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/*
This file is a part of KMC software distributed under GNU GPL 3 licence.
The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Marek Kokot
Version: 3.2.4
Date : 2024-02-09
*/
#ifndef _DEFS_H
#define _DEFS_H
#include <cinttypes>
#define KMC_VER "3.2.4"
#define KMC_DATE "2024-02-09"
#define _CRT_SECURE_NO_WARNINGS
#define MIN(x,y) ((x) < (y) ? (x) : (y))
#define MAX(x,y) ((x) > (y) ? (x) : (y))
#define NORM(x, lower, upper) ((x) < (lower) ? (lower) : (x) > (upper) ? (upper) : (x))
#define uchar unsigned char
#include <time.h>
//#define DEBUG_MODE
//#define USE_META_PROG
#define COMPACT_CUMSUM_PART_SIZE (1<<10)
#define KMER_X 3
#define STATS_FASTQ_SIZE (1 << 28)
#define EXPAND_BUFFER_RECS (1 << 16)
#define MIN_N_BINS 64
#define MAX_N_BINS 2000
#ifndef MAX_K
#define MAX_K 256
#endif
#define MIN_K 1
#define MIN_MEM 2
// Range of number of FASTQ/FASTA reading threads
#define MIN_SF 1
#define MAX_SF 32
// Range of number of signature length
#define MIN_SL 5
#define MAX_SL 11
// Range of number of splitting threads
#define MIN_SP 1
#define MAX_SP 64
// Range of number of threads for 2nd stage
#define MIN_SR 1
#define MAX_SR 128
//Range of number of sorter threads pre sorter in strict memory mode
#define MIN_SMSO 1
#define MAX_SMSO 16
//Range of number of uncompactor threads in strict memory mode
#define MIN_SMUN 1
#define MAX_SMUN 16
//Range of number of merger threads in strict memory mode
#define MIN_SMME 1
#define MAX_SMME 16
typedef float count_t;
#define KMER_WORDS ((MAX_K + 31) / 32)
#ifdef _WIN32
#define my_fopen fopen
#define my_fseek _fseeki64
#define my_ftell _ftelli64
using int32 = int32_t;
using uint32 = uint32_t;
using int64 = int64_t;
using uint64 = uint64_t;
#else
#define my_fopen fopen
#define my_fseek fseek
#define my_ftell ftell
using int32 = int32_t;
using uint32 = uint32_t;
using int64 = int64_t;
using uint64 = uint64_t;
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <stdio.h>
#include <ext/algorithm>
using __gnu_cxx::copy_n;
#endif
const int32 MAX_STR_LEN = 32768;
#define ALIGNMENT 0x100
#define BYTE_LOG(x) (((x) < (1 << 8)) ? 1 : ((x) < (1 << 16)) ? 2 : ((x) < (1 << 24)) ? 3 : 4)
#define BYTE_LOG_ULL(x) (((x) < (1ull << 8)) ? 1 : ((x) < (1ull << 16)) ? 2 : ((x) < (1ull << 24)) ? 3 : ((x) < (1ull << 32)) ? 4 : ((x) < (1ull << 40) ? 5 : ((x) < (1ull << 48) ? 6 : ((x) < (1ull << 56)) ? 7 : 8)))
#ifdef _WIN32
#define FORCE_INLINE __forceinline
#else
#define FORCE_INLINE inline __attribute__((always_inline))
#endif
//for radix
#define WIN_ALIGNMENT 64
//designated experimentally
constexpr int32 BUFFER_WIDTHS[] = { -1, 32, 16, 16, 8, 8, 4, 8, 4 };
constexpr int32_t BUFFER_WIDTHS_ABOVE_CACHE_LINE_SIZE[] = { -1, 8, 4, 8, 2, 8, 4, 8, 1 };
constexpr uint32_t GetBufferWidth(uint32_t index)
{
return (index <= 8) ? BUFFER_WIDTHS[index] : BUFFER_WIDTHS_ABOVE_CACHE_LINE_SIZE[(index - 1) % 8 + 1];
}
#ifdef _WIN32
#define ALIGN_ARRAY __declspec(align(WIN_ALIGNMENT))
#else
#define ALIGN_ARRAY __attribute__((aligned(ALIGNMENT)))
#endif
#ifdef _WIN32
typedef unsigned __int8 uint8_t;
#else
#include <stdint.h>
#endif
inline uint32 calc_counter_size(int64 cutoff_max, int64 counter_max)
{
if (counter_max == 1)
return 0;
return MIN(BYTE_LOG(cutoff_max), BYTE_LOG(counter_max));
}
inline uint32 calc_counter_size_ull(int64 cutoff_max, int64 counter_max)
{
if (counter_max == 1)
return 0;
return MIN(BYTE_LOG_ULL((uint64)cutoff_max), BYTE_LOG_ULL((uint64)counter_max));
}
#endif
// ***** EOF
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