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#ifndef _sml_h_
#define _sml_h_
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/dmSML/asyncio.h"
#include <string.h>
#include "libGenome/gnDefs.h"
#ifndef UINT8_MAX
#define UINT8_MAX 256
typedef unsigned char uint8;
typedef unsigned uint32;
typedef unsigned long long uint64;
#endif
static uint8* CreateBasicDNATable(){
uint8* bdt = (uint8*)malloc( sizeof(uint8) * UINT8_MAX );
memset(bdt, 0, UINT8_MAX);
bdt['c'] = 1;
bdt['C'] = 1;
bdt['b'] = 1;
bdt['B'] = 1;
bdt['y'] = 1;
bdt['Y'] = 1;
bdt['g'] = 2;
bdt['G'] = 2;
bdt['s'] = 2;
bdt['S'] = 2;
bdt['k'] = 2;
bdt['K'] = 2;
bdt['t'] = 3;
bdt['T'] = 3;
return bdt;
}
static uint8* DNA_TABLE;
typedef unsigned position_t;
typedef unsigned long long mask_t;
#define MASK_T_BYTES 8
static mask_t seed_mask = 0x7FFFFFFF;
static int mask_length = 31;
static int mask_weight = 31;
#define DESCRIPTION_SIZE 2048 /**< Number of bytes for the freeform text description of an SML */
typedef signed short sarID_t;
typedef struct SMLHeader_s{
uint32 version; /**< Format version - 4 bytes */
uint32 alphabet_bits; /**< Bits per character in the alphabet - 4 bytes */
uint64 seed; /**< The pattern used in each seed */
uint32 seed_length; /**< The length of the seed mask */
uint32 seed_weight; /**< The weight of the seed mask */
uint64 length; /**< length of the sequence before circularity - 8 bytes */
uint32 unique_mers; /**< Number of unique mers in the sequence 4 bytes */
uint32 word_size; /**< Word size on the machine the sequence was translated */
boolean little_endian; /**< Is the byte order little endian? 0==no, !0==yes */
signed short id; /**< Obsolete ID value - 1 byte, eaten by alignment? */
boolean circular; /**< Circularity of sequence - 1 byte */
uint8 translation_table[UINT8_MAX]; /**< Translation table for ascii characters to binary values -- 256 bytes */
char description[DESCRIPTION_SIZE]; /**< Freeform text description of sequence data -- 2048 bytes */
} SMLHeader_t;
typedef struct sml_s {
char key[8];
position_t pos;
} sml_t;
SMLHeader_t InitSML( aFILE* file, uint64 file_size, uint64 seed );
#endif /* _sml_h_ */
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