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MICA-PE.h
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//
// MICA.h
//
// mica
//
// Copyright (C) 2013, HKU
//
// 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; either version 2
// of the License, or (at your option) any later version.
//
// 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 should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
///////////////////////////////////////////////////////////////////////////////////////////////
#ifndef __MICA_PE_H__
#define __MICA_PE_H__
///////////////////////////////////////
// Including Standard Libraries
///////////////////////////////////////
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <unistd.h>
#include <time.h>
#include <omp.h>
///////////////////////////////////////
// Including 2BWT Libraries
///////////////////////////////////////
#include "2bwt-flex/2bwt-lib/iniparser.h"
#include "2bwt-flex/2bwt-lib/2BWT-Interface.h"
#include "2bwt-flex/2bwt-lib/Timing.h"
///////////////////////////////////////
// Including SOAP2-DP Libraries
///////////////////////////////////////
#include "2bwt-flex/2BWT-PEAlgnmt.h"
#include "2bwt-flex/2BWT-SRAAlgnmt.h"
#include "2bwt-flex/SRAQueryParser.h"
#include "2bwt-flex/utilities/Logging.h"
///////////////////////////////////////
// Including MIC Libraries
///////////////////////////////////////
#include "MIC-SRA2BWTMdl.h"
#include "MIC-SRAAlgnmt.h"
#include "MIC-PEAlgnmt.h"
#include "MIC-DPAlgnmt.h"
#include "MICA-PE-ReadThread.h"
#include "MICA-PE-WriteThread.h"
#include "MICControllerThread.h"
#include "CPUControllerThread.h"
#include "MICA-Health.h"
#include "MemMan.h"
///////////////////////////////////////
// Constants
///////////////////////////////////////
#define SRA_READ_SKIP_INVALID 0
#define SRA_READ_REPLACE_INVALID 1
///////////////////////////////////////
// DEBUG FLAGS
///////////////////////////////////////
// Define to disable the output handler
// The output will be discarded after MIC round
//#define MICA_PE_DISCARD_OUTPUT_FROM_MIC
#endif