BWA-MEM program accelerated with the GASAL2 library
License: GNU General Public License v3.0
In order to match the way results are computed in bwa-mem, the KSW kernel must enforce computation in the beginning of both query and target. To do so, a filter is set depending on the values of the score for each cell.
After discussion with @nahmedraja we agreed on removing the tile-based computing since this would make impossible to reproduce the per-cell filtering.
This is done by the following code that ksw_extend runs after computing every column of te matrix, to check where to begin the next column:
for (i = 0; LIKELY(i < tlen); ++i) {
int t, f = 0, h1, m = 0, mj = -1;
int8_t *q = &qp[target[i] * qlen];
// apply the band and the constraint (if provided)
if (beg < i - w) beg = i - w;
if (end > i + w + 1) end = i + w + 1;
if (end > qlen) end = qlen;
if (beg == 0) {
h1 = h0 - (o_del + e_del * (i + 1));
if (h1 < 0) h1 = 0;
} else h1 = 0;
for (j = beg; LIKELY(j < end); ++j) {
// compute cell
}
[...]
for (j = beg; j < end && eh[j].h == 0 && eh[j].e == 0; ++j)
;
beg = j;
for (j = end; j >= beg && eh[j].h == 0 && eh[j].e == 0; --j)
;
end = j + 2 < ref_len ? j + 2 : query_len;
[...]
}Implementing it should provide better results
Hi, I encoutered an error when try to compile with make.
First I clone GASAL2 and then compile it successfully by running ./configure.sh and ./run_all.sh
But when I compile bwa-gasal2, I encountered this error:
If you donot see anything below this line then there is nothing to "make"
g++ -c -g -Wall -Wno-unused-function -O2 -msse4.2 -std=c++11 -fpermissive -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -I./GASAL2/include/ src/bwamem.c -o ./obj/bwamem.o
In file included from src/bwamem.c:18:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^~~~~~~
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/xmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/8/include/mmintrin.h:45:85: error: expected ‘)’ before ‘(’ token
typedef int __m64_u __attribute__ ((__vector_size__ (8), __may_alias__, __aligned__ (1)));
~ ^
/usr/lib/gcc/x86_64-linux-gnu/8/include/mmintrin.h:45:85: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^~~~~~~
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/8/include/xmmintrin.h:72:89: error: expected ‘)’ before ‘(’ token
typedef float __m128_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
~ ^
/usr/lib/gcc/x86_64-linux-gnu/8/include/xmmintrin.h:72:89: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^~~~~~~
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:57:94: error: expected ‘)’ before ‘(’ token
typedef long long __m128i_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
~ ^
/usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:57:94: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^~~~~~~
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/pmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/tmmintrin.h:31,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/smmintrin.h:32,
from /usr/lib/gcc/x86_64-linux-gnu/8/include/nmmintrin.h:31,
from src/vector_filter.h:16,
from src/bwamem.c:18:
/usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:58:91: error: expected ‘)’ before ‘(’ token
typedef double __m128d_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
~ ^
/usr/lib/gcc/x86_64-linux-gnu/8/include/emmintrin.h:58:91: error: expected ‘)’ before ‘(’ token
In file included from src/kstring.h:8,
from src/bwamem.c:11:
src/bwamem.c: In function ‘mem_opt_t* mem_opt_init()’:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘mem_opt_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:52:6: note: in expansion of macro ‘calloc’
o = calloc(1, sizeof(mem_opt_t));
^~~~~~
src/bwamem.c: In function ‘smem_aux_t* smem_aux_init()’:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘smem_aux_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:110:6: note: in expansion of macro ‘calloc’
a = calloc(1, sizeof(smem_aux_t));
^~~~~~
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘bwtintv_v*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:111:15: note: in expansion of macro ‘calloc’
