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Heng Li
2018-07-14 22:52:36 -04:00
parent 1a55227d5a
commit e5277dbf5c
4 changed files with 181 additions and 39 deletions
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mmpriv.h
+5
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@@ -28,6 +28,9 @@
#define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
#define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
#define MALLOC(type, len) ((type*)malloc((len) * sizeof(type)))
#define CALLOC(type, len) ((type*)calloc((len), sizeof(type)))
#ifdef __cplusplus
extern "C" {
#endif
@@ -87,6 +90,8 @@ void mm_seg_free(void *km, int n_segs, mm_seg_t *segs);
void mm_pair(void *km, int max_gap_ref, int dp_bonus, int sub_diff, int match_sc, const int *qlens, int *n_regs, mm_reg1_t **regs);
FILE *mm_split_init(const char *prefix, const mm_idx_t *mi);
FILE **mm_split_merge_prep(const char *prefix, int n_splits, mm_idx_t **mi_);
int mm_split_merge(int n_segs, const char **fn, const mm_mapopt_t *opt, int n_split_idx);
void mm_err_puts(const char *str);
void mm_err_fwrite(const void *p, size_t size, size_t nitems, FILE *fp);