ or ‘;’ before ‘)’ token
typedef double __m128d_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
src/bwamem.c: In function ‘mem_collect_intv’:
src/bwamem.c:162:21: warning: unused variable ‘w’ [-Wunused-variable]
bwt_mem_width_t *w;
^
src/bwamem.c:161:8: warning: unused variable ‘min_miss_match’ [-Wunused-variable]
int min_miss_match = 0;
^~~~~~~~~~~~~~
src/bwamem.c:158:33: warning: unused variable ‘max_i’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~~~
src/bwamem.c:158:28: warning: unused variable ‘max’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~
src/bwamem.c: In function ‘mem_shd_flt_chained_seeds’:
src/bwamem.c:880:18: warning: variable ‘ref_display’ set but not used [-Wunused-but-set-variable]
char ref_display[320] __aligned__;
^~~~~~~~~~~
src/bwamem.c:851:18: warning: variable ‘read_display’ set but not used [-Wunused-but-set-variable]
char read_display[320] __aligned__;
^~~~~~~~~~~~
src/bwamem.c:947:18: warning: variable ‘ref_display’ set but not used [-Wunused-but-set-variable]
char ref_display[320] __aligned__;
^~~~~~~~~~~
src/bwamem.c:919:18: warning: variable ‘read_display’ set but not used [-Wunused-but-set-variable]
char read_display[320] __aligned__;
^~~~~~~~~~~~
src/bwamem.c:840:15: warning: variable ‘seed’ set but not used [-Wunused-but-set-variable]
char seed[s->len+1];
^~~~
src/bwamem.c:833:74: warning: variable ‘left_len’ set but not used [-Wunused-but-set-variable]
int qb, qe, is_right_pass = 1, is_left_pass = 1, right_len = 0, left_len = 0;
^~~~~~~~
src/bwamem.c:833:59: warning: variable ‘right_len’ set but not used [-Wunused-but-set-variable]
int qb, qe, is_right_pass = 1, is_left_pass = 1, right_len = 0, left_len = 0;
^~~~~~~~~
Makefile:36: recipe for target 'bwamem.o' failed
make: *** [bwamem.o] Error 1
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