a->tmpv[0] = calloc(1, sizeof(bwtintv_v));
^~~~~~
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘bwtintv_v*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:112:15: note: in expansion of macro ‘calloc’
a->tmpv[1] = calloc(1, sizeof(bwtintv_v));
^~~~~~
src/bwamem.c: In function ‘void mem_collect_intv(mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)’:
src/bwamem.c:202:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i) {
~~^~~~~~~~~~~
src/bwamem.c:217:43: warning: comparison of integer expressions of different signedness: ‘bwtint_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
if (end - start < split_len || p->x[2] > opt->split_width)
~~~~~~~~^~~~~~~~~~~~~~~~~~
src/bwamem.c:220:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i)
~~^~~~~~~~~~~
src/bwamem.c:221:66: warning: comparison of integer expressions of different signedness: ‘bwtint_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
if ((uint32_t) a->mem1.a[i].info - (a->mem1.a[i].info >> 32) >= opt->min_seed_len)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
src/bwamem.c:236:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i)
~~^~~~~~~~~~~
src/bwamem.c:164:26: warning: unused variable ‘max’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~
src/bwamem.c:164:31: warning: unused variable ‘max_i’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~~~
src/bwamem.c:167:6: warning: unused variable ‘min_miss_match’ [-Wunused-variable]
int min_miss_match = 0;
^~~~~~~~~~~~~~
src/bwamem.c:168:19: warning: unused variable ‘w’ [-Wunused-variable]
bwt_mem_width_t *w;
^
In file included from src/kstring.h:8,
from src/bwamem.c:11:
src/bwamem.c: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int)’:
src/malloc_wrap.h:38:37: warning: invalid conversion from ‘void*’ to ‘mem_seed_t*’ [-fpermissive]
# define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:374:16: note: in expansion of macro ‘realloc’
c->seeds = realloc(c->seeds, c->m * sizeof(mem_seed_t));
^~~~~~~
src/bwamem.c: In function ‘void mem_print_chain(const bntseq_t*, mem_chain_v*)’:
src/bwamem.c:409:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < chn->n; ++i) {
~~^~~~~~~~
src/bwamem.c: In function ‘mem_chain_v mem_chain(const mem_opt_t*, const bwt_t*, const bntseq_t*, int, const uint8_t*, void*)’:
src/bwamem.c:438:19: warning: invalid conversion from ‘const mem_opt_t*’ to ‘mem_opt_t*’ [-fpermissive]
mem_collect_intv(opt, bwt, len, seq, aux);
^~~
src/bwamem.c:163:41: note: initializing argument 1 of ‘void mem_collect_intv(mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)’
static void mem_collect_intv(mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq, smem_aux_t *a) {
~~~~~~~~~~~^~~
src/bwamem.c:439:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0, b = e = l_rep = 0; i < aux->mem.n; ++i) { // compute frac_rep
~~^~~~~~~~~~~~
src/bwamem.c:442:15: warning: comparison of integer expressions of different signedness: ‘bwtint_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
if (p->x[2] <= opt->max_occ)
~~~~~~~~^~~~~~~~~~~~~~~
src/bwamem.c:450:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < aux->mem.n; ++i) {
~~^~~~~~~~~~~~
src/bwamem.c:455:18: warning: comparison of integer expressions of different signedness: ‘bwtint_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
step = p->x[2] > opt->max_occ ? p->x[2] / opt->max_occ : 1;
~~~~~~~~^~~~~~~~~~~~~~
src/bwamem.c:456:25: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘bwtint_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = count = 0; k < p->x[2] && count < opt->max_occ; k += step, ++count) {
~~^~~~~~~~~
In file included from src/kstring.h:8,
from src/bwamem.c:11:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘mem_seed_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:476:17: note: in expansion of macro ‘calloc’
tmp.seeds = calloc(tmp.m, sizeof(mem_seed_t));
^~~~~~
src/bwamem.c:493:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < chain.n; ++i)
~~^~~~~~~~~
src/bwamem.c: In function ‘int mem_chain_flt(const mem_opt_t*, int, mem_chain_t*)’:
