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r573: prepare to generalize index

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Heng Li
2017-11-11 19:54:06 -05:00
parent 3b518271ee
commit 2f463b1db0
6 changed files with 38 additions and 35 deletions
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minimap.h
+7 -3
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@@ -26,6 +26,10 @@
#define MM_F_SPLICE_FLANK 0x40000
#define MM_F_SOFTCLIP 0x80000
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2
#define MM_I_NO_NAME 0x4
#define MM_IDX_MAGIC "MMI\2"
#define MM_MAX_SEG 255
@@ -46,7 +50,7 @@ typedef struct {
} mm_idx_seq_t;
typedef struct {
int32_t b, w, k, is_hpc;
int32_t b, w, k, flag;
uint32_t n_seq; // number of reference sequences
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
@@ -80,7 +84,7 @@ typedef struct {
// indexing and mapping options
typedef struct {
short k, w, is_hpc, bucket_bits;
short k, w, flag, bucket_bits;
int mini_batch_size;
uint64_t batch_size;
} mm_idxopt_t;
@@ -269,7 +273,7 @@ int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_
// 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 is_hpc, int n_threads);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads);
#ifdef __cplusplus
}