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/*
Ray -- Parallel genome assemblies for parallel DNA sequencing
Copyright (C) 2011, 2012, 2013 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#ifndef _constants
#define _constants
#ifndef CONFIG_RAY_VERSION
#define CONFIG_RAY_VERSION "Unknown"
#endif
/*
* Define the maximum k-mer length when
* the compiler/make does not.
*/
#ifndef CONFIG_MAXKMERLENGTH
#define CONFIG_MAXKMERLENGTH 32
#endif
// some multipliers
/** something occuring twice is repeated */
#define REPEAT_MULTIPLIER 2
/** 3 standard deviations on both sides of a normal distribution include most points */
#define FRAGMENT_MULTIPLIER 3
#include <stdlib.h> /* for __WORDSIZE hopefully */
#include <stdint.h>
/* exit codes */
/*
* Include those libraries for Microsoft Visual C++
*/
#ifdef _MSC_VER
#include <xiosbase>
#include <stdexcept>
/* http://msdn.microsoft.com/en-us/library/b0084kay%28VS.80%29.aspx */
#define __func__ __FUNCTION__
#endif
#ifdef CONFIG_FORCE_PACKING
/*
* With gcc, one can pack data structures.
*/
#ifdef __GNUC__
#define ATTRIBUTE_PACKED __attribute__ ((packed))
/*
* For Microsoft Visual C++
*/
#elif defined(_MSC_VER)
#define ATTRIBUTE_PACKED /* sorry, not available yet */
#else
#define ATTRIBUTE_PACKED
#endif
#else
#define ATTRIBUTE_PACKED
#endif
#define DUMMY_LIBRARY 40000
#define RAY_NUCLEOTIDE_A 0 /* ~00 == 11 */
#define RAY_NUCLEOTIDE_C 1 /* ~01 == 10 */
#define RAY_NUCLEOTIDE_G 2 /* ~10 == 01 */
#define RAY_NUCLEOTIDE_T 3 /* ~11 == 00 */
#define SYMBOL_A 'A'
#define SYMBOL_T 'T'
#define SYMBOL_G 'G'
#define SYMBOL_C 'C'
#define SYMBOL_LOWER_A 'a'
#define SYMBOL_LOWER_T 't'
#define SYMBOL_LOWER_G 'g'
#define SYMBOL_LOWER_C 'c'
#define DOUBLE_ENCODING_A_COLOR '0'
#define DOUBLE_ENCODING_C_COLOR '1'
#define DOUBLE_ENCODING_G_COLOR '2'
#define DOUBLE_ENCODING_T_COLOR '3'
/* maximum value for a uint16_t */
#define RAY_MAXIMUM_READ_LENGTH 65535
#define MAX_VERTICES_TO_VISIT 500
#define TIP_LIMIT 40
/*
* this is the type used to store coverage values
*
* possible values are:
*
* - uint8_t for coverage values from 0 to 256-1
* - uint16_t for coverage values from 0 to 65536-1
* - uint32_t for coverage values from 0 to 4294967296-1
*
*
*/
#ifndef CONFIG_MAXIMUM_COVERAGE
#define CONFIG_MAXIMUM_COVERAGE 99999
#endif
#if CONFIG_MAXIMUM_COVERAGE < 256
typedef uint8_t CoverageDepth ;
#elif CONFIG_MAXIMUM_COVERAGE < 65536
typedef uint16_t CoverageDepth;
#elif CONFIG_MAXIMUM_COVERAGE < 4294967296
typedef uint32_t CoverageDepth;
#else
typedef uint64_t CoverageDepth;
#endif
/** 32-bit or 64-bit system */
#if defined(__WORDSIZE)
/** use __WORDSIZE */
#define NUMBER_OF_BITS __WORDSIZE
#elif defined(_WIN64)
#define NUMBER_OF_BITS 64
#elif defined (_WIN32)
#define NUMBER_OF_BITS 32
/** assume 64 bits */
/* you may get some compilation warnings about printf and fprintf */
#else
#define NUMBER_OF_BITS 64
#endif
/* 64-bit system */
#if NUMBER_OF_BITS == 64
#define RAY_64_BITS
/* 32-bit system */
#elif NUMBER_OF_BITS == 32
#define RAY_32_BITS
/* assume a 64-bit system */
#else
#define RAY_64_BITS
#endif
/* since Lustre is not very good at caching file input/output operations
* Ray agglomerates these operations */
#define SIZE_1M 1048576
#define SIZE_2M 2097152
#define SIZE_4M 4194304
#define SIZE_8M 8388608
#define SIZE_16M 16777216
#define SIZE_32M 33554432
#define SIZE_64M 67108864
#define SIZE_128M 134217728
#define CONFIG_FILE_IO_BUFFER_SIZE SIZE_16M
/* a DNA strand */
typedef char Strand;
/* a datatype for counts */
typedef uint64_t LargeCount;
/* a datatype for an index */
typedef uint64_t LargeIndex;
typedef uint16_t LibraryHandle;
typedef int SampleIdentifier;
/*
* path storage engine
* CONFIG_PATH_STORAGE_DEFAULT uses arrays of vertices, which consumes memory a lot.
* CONFIG_PATH_STORAGE_BLOCK uses a block approach for vertices.
*/
#define CONFIG_PATH_STORAGE_BLOCK
//#define CONFIG_PATH_STORAGE_DEFAULT
#define BITS_PER_NUCLEOTIDE 2
#define BITS_PER_BYTE 8
#endif
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