src/bwamem.c:536:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = 0; k < chains.n; ++k) {
~~^~~~~~~~~~
src/bwamem.c:555:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
if (k == chains.n) {
~~^~~~~~~~~~~
src/bwamem.c:560:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < chains.n; ++i) {
~~^~~~~~~~~~
src/bwamem.c: In function ‘void mem_mark_primary_se_core(const mem_opt_t*, int, mem_alnreg_t*, int_v*)’:
src/bwamem.c:717:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = 0; k < z->n; ++k) {
~~^~~~~~
src/bwamem.c:732:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
if (k == z->n)
~~^~~~~~~
In file included from src/kstring.h:8,
from src/bwamem.c:11:
src/bwamem.c: In function ‘void mem_chain2aln(const mem_opt_t*, const bntseq_t*, const uint8_t*, int, const uint8_t*, const mem_chain_t*, mem_alnreg_v*, int*, int*, gpu_batch*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘uint64_t*’ {aka ‘long unsigned int*’} [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1087:8: note: in expansion of macro ‘malloc’
srt = malloc(c->n * 8);
^~~~~~
src/bwamem.c:1098:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < av->n; ++i) // test whether extension has been made before
~~^~~~~~~
src/bwamem.c:1119:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
if (i < av->n)
~~^~~~~~~
src/bwamem.c:1226:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (curr_gpu_batch->n_target_batch < curr_gpu_batch->gpu_storage->host_max_target_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1246:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1253:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1260:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1267:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1211:8: warning: unused variable ‘j’ [-Wunused-variable]
int j;
^
src/bwamem.c:1048:12: warning: unused variable ‘rid’ [-Wunused-variable]
int i, k, rid, max_off[2], aw[2]; // aw: actual bandwidth used in extension
^~~
src/bwamem.c:1048:17: warning: unused variable ‘max_off’ [-Wunused-variable]
int i, k, rid, max_off[2], aw[2]; // aw: actual bandwidth used in extension
^~~~~~~
src/bwamem.c:1049:39: warning: unused variable ‘tmp’ [-Wunused-variable]
int64_t l_pac = bns->l_pac, rmax[2], tmp, max = 0;
^~~
src/bwamem.c:1051:11: warning: unused variable ‘rseq’ [-Wunused-variable]
uint8_t *rseq = NULL;
^~~~
src/bwamem.c: In function ‘void mem_aln2sam(const mem_opt_t*, const bntseq_t*, kstring_t*, bseq1_t*, int, const mem_aln_t*, int, const mem_aln_t*)’:
src/bwamem.c:1563:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = tmp; i < str->l; ++i) // replace TAB in the comment to SPACE
~~^~~~~~~~
src/bwamem.c: In function ‘void mem_reg2sam(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, mem_alnreg_v*, int, const mem_aln_t*)’:
src/bwamem.c:1621:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = l = 0; k < a->n; ++k) {
~~^~~~~~
src/bwamem.c:1649:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = 0; k < aa.n; ++k)
~~^~~~~~
src/bwamem.c:1651:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = 0; k < aa.n; ++k)
~~^~~~~~
src/bwamem.c:1657:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (k = 0; k < a->n; ++k)
~~^~~~~~
src/bwamem.c: In function ‘void mem_gasal_fill(gpu_batch*, int, int, char*, int)’:
src/bwamem.c:1679:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (gpu_batch_arr[gpu_batch_arr_idx].n_query_batch < gpu_batch_arr[gpu_batch_arr_idx].gpu_storage->host_max_query_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1697:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
if (gpu_batch_arr[gpu_batch_arr_idx].n_query_batch < gpu_batch_arr[gpu_batch_arr_idx].gpu_storage->host_max_query_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c: In function ‘void mem_align1_core(const mem_opt_t*, const bwt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, void*, int, int, mem_alnreg_v*, int, gasal_gpu_storage_v*)’:
src/bwamem.c:1803:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < chn.n; ++i) {
~~^~~~~~~
src/bwamem.c:1851:16: warning: unused variable ‘cur’ [-Wunused-variable]
