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BED I/O

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Heng Li
2019-04-28 16:47:12 -04:00
parent 371bc9513a
commit 6420acca6d
4 changed files with 125 additions and 2 deletions
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minimap.h
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@@ -66,6 +66,7 @@ typedef struct {
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
struct mm_idx_bucket_s *B; // index (hidden)
struct mm_idx_intv_s *I; // intervals (hidden)
void *km, *h;
} mm_idx_t;
@@ -365,6 +366,9 @@ int mm_idx_index_name(mm_idx_t *mi);
int mm_idx_name2id(const mm_idx_t *mi, const char *name);
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
int mm_idx_bed_read(mm_idx_t *mi, const char *fn);
int mm_idx_bed_junc(const mm_idx_t *mi, int32_t ctg, int32_t st, int32_t en, int32_t strand, int8_t *s);
// deprecated APIs for backward compatibility
void mm_mapopt_init(mm_mapopt_t *opt);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads);