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AS_global.H
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AS_global.H
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/******************************************************************************
*
* This file is part of canu, a software program that assembles whole-genome
* sequencing reads into contigs.
*
* This software is based on:
* 'Celera Assembler' (http://wgs-assembler.sourceforge.net)
* the 'kmer package' (http://kmer.sourceforge.net)
* both originally distributed by Applera Corporation under the GNU General
* Public License, version 2.
*
* Canu branched from Celera Assembler at its revision 4587.
* Canu branched from the kmer project at its revision 1994.
*
* Modifications by:
*
* Brian P. Walenz from 2006-OCT-08 to 2014-MAR-05
* are Copyright 2006-2014 J. Craig Venter Institute, and
* are subject to the GNU General Public License version 2
*
* Eli Venter on 2006-NOV-14
* are Copyright 2006 J. Craig Venter Institute, and
* are subject to the GNU General Public License version 2
*
* Sergey Koren from 2011-MAY-02 to 2011-OCT-11
* are Copyright 2011 Battelle National Biodefense Institute, and
* are subject to the BSD 3-Clause License
*
* Brian P. Walenz from 2014-AUG-11 to 2015-MAR-31
* are Copyright 2014-2015 Battelle National Biodefense Institute, and
* are subject to the BSD 3-Clause License
*
* Brian P. Walenz beginning on 2015-OCT-29
* are a 'United States Government Work', and
* are released in the public domain
*
* File 'README.licenses' in the root directory of this distribution contains
* full conditions and disclaimers for each license.
*/
// This is the global include file that all C files in the AS
// subsystem should include.
#ifndef AS_GLOBAL_H
#define AS_GLOBAL_H
// ISO C99 says that to get INT32_MAX et al, these must be defined. (7.18.2, 7.18.4, 7.8.1)
#ifndef __STDC_CONSTANT_MACROS
#define __STDC_CONSTANT_MACROS
#endif
#ifndef __STDC_LIMIT_MACROS
#define __STDC_LIMIT_MACROS
#endif
#ifndef __STDC_FORMAT_MACROS
#define __STDC_FORMAT_MACROS
#endif
// Check for GCC parallel STL support. This appeared in version 4.3, but the lowest we've tested
// with is 4.6.
//
#if ((__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ > 2)))
// Not by default!
//#ifndef _GLIBCXX_PARALLEL
//#define _GLIBCXX_PARALLEL
//#endif
#else
#undef _GLIBCXX_PARALLEL
#endif
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include <inttypes.h>
#include <limits.h>
#include <unistd.h>
#include <string.h>
#include <ctype.h>
#include <float.h>
#include <math.h>
#include <assert.h>
#include <errno.h>
#include <time.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <sys/types.h>
#ifndef TRUE
#define TRUE true
#endif
#ifndef FALSE
#define FALSE false
#endif
#ifndef MIN
#define MIN(a,b) (((a) < (b)) ? (a) : (b))
#endif
#ifndef MAX
#define MAX(a,b) (((a) > (b)) ? (a) : (b))
#endif
typedef int8_t int8;
typedef int16_t int16;
typedef int32_t int32;
typedef int64_t int64;
typedef uint8_t uint8;
typedef uint16_t uint16;
typedef uint32_t uint32;
typedef uint64_t uint64;
//typedef void* PtrT;
// Correct? Or should it be LLU and LU?