gpu_batch *cur = &gpu_batch_arr[gpu_batch_arr_idx];
^~~
src/bwamem.c:1857:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
fprintf(stderr, "Thread no. %d is here with internal batch size %d, regs.n %d \n", tid, internal_batch_size, regs.n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~
In file included from src/bntseq.h:31,
from src/bwamem.h:5,
from src/bwamem.c:12:
src/bwamem.c:1865:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
assert(kv_size(regs_vec) == batch_processed);
src/bwamem.c:1902:91: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
if (gpu_batch_arr[internal_batch_idx].no_extend == 1) fprintf(stderr, "I am here too as well with regs.n %d\n", regs.n);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~
src/bwamem.c:1903:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for(i = 0; i < regs.n; ++i){
~~^~~~~~~~
src/bwamem.c:1923:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < regs.n; ++i) {
~~^~~~~~~~
src/bwamem.c:1928:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < regs.n; ++i) {
~~^~~~~~~~
In file included from src/kstring.h:8,
from src/bwamem.c:11:
src/bwamem.c: In function ‘mem_aln_t mem_reg2aln(const mem_opt_t*, const bntseq_t*, const uint8_t*, int, const char*, const mem_alnreg_t*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘uint8_t*’ {aka ‘unsigned char*’} [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1970:13: note: in expansion of macro ‘malloc’
query = malloc(l_query);
^~~~~~
src/malloc_wrap.h:38:37: warning: invalid conversion from ‘void*’ to ‘uint32_t*’ {aka ‘unsigned int*’} [-fpermissive]
# define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2027:19: note: in expansion of macro ‘realloc’
a.cigar = realloc(a.cigar, 4 * (a.n_cigar + 2) + l_MD);
^~~~~~~
src/bwamem.c: In function ‘void mem_process_seqs(const mem_opt_t*, const bwt_t*, const bntseq_t*, const uint8_t*, int64_t, int, bseq1_t*, const mem_pestat_t*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘mem_alnreg_v*’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2104:14: note: in expansion of macro ‘malloc’
w.regs = malloc(n * sizeof(mem_alnreg_v));
^~~~~~
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘smem_aux_t**’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2112:13: note: in expansion of macro ‘malloc’
w.aux = malloc(opt->n_threads * sizeof(smem_aux_t));
^~~~~~
src/bwamem.c:2116:28: warning: invalid conversion from ‘void (*)(void*, int, int, int, int, gasal_gpu_storage_v*)’ to ‘void (*)(void*, int, int, int, int)’ [-fpermissive]
kt_for(opt->n_threads, worker1, &w, /*(opt->flag & MEM_F_PE) ? n >> 1 : */n); // find mapping positions
^~~~~~~
In file included from src/bwamem.c:12:
src/bwamem.h:197:43: note: initializing argument 2 of ‘void kt_for(int, void (*)(void*, int, int, int, int), void*, int)’
extern void kt_for(int n_threads, void (*func)(void*, int, int, int, int), void *data, int n);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2136:28: warning: invalid conversion from ‘void (*)(void*, int, int, int, int, gasal_gpu_storage_v*)’ to ‘void (*)(void*, int, int, int, int)’ [-fpermissive]
kt_for(opt->n_threads, worker2, &w, (opt->flag & MEM_F_PE) ? n >> 1 : n); // generate alignment
^~~~~~~
In file included from src/bwamem.c:12:
src/bwamem.h:197:43: note: initializing argument 2 of ‘void kt_for(int, void (*)(void*, int, int, int, int), void*, int)’
extern void kt_for(int n_threads, void (*func)(void*, int, int, int, int), void *data, int n);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [Makefile:57: bwamem.o] Error 1
My system information is:
$uname -a
Linux TGD 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/8/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 8.4.0-3ubuntu2' --with-bugurl=file:///usr/share/doc/gcc-8/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-8 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 8.4.0 (Ubuntu 8.4.0-3ubuntu2)
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Sun_Jul_28_19:07:16_PDT_2019
Cuda compilation tools, release 10.1, V10.1.243
Hi all, I tried to build bwa-gasal2 on my system but I'm getting errors in the procedure.
