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

reduced a heap allocation 

which *might* be frequent for short reads
This commit is contained in:
Heng Li 2017-09-02 18:32:45 -04:00
parent 00416c76d1
commit 3d48516885
1 changed files with 2 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
sketch.c
View File

@ -77,11 +77,10 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
{
uint64_t shift1 = 2 * (k - 1), mask = (1ULL<<2*k) - 1, kmer[2] = {0,0};
int i, j, l, buf_pos, min_pos, kmer_span = 0;
mm128_t *buf, min = { UINT64_MAX, UINT64_MAX };
mm128_t buf[256], min = { UINT64_MAX, UINT64_MAX };
tiny_queue_t tq;
assert(len > 0 && w > 0 && k > 0 && k <= 28); // 56 bits for k-mer; could use long k-mers, but 28 enough in practice
buf = (mm128_t*)calloc(w, 16);
assert(len > 0 && (w > 0 && w < 256) && (k > 0 && k <= 28)); // 56 bits for k-mer; could use long k-mers, but 28 enough in practice
memset(buf, 0xff, w * 16);
memset(&tq, 0, sizeof(tiny_queue_t));
kv_resize(mm128_t, km, *p, p->n + len/w);
@ -140,5 +139,4 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
}
if (min.x != UINT64_MAX)
kv_push(mm128_t, km, *p, min);
free(buf);
}