File: Mosaik.h

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#pragma once

#ifndef WIN32
//#include "SafeFunctions.h"
#endif

// ==============
// MOSAIK version
// ==============

#define MOSAIK_VERSION_DATE "2009-02-11"

// adopt a major.minor.build version number [1].[1].[3]
const unsigned char  MOSAIK_MAJOR_VERSION = 0;
const unsigned char  MOSAIK_MINOR_VERSION = 9;
const unsigned short MOSAIK_BUILD_VERSION = 899;

// ================================
// Platform specific variable sizes
// ================================

// Windows Vista 32-bit
// Fedora Core 7 32-bit
// Fedora Core 6 64-bit
// Itanium2      64-bit
#define SIZEOF_CHAR          1
#define SIZEOF_WCHAR         2
#define SIZEOF_SHORT         2
#define SIZEOF_INT           4
#define SIZEOF_FLOAT         4
#define SIZEOF_DOUBLE        8
#define SIZEOF_UINT64        8
#define MOSAIK_LITTLE_ENDIAN 1

#ifdef WIN32
typedef signed long long    int64_t;
typedef unsigned long long uint64_t;
#endif

#define NEGATIVE_ONE_INT     0xffffffff
#define NEGATIVE_TWO_INT     0xfffffffe
#define NEGATIVE_THREE_INT   0xfffffffd
#define NEGATIVE_FOUR_INT    0xfffffffc
#define MAX_SHORT            0xffff

// ==========================
// Platform specific file I/O 
// ==========================

#ifdef WIN32
const char OS_DIRECTORY_SEPARATOR = '\\';
#else
const char OS_DIRECTORY_SEPARATOR = '/';
#endif

#define DIRECTORY_NAME_LENGTH    255

// ====================================
// Enable unit test diagnostic messages
// ====================================

#ifdef UNITTEST
#define SILENTMODE if(0)
#else
#define SILENTMODE
#endif

// =================
// Aligner constants
// =================

const double HASH_REGION_EXTENSION_PERCENT     = 0.025;
const unsigned char REFERENCE_SEQUENCE_QUALITY = 40;