I cloned the repo, built GASAL2 library for my platform (it seems to work), although I had to substitute this
g++ -std=c++11 -O3 -o test_prog.out -L/usr/local/cuda//targets/x86_64-linux/lib -L../lib test_prog.o -fopenmp -lcudart -lgasal
with this in the Makefile
nvcc -std=c++11 -O3 -o test_prog.out -L/usr/local/cuda//targets/x86_64-linux/lib -L../lib test_prog.o -lgomp -lcudart -lgasal.
Nevertheless, when issuing make at bwa-gasal2 level, I have this error:
$ make
If you donot see anything below this line then there is nothing to "make"
g++ -c -g -Wall -Wno-unused-function -O2 -msse4.2 -std=c++11 -fpermissive -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -I./GASAL2/include/ -I/beegfs/scratch/ric.cosr/cittaro.davide/src/boost_1_74_0 src/bwamem.c -o ./obj/bwamem.o
Makefile:57: recipe for target 'bwamem.o' failed
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
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:45:85: error: expected ‘)’ before ‘(’ token
typedef int __m64_u __attribute__ ((__vector_size__ (8), __may_alias__, __aligned__ (1)));
^
/usr/lib/gcc/x86_64-linux-gnu/7/include/mmintrin.h:45:85: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
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:72:89: error: expected ‘)’ before ‘(’ token
typedef float __m128_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:72:89: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
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:57:94: error: expected ‘)’ before ‘(’ token
typedef long long __m128i_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:57:94: error: expected ‘)’ before ‘(’ token
In file included from src/bwamem.c:18:0:
src/vector_filter.h:12:36: error: ‘aligned’ was not declared in this scope
#define __aligned__ __attribute__((aligned(16)))
^
src/vector_filter.h:12:36: note: suggested alternative: ‘signed’
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:58:91: error: expected ‘)’ before ‘(’ token
typedef double __m128d_u __attribute__ ((__vector_size__ (16), __may_alias__, __aligned__ (1)));
^
/usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:58:91: error: expected ‘)’ before ‘(’ token
In file included from src/kstring.h:8:0,
from src/bwamem.c:11:
src/bwamem.c: In function ‘mem_opt_t* mem_opt_init()’:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘mem_opt_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:52:6: note: in expansion of macro ‘calloc’
o = calloc(1, sizeof(mem_opt_t));
^~~~~~
src/bwamem.c: In function ‘smem_aux_t* smem_aux_init()’:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘smem_aux_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:110:6: note: in expansion of macro ‘calloc’
a = calloc(1, sizeof(smem_aux_t));
^~~~~~
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘bwtintv_v*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:111:15: note: in expansion of macro ‘calloc’
a->tmpv[0] = calloc(1, sizeof(bwtintv_v));
^~~~~~
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘bwtintv_v*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:112:15: note: in expansion of macro ‘calloc’
a->tmpv[1] = calloc(1, sizeof(bwtintv_v));
^~~~~~
src/bwamem.c: In function ‘void mem_collect_intv(mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)’:
src/bwamem.c:202:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i) {
~~^~~~~~~~~~~
src/bwamem.c:217:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (end - start < split_len || p->x[2] > opt->split_width)
~~~~~~~~^~~~~~~~~~~~~~~~~~
src/bwamem.c:220:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i)
~~^~~~~~~~~~~
src/bwamem.c:221:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if ((uint32_t) a->mem1.a[i].info - (a->mem1.a[i].info >> 32) >= opt->min_seed_len)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
