minimap2/sdust.h at v2.12 · Triadai/minimap2

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#ifndef SDUST_H

#define SDUST_H

#include <stdint.h>

#ifdef __cplusplus

extern "C" {

#endif

struct sdust_buf_s;

typedef struct sdust_buf_s sdust_buf_t;

// the simple interface

uint64_t *sdust(void *km, const uint8_t *seq, int l_seq, int T, int W, int *n);

// the following interface dramatically reduce heap allocations when sdust is frequently called.

sdust_buf_t *sdust_buf_init(void *km);

void sdust_buf_destroy(sdust_buf_t *buf);

const uint64_t *sdust_core(const uint8_t *seq, int l_seq, int T, int W, int *n, sdust_buf_t *buf);

#ifdef __cplusplus

}

#endif