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r819: mappy to support cs/MD

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Heng Li
2018-07-24 23:29:55 -04:00
parent 8c064a5f29
commit ff9917a1c4
11 changed files with 115 additions and 28 deletions
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minimap.h
+18
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@@ -301,6 +301,8 @@ mm_tbuf_t *mm_tbuf_init(void);
*/
void mm_tbuf_destroy(mm_tbuf_t *b);
void *mm_tbuf_get_km(mm_tbuf_t *b);
/**
* Align a query sequence against an index
*
@@ -337,6 +339,22 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads);
/**
* Generate the cs tag (new in 2.12)
*
* @param km memory blocks; set to NULL if unsure
* @param buf buffer to write the cs/MD tag; typicall NULL on the first call
* @param max_len max length of the buffer; typically set to 0 on the first call
* @param mi index
* @param r alignment
* @param seq query sequence
* @param no_iden true to use : instead of =
*
* @return the length of cs
*/
int mm_gen_cs(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq, int no_iden);
int mm_gen_MD(void *km, char **buf, int *max_len, const mm_idx_t *mi, const mm_reg1_t *r, const char *seq);
// query sequence name and sequence in the minimap2 index
int mm_idx_index_name(mm_idx_t *mi);
int mm_idx_name2id(const mm_idx_t *mi, const char *name);