src/bwamem.c:236:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < a->mem1.n; ++i)
~~^~~~~~~~~~~
src/bwamem.c:164:26: warning: unused variable ‘max’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~
src/bwamem.c:164:31: warning: unused variable ‘max_i’ [-Wunused-variable]
int i, k, x = 0, old_n, max, max_i;
^~~~~
src/bwamem.c:167:6: warning: unused variable ‘min_miss_match’ [-Wunused-variable]
int min_miss_match = 0;
^~~~~~~~~~~~~~
src/bwamem.c:168:19: warning: unused variable ‘w’ [-Wunused-variable]
bwt_mem_width_t *w;
^
In file included from src/kstring.h:8:0,
from src/bwamem.c:11:
src/bwamem.c: In function ‘int test_and_merge(const mem_opt_t*, int64_t, mem_chain_t*, const mem_seed_t*, int)’:
src/malloc_wrap.h:38:37: warning: invalid conversion from ‘void*’ to ‘mem_seed_t*’ [-fpermissive]
# define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:374:16: note: in expansion of macro ‘realloc’
c->seeds = realloc(c->seeds, c->m * sizeof(mem_seed_t));
^~~~~~~
src/bwamem.c: In function ‘void mem_print_chain(const bntseq_t*, mem_chain_v*)’:
src/bwamem.c:409:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < chn->n; ++i) {
~~^~~~~~~~
src/bwamem.c: In function ‘mem_chain_v mem_chain(const mem_opt_t*, const bwt_t*, const bntseq_t*, int, const uint8_t*, void*)’:
src/bwamem.c:438:42: warning: invalid conversion from ‘const mem_opt_t*’ to ‘mem_opt_t*’ [-fpermissive]
mem_collect_intv(opt, bwt, len, seq, aux);
^
src/bwamem.c:163:13: note: initializing argument 1 of ‘void mem_collect_intv(mem_opt_t*, const bwt_t*, int, const uint8_t*, smem_aux_t*)’
static void mem_collect_intv(mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq, smem_aux_t *a) {
^~~~~~~~~~~~~~~~
src/bwamem.c:439:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0, b = e = l_rep = 0; i < aux->mem.n; ++i) { // compute frac_rep
~~^~~~~~~~~~~~
src/bwamem.c:442:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (p->x[2] <= opt->max_occ)
~~~~~~~~^~~~~~~~~~~~~~~
src/bwamem.c:450:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < aux->mem.n; ++i) {
~~^~~~~~~~~~~~
src/bwamem.c:455:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
step = p->x[2] > opt->max_occ ? p->x[2] / opt->max_occ : 1;
~~~~~~~~^~~~~~~~~~~~~~
src/bwamem.c:456:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = count = 0; k < p->x[2] && count < opt->max_occ; k += step, ++count) {
~~^~~~~~~~~
In file included from src/kstring.h:8:0,
from src/bwamem.c:11:
src/malloc_wrap.h:28:36: warning: invalid conversion from ‘void*’ to ‘mem_seed_t*’ [-fpermissive]
# define calloc(n, s) wrap_calloc( (n), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:476:17: note: in expansion of macro ‘calloc’
tmp.seeds = calloc(tmp.m, sizeof(mem_seed_t));
^~~~~~
src/bwamem.c:493:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < chain.n; ++i)
~~^~~~~~~~~
src/bwamem.c: In function ‘int mem_chain_flt(const mem_opt_t*, int, mem_chain_t*)’:
src/bwamem.c:536:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = 0; k < chains.n; ++k) {
~~^~~~~~~~~~
src/bwamem.c:555:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k == chains.n) {
~~^~~~~~~~~~~
src/bwamem.c:560:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < chains.n; ++i) {
~~^~~~~~~~~~
src/bwamem.c: In function ‘void mem_mark_primary_se_core(const mem_opt_t*, int, mem_alnreg_t*, int_v*)’:
src/bwamem.c:717:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = 0; k < z->n; ++k) {
~~^~~~~~
src/bwamem.c:732:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (k == z->n)
~~^~~~~~~
In file included from src/kstring.h:8:0,
from src/bwamem.c:11:
