fasta.h

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#ifndef FASTA_H
#define FASTA_H
 
#include <limits.h>
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
 
#define firstEl(b) (b & 0x0F) // first 4 bits
 
#define secondEl(b) (b & 0xF0) >> 4 // second 4 bits
 
#define toByte(a, b) (uint8_t)a | (b << 4)
 
typedef uint64_t packing_t;
 
#define PACKING_WIDTH sizeof(packing_t) * 2
 
#define ROUND_NUM 7
 
#define PACKING_ROUND(packed_size) (((packed_size) + ROUND_NUM) & ~ROUND_NUM)
 
static inline void pack(uint8_t values[PACKING_WIDTH], packing_t *packed) {
    *packed = values[0];
    for (uint8_t i = 1; i < PACKING_WIDTH; i++) {
        *packed |= (packing_t)(values[i]) << (i * 4);
    }
}
 
#define i_Index 0xFF // invalid FASTA index
 
extern uint8_t fasta_binary_mapping[CHAR_MAX + 1];
 
bool is_valid_title(const char *title, size_t len);
 
char getIUPACchar(uint8_t index, bool rna);
 
void initialize_fasta_binary_mapping();
 
#endif