zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

make sdust work (it didn't)

This commit is contained in:
Heng Li 2017-04-07 10:45:50 -04:00
parent bacb7534d2
commit 0f160151c7
2 changed files with 7 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
sdust.c
View File

@ -50,11 +50,9 @@ struct sdust_buf_s {
void *km; // memory pool void *km; // memory pool
}; };
sdust_buf_t *sdust_buf_init(void) sdust_buf_t *sdust_buf_init(void *km)
{ {
sdust_buf_t *buf; sdust_buf_t *buf;
void *km;
km = km_init();
buf = (sdust_buf_t*)kcalloc(km, 1, sizeof(sdust_buf_t)); buf = (sdust_buf_t*)kcalloc(km, 1, sizeof(sdust_buf_t));
buf->km = km; buf->km = km;
buf->w = kdq_init(int, buf->km); buf->w = kdq_init(int, buf->km);
@ -64,9 +62,7 @@ sdust_buf_t *sdust_buf_init(void)
void sdust_buf_destroy(sdust_buf_t *buf) void sdust_buf_destroy(sdust_buf_t *buf)
{ {
if (buf == 0) return; if (buf == 0) return;
if (buf->km == 0) { // then fall back to the default allocator for which we need free all arrays manually kfree(buf->km, buf->P.a); kfree(buf->km, buf->res.a); kfree(buf->km, buf);
kfree(buf->km, buf->P.a); kfree(buf->km, buf->res.a); kfree(buf->km, buf);
} else km_destroy(buf->km); // This deallocate all memory allocated from buf->km
} }
static inline void shift_window(int t, kdq_t(int) *w, int T, int W, int *L, int *rw, int *rv, int *cw, int *cv) static inline void shift_window(int t, kdq_t(int) *w, int T, int W, int *L, int *rw, int *rv, int *cw, int *cv)
@ -165,11 +161,11 @@ const uint64_t *sdust_core(const uint8_t *seq, int l_seq, int T, int W, int *n,
return buf->res.a; return buf->res.a;
} }
uint64_t *sdust(const uint8_t *seq, int l_seq, int T, int W, int *n) uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n)
{ {
uint64_t *ret; uint64_t *ret;
sdust_buf_t *buf; sdust_buf_t *buf;
buf = sdust_buf_init(); buf = sdust_buf_init(km);
ret = (uint64_t*)sdust_core(seq, l_seq, T, W, n, buf); ret = (uint64_t*)sdust_core(seq, l_seq, T, W, n, buf);
buf->res.a = 0; buf->res.a = 0;
sdust_buf_destroy(buf); sdust_buf_destroy(buf);
@ -202,7 +198,7 @@ int main(int argc, char *argv[])
while (kseq_read(ks) >= 0) { while (kseq_read(ks) >= 0) {
uint64_t *r; uint64_t *r;
int i, n; int i, n;
r = sdust((uint8_t*)ks->seq.s, -1, T, W, &n); r = sdust(0, (uint8_t*)ks->seq.s, -1, T, W, &n);
for (i = 0; i < n; ++i) for (i = 0; i < n; ++i)
printf("%s\t%d\t%d\n", ks->name.s, (int)(r[i]>>32), (int)r[i]); printf("%s\t%d\t%d\n", ks->name.s, (int)(r[i]>>32), (int)r[i]);
free(r); free(r);

4
sdust.h
View File

@ -9,10 +9,10 @@ extern "C" {
#endif #endif
// the simple interface // the simple interface
uint64_t *sdust(const uint8_t *seq, int l_seq, int T, int W, int *n); uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n);
// the following interface dramatically reduce heap allocations when sdust is frequently called. // the following interface dramatically reduce heap allocations when sdust is frequently called.
sdust_buf_t *sdust_buf_init(void); sdust_buf_t *sdust_buf_init(void *km);
void sdust_buf_destroy(sdust_buf_t *buf); void sdust_buf_destroy(sdust_buf_t *buf);
const uint64_t *sdust_core(const uint8_t *seq, int l_seq, int T, int W, int *n, sdust_buf_t *buf); const uint64_t *sdust_core(const uint8_t *seq, int l_seq, int T, int W, int *n, sdust_buf_t *buf);