src/bwamem.c: In function ‘void mem_chain2aln(const mem_opt_t*, const bntseq_t*, const uint8_t*, int, const uint8_t*, const mem_chain_t*, mem_alnreg_v*, int*, int*, gpu_batch*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘uint64_t* {aka long unsigned int*}’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1087:8: note: in expansion of macro ‘malloc’
srt = malloc(c->n * 8);
^~~~~~
src/bwamem.c:1098:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < av->n; ++i) // test whether extension has been made before
~~^~~~~~~
src/bwamem.c:1119:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < av->n)
~~^~~~~~~
src/bwamem.c:1226:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curr_gpu_batch->n_target_batch < curr_gpu_batch->gpu_storage->host_max_target_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1246:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1253:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1260:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1267:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (curr_gpu_batch->n_seqs < curr_gpu_batch->gpu_storage->host_max_n_alns)
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1211:8: warning: unused variable ‘j’ [-Wunused-variable]
int j;
^
src/bwamem.c:1048:12: warning: unused variable ‘rid’ [-Wunused-variable]
int i, k, rid, max_off[2], aw[2]; // aw: actual bandwidth used in extension
^~~
src/bwamem.c:1048:17: warning: unused variable ‘max_off’ [-Wunused-variable]
int i, k, rid, max_off[2], aw[2]; // aw: actual bandwidth used in extension
^~~~~~~
src/bwamem.c:1049:39: warning: unused variable ‘tmp’ [-Wunused-variable]
int64_t l_pac = bns->l_pac, rmax[2], tmp, max = 0;
^~~
src/bwamem.c:1051:11: warning: unused variable ‘rseq’ [-Wunused-variable]
uint8_t *rseq = NULL;
^~~~
src/bwamem.c: In function ‘void mem_aln2sam(const mem_opt_t*, const bntseq_t*, kstring_t*, bseq1_t*, int, const mem_aln_t*, int, const mem_aln_t*)’:
src/bwamem.c:1563:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = tmp; i < str->l; ++i) // replace TAB in the comment to SPACE
~~^~~~~~~~
src/bwamem.c: In function ‘void mem_reg2sam(const mem_opt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, mem_alnreg_v*, int, const mem_aln_t*)’:
src/bwamem.c:1621:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = l = 0; k < a->n; ++k) {
~~^~~~~~
src/bwamem.c:1649:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = 0; k < aa.n; ++k)
~~^~~~~~
src/bwamem.c:1651:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = 0; k < aa.n; ++k)
~~^~~~~~
src/bwamem.c:1657:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (k = 0; k < a->n; ++k)
~~^~~~~~
src/bwamem.c: In function ‘void mem_gasal_fill(gpu_batch*, int, int, char*, int)’:
src/bwamem.c:1679:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gpu_batch_arr[gpu_batch_arr_idx].n_query_batch < gpu_batch_arr[gpu_batch_arr_idx].gpu_storage->host_max_query_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1697:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (gpu_batch_arr[gpu_batch_arr_idx].n_query_batch < gpu_batch_arr[gpu_batch_arr_idx].gpu_storage->host_max_query_batch_bytes)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c: In function ‘void mem_align1_core(const mem_opt_t*, const bwt_t*, const bntseq_t*, const uint8_t*, bseq1_t*, void*, int, int, mem_alnreg_v*, int, gasal_gpu_storage_v*)’:
src/bwamem.c:1803:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < chn.n; ++i) {
~~^~~~~~~
src/bwamem.c:1851:16: warning: unused variable ‘cur’ [-Wunused-variable]
gpu_batch *cur = &gpu_batch_arr[gpu_batch_arr_idx];
^~~
src/bwamem.c:1857:132: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
fprintf(stderr, "Thread no. %d is here with internal batch size %d, regs.n %d \n", tid, internal_batch_size, regs.n);
~~~~~~^
In file included from src/bntseq.h:31:0,
from src/bwamem.h:5,
