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compilable again

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This commit is contained in:
Heng Li
2017-04-26 19:36:46 +08:00
parent 56723ad580
commit de367a340c
4 changed files with 206 additions and 37 deletions
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minimap.h
+10 -4
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@@ -50,13 +50,18 @@ typedef struct {
} mm_reg1_t;
typedef struct {
int n_frag_mini;
float max_occ_frac;
float mid_occ_frac;
int sdust_thres; // score threshold for SDUST; 0 to disable
int flag; // see MM_F_* macros
int radius; // bandwidth to cluster hits
int max_gap; // break a chain if there are no minimizers in a max_gap window
int min_cnt; // minimum number of minimizers to start a chain
int min_match;
int sdust_thres; // score threshold for SDUST; 0 to disable
int flag; // see MM_F_* macros
float merge_frac; // merge two chains if merge_frac fraction of minimzers are shared between the chains
int max_occ;
int mid_occ;
} mm_mapopt_t;
extern int mm_verbose;
@@ -81,7 +86,7 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc);
void mm_idx_destroy(mm_idx_t *mi);
mm_idx_t *mm_idx_gen(struct bseq_file_s *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name);
void mm_idx_set_max_occ(mm_idx_t *mi, float f);
uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
@@ -92,6 +97,7 @@ mm_idx_t *mm_idx_load(FILE *fp);
// mapping
void mm_mapopt_init(mm_mapopt_t *opt);
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
mm_tbuf_t *mm_tbuf_init(void);
void mm_tbuf_destroy(mm_tbuf_t *b);
const mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);