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Release the GIL to allow native Python threading.

This commit is contained in:
Hyeshik Chang 2018-06-27 02:09:58 +09:00 committed by Heng Li
parent 6908dc59a5
commit c92a6866f3
1 changed files with 9 additions and 2 deletions
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11
python/cmappy.h
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@ -73,13 +73,17 @@ static inline void mm_reset_timer(void)
extern unsigned char seq_comp_table[256]; extern unsigned char seq_comp_table[256];
static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt) static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const char *seq2, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt)
{ {
mm_reg1_t *r;
Py_BEGIN_ALLOW_THREADS
if (seq2 == 0) { if (seq2 == 0) {
return mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, NULL); r = mm_map(mi, strlen(seq1), seq1, n_regs, b, opt, NULL);
} else { } else {
int _n_regs[2]; int _n_regs[2];
mm_reg1_t *regs[2]; mm_reg1_t *regs[2];
char *seq[2]; char *seq[2];
int i, len[2]; int i, len[2];
len[0] = strlen(seq1); len[0] = strlen(seq1);
len[1] = strlen(seq2); len[1] = strlen(seq2);
seq[0] = (char*)seq1; seq[0] = (char*)seq1;
@ -97,8 +101,11 @@ static inline mm_reg1_t *mm_map_aux(const mm_idx_t *mi, const char *seq1, const
regs[0] = (mm_reg1_t*)realloc(regs[0], sizeof(mm_reg1_t) * (*n_regs)); regs[0] = (mm_reg1_t*)realloc(regs[0], sizeof(mm_reg1_t) * (*n_regs));
memcpy(&regs[0][_n_regs[0]], regs[1], _n_regs[1] * sizeof(mm_reg1_t)); memcpy(&regs[0][_n_regs[0]], regs[1], _n_regs[1] * sizeof(mm_reg1_t));
free(regs[1]); free(regs[1]);
return regs[0]; r = regs[0];
} }
Py_END_ALLOW_THREADS
return r;
} }
static inline char *mappy_revcomp(int len, const uint8_t *seq) static inline char *mappy_revcomp(int len, const uint8_t *seq)