from src/bwamem.c:12:
src/bwamem.c:1865:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
assert(kv_size(regs_vec) == batch_processed);
src/bwamem.c:1902:139: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
if (gpu_batch_arr[internal_batch_idx].no_extend == 1) fprintf(stderr, "I am here too as well with regs.n %d\n", regs.n);
~~~~~~^
src/bwamem.c:1903:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i = 0; i < regs.n; ++i){
~~^~~~~~~~
src/bwamem.c:1923:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < regs.n; ++i) {
~~^~~~~~~~
src/bwamem.c:1928:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 0; i < regs.n; ++i) {
~~^~~~~~~~
In file included from src/kstring.h:8:0,
from src/bwamem.c:11:
src/bwamem.c: In function ‘mem_aln_t mem_reg2aln(const mem_opt_t*, const bntseq_t*, const uint8_t*, int, const char*, const mem_alnreg_t*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘uint8_t* {aka unsigned char*}’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:1970:13: note: in expansion of macro ‘malloc’
query = malloc(l_query);
^~~~~~
src/malloc_wrap.h:38:37: warning: invalid conversion from ‘void*’ to ‘uint32_t* {aka unsigned int*}’ [-fpermissive]
# define realloc(p, s) wrap_realloc((p), (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2027:19: note: in expansion of macro ‘realloc’
a.cigar = realloc(a.cigar, 4 * (a.n_cigar + 2) + l_MD);
^~~~~~~
src/bwamem.c: In function ‘void mem_process_seqs(const mem_opt_t*, const bwt_t*, const bntseq_t*, const uint8_t*, int64_t, int, bseq1_t*, const mem_pestat_t*)’:
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘mem_alnreg_v*’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2104:14: note: in expansion of macro ‘malloc’
w.regs = malloc(n * sizeof(mem_alnreg_v));
^~~~~~
src/malloc_wrap.h:33:36: warning: invalid conversion from ‘void*’ to ‘smem_aux_t**’ [-fpermissive]
# define malloc(s) wrap_malloc( (s), __FILE__, __LINE__, __func__)
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/bwamem.c:2112:13: note: in expansion of macro ‘malloc’
w.aux = malloc(opt->n_threads * sizeof(smem_aux_t));
^~~~~~
src/bwamem.c:2116:80: warning: invalid conversion from ‘void (*)(void*, int, int, int, int, gasal_gpu_storage_v*)’ to ‘void (*)(void*, int, int, int, int)’ [-fpermissive]
kt_for(opt->n_threads, worker1, &w, /*(opt->flag & MEM_F_PE) ? n >> 1 : */n); // find mapping positions
^
In file included from src/bwamem.c:12:0:
src/bwamem.h:197:14: note: initializing argument 2 of ‘void kt_for(int, void (*)(void*, int, int, int, int), void*, int)’
extern void kt_for(int n_threads, void (*func)(void*, int, int, int, int), void *data, int n);
^~~~~~
src/bwamem.c:2136:76: warning: invalid conversion from ‘void (*)(void*, int, int, int, int, gasal_gpu_storage_v*)’ to ‘void (*)(void*, int, int, int, int)’ [-fpermissive]
kt_for(opt->n_threads, worker2, &w, (opt->flag & MEM_F_PE) ? n >> 1 : n); // generate alignment
^
In file included from src/bwamem.c:12:0:
src/bwamem.h:197:14: note: initializing argument 2 of ‘void kt_for(int, void (*)(void*, int, int, int, int), void*, int)’
extern void kt_for(int n_threads, void (*func)(void*, int, int, int, int), void *data, int n);
^~~~~~
make: *** [bwamem.o] Error 1
Here's some system info:
$ uname -a
Linux dgx01 4.15.0-130-generic #134-Ubuntu SMP Tue Jan 5 20:46:26 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2020 NVIDIA Corporation
Built on Tue_Sep_15_19:10:02_PDT_2020
Cuda compilation tools, release 11.1, V11.1.74
Build cuda_11.1.TC455_06.29069683_0
Hi, I really appreciate your work. However, I just wonder why you don't integrate the globol alignment, which may lead to more acceleration to BWA.
I am looking forward to your reply.
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