#define uint64NUMBER(X) X ## LU
#define uint32NUMBER(X) X ## U
#define uint64ZERO uint64NUMBER(0x0000000000000000)
#define uint64ONE uint64NUMBER(0x0000000000000001)
#define uint64MAX uint64NUMBER(0xffffffffffffffff)
#define uint64MASK(X) ((~uint64ZERO) >> (64 - (X)))
#define uint32ZERO uint32NUMBER(0x00000000)
#define uint32ONE uint32NUMBER(0x00000001)
#define uint32MAX uint32NUMBER(0xffffffff)
#define uint32MASK(X) ((~uint32ZERO) >> (32 - (X)))
#define uint16ZERO (0x0000)
#define uint16ONE (0x0001)
#define uint16MAX (0xffff)
#define uint16MASK(X) ((~uint16ZERO) >> (16 - (X)))
#define uint8ZERO (0x00)
#define uint8ONE (0x01)
#define uint8MAX (0xff)
#define uint8MASK(X) ((~uint8ZERO) >> (8 - (X)))
#define strtouint32(N) (uint32)strtoul (N, NULL, 10)
#define strtouint64(N) (uint64)strtoull(N, NULL, 10)
#define strtodouble(N) (double)strtod (N, NULL)
//inline uint32 strtouint32(char *N, O) (uint32)strtoul (N, O, 10)
//inline uint64 strtouint64(char *N, O) (uint64)strtoull(N, O, 10)
//inline double strtodouble(char *N, O) (double)strtod (N, O)
// Pointers
#define F_PTR "0x%016p"
// Characters
#define F_C "%c"
#define F_CP "c"
#define F_CI "%*c"
// Strings
#define F_STR "%s"
#define F_STRP "s"
#define F_STRI "%*s"
// Integers
#define F_S16 "%"PRId16
#define F_S16P PRId16
#define F_S16I "%*"PRId16
#define F_U16 "%"PRIu16
#define F_U16P PRIu16
#define F_U16I "%*"PRIu16
#define F_S32 "%"PRId32
#define F_S32P PRId32
#define F_S32I "%*"PRId32
#define F_U32 "%"PRIu32
#define F_U32P PRIu32
#define F_U32I "%*"PRIu32
#define F_S64 "%"PRId64
#define F_S64P PRId64
#define F_S64I "%*"PRId64
#define F_U64 "%"PRIu64
#define F_U64P PRIu64
#define F_U64I "%*"PRIu64
#define F_X64 "%016"PRIx64
#define F_X64P PRIx64
#define F_X64I "%*"PRIx64
// Floating points
#define F_F32 "%f"
#define F_F32P "f"
#define F_F32I "%*f"
#define F_F64 "%lf"
#define F_F64P "lf"
#define F_F64I "%*lf"
// Standard typedefs
#define F_SIZE_T "%zu"
#define F_SIZE_TP "zu"
#define F_SIZE_TI "%*zu"
#define F_OFF_T F_S64
#define F_OFF_TP F_S64P
#define F_OFF_TI F_S64I
typedef uintptr_t INTPTR;
// These are used to pad various structs to specific sizes
#if ULONG_MAX == 0xffffffff
#define TRUE32BIT
#else
#define TRUE64BIT
#endif
#if defined(_FILE_OFFSET_BITS) && (_FILE_OFFSET_BITS == 32)
#error I do not support 32-bit off_t.
#endif
// Enable troublesome asserts. These typically have work arounds, and occasionally trigger.
// They're really only useful if the assembly can be debugged.
#undef AGGRESSIVE_ASSERT
// perl's chomp is pretty nice
// Not a great place to put this, but it's getting used all over.
#ifndef chomp
#define chomp(S) { char *t=(S); while (*t) t++; t--; while (t >= S && isspace(*t)) *t--=0; }
#endif
#ifndef munch
#define munch(S) { while (*(S) && isspace(*(S))) (S)++; }
#endif
#ifndef crunch
#define crunch(S) { while (*(S) && !isspace(*(S))) (S)++; }
#endif
int AS_configure(int argc, char **argv);
// These macros are use to eliminate inter-platform differnces between
// calculated results
#define DBL_TO_INT(X) ((int)((1.0+16.0*DBL_EPSILON)*(X)))
#define ROUNDPOS(X) (DBL_TO_INT((X)+0.5) )
#define ROUND(X) (((X)>0.0) ? ROUNDPOS(X) : -ROUNDPOS(-(X)) )
#define ZERO_PLUS ( 16.0*DBL_EPSILON)
#define ZERO_MINUS (-16.0*DBL_EPSILON)
#define ONE_PLUS (1.0+ZERO_PLUS)
#define ONE_MINUS (1.0+ZERO_MINUS)
#define INT_EQ_DBL(I,D) (fabs((double)(I)-(D)) < 16.0*DBL_EPSILON )
#define DBL_EQ_DBL(A,B) (fabs((A)-(B))<16.0*DBL_EPSILON)
// Tell gcc (and others, maybe) about unused parameters. This is important for gcc (especially
// newer ones) that complain about unused parameters. Thanks to ideasman42 at
// http://stackoverflow.com/questions/3599160/unused-parameter-warnings-in-c-code.
#ifdef __GNUC__
#define UNUSED(x) UNUSED_ ## x __attribute__((__unused__))
#else
#define UNUSED(x) UNUSED_ ## x
#endif
#include "AS_UTL_alloc.H"
// Stubs for ignoring OpenMP on clang.
#ifdef BROKEN_CLANG_OpenMP
static
int
omp_get_max_threads(void) {
return(1);
}
static
void
omp_set_num_threads(int x) {
}
static
int
omp_get_num_threads(void) {
return(1);
}
static
int
omp_get_thread_num(void) {
return(0);
}
typedef int omp_lock_t;
static
void
omp_init_lock(omp_lock_t *a) {
}
static
void
omp_set_lock(omp_lock_t *a) {
}
static
void
omp_unset_lock(omp_lock_t *a) {
}
static
void
omp_destroy_lock(omp_lock_t *a) {
}
#endif
#endif