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MICA-PE.c
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MICA-PE.c
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//
// MICA.c
//
// 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.
//
// Modification History
//
// Date : 4th June 2013
// Changes : Correctly distribute the bucket. Currently the numReadPerCore for each core is
// hardcoded causing inefficient load balancing while the number of reads is not
// a multiple of the numReadPerCore.
//
// Date : 6th June 2013
// Changes : Add Occurrence Collector to gather output but discard them to avoid IO
//
// To-do : 1. Construct the BWT structure outside the pragma offload.
// 2. Don't need inout saCount everytime
//
///////////////////////////////////////////////////////////////////////////////////////////////
#include "MICA-PE.h"
#include "Release.h"
#define MIC_MAIN_NON_INPUT_VALUE 99999999
// Input Arguments for MICA
#define MICA_INPUT_FILE_ARG_FILE 0
#define MICA_INPUT_FILE_ARG_LIST 1
// -----------------------------
// Compile-time Configurable #1
// -----------------------------
// Maximum number of reads to be processed by
// each MIC controller batch run.
#define MIC_MAX_BATCH_SIZE 1000000
// -----------------------------
// Compile-time Configurable #2
// -----------------------------
// Number of MIC card equipped in the machine.
// User may set the numOfMICThread to 0 in mica-pe.ini to disable
// a particular MIC card.
#define NUM_MIC_EQUIPPED 3
// -----------------------------
// Compile-time Configurable #3
// -----------------------------
// Enable the core health checker to poll
// multiple component and get health status on stdout.
//#define MICA_PE_ENABLE_HEALTH_CHECK
//-----------------------------------
// DEBUG FLAGS
//-----------------------------------
// Define to print output statistics
//#define MIC_DEBUG_PRINT_OUTPUT_COUNTS
// Declaration of Global Variables
// Global Variables should NEVER be referenced outside of
// this file though they can be.
// Number of CPU thread allocated to aid MIC alignment
// It's common for nowadays computer to equip with a multi-
// core CPU. MICA supports to definition of extra aligner
// utilising CPU processing power to perform alignment
// alongside the MIC processing unit.
int InputNumOfCPUThreads = 1;
int InputFileArgument = MICA_INPUT_FILE_ARG_FILE;
char ReadFileName[MAX_FILENAME_LEN+1] = "";
char MateFileName[MAX_FILENAME_LEN+1] = "";
char ListFileName[MAX_FILENAME_LEN+1] = "";
char OutputFileName[MAX_FILENAME_LEN+1] = "*.out";
char DatabaseName[MAX_FILENAME_LEN+1] = "";
char InputSaValueFileName[MAX_FILENAME_LEN+1] = ".sa8";
char InputCPUSaValueFileName[MAX_FILENAME_LEN+1] = ".sa";
int InputCPULoadSAValue = 1;
int InputSRAInvalidReadHandling = SRA_READ_SKIP_INVALID;
int InputQueryStrand = QUERY_BOTH_STRAND;
int InputAlignmentModel = SRA_MODEL_8G;
int InputMaxNumOfAlignment = -1;
int InputReportType = PE_REPORT_ALL_BEST;
int InputErrorType = SRA_TYPE_MISMATCH_ONLY;
int InputMaxError = 2;
int InputMaxNBMismatch = 0;
int InputOutputFileName = MIC_MAIN_NON_INPUT_VALUE;
int InputOutputFormat = SRA_OUTPUT_FORMAT_SAM;
int InputOutputNumSamThreads = 1;
int InputPEInsertionUpperBound = MIC_MAIN_NON_INPUT_VALUE;
int InputPEInsertionLowerBound = MIC_MAIN_NON_INPUT_VALUE;
int InputPEStrandLeftLeg = QUERY_POS_STRAND;
int InputPEStrandRightLeg = QUERY_NEG_STRAND;
int InputSGAOrphanEnhancement = 0;
double InputSGAOrphanTriggerTF = 0.30f;
double InputSGAScoreTF = 0.30f;
int InputSGAOrphanExtendEnhancement = 0;
double InputSGAOrphanExtendTriggerTF = 0.30f;
int InputSGAScoreMatch = 1;
int InputSGAScoreMismatch = -2;
int InputSGAScoreGapOpen = -3;
int InputSGAScoreGapExtend = -1;
double InputSGASoftHeadClipLength = 0.0;
double InputSGASoftTailClipLength = 0.40;
double InputSGASoftTotalClipLength = 0.40;
int InputSGASeedEnhancement = 0;
double InputSGASeedLength = 0.30f;
double InputSGASeedLengthOverlap = 0.15f;
int InputSGASeedLooseCriteria = -1;
int InputSGASeedOccLimitation = 4096;
int InputSGASeedEnhancement_1 = 0;
double InputSGASeedLength_1 = 0.30f;
double InputSGASeedLengthOverlap_1 = 0.15f;
int InputSGASeedLooseCriteria_1 = -1;
int InputSGASeedOccLimitation_1 = 4096;
unsigned int InputMemoryCPUMaxUsageMBytes = -1;
unsigned int InputMemoryMICMaxUsageMBytes = 3600;
unsigned int InputMICThreads[NUM_MIC_EQUIPPED];
void PrintHelp();
dictionary *ParseInput(int argc, char** argv);
void ParseIniFile(char *iniFileName);
void SRAFillCharMap(unsigned char * charMap);
void PrintAlignmentSettings(Logging * logger, SRAArguments * sArgs, PEArguments * peArgs);
void SRAGetFileSuffix(int threadId, char * suffixStr);
void ParameterVerification();
int main(int argc, char** argv) {
// Start Audit Logging
Logging * logger = LOGCreate("mica-pe.log",LOGGING_MODE_RUNNING);
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"\n%s v%d.%d.%d (%s)\n",PROJECT_NAME,PROJECT_MAJOR,PROJECT_MINOR,PROJECT_REV,PROJECT_SPECIAL);
////////////////////////////////////////////////////////////
// Declaration of Variables
////////////////////////////////////////////////////////////
// Program input
dictionary *programInput;
double startTime, lastEventTime, timestamp;
startTime = setStartTime();
lastEventTime = 0;
unsigned long long i,j,k;
unsigned int u,v,w;
unsigned char charMap[256];
unsigned char complementMap[256];
//Initial Environmental Parameters for Intel MIC
MICSetParameters();
////////////////////////////////////////////////////////////
// Ini Configuration
////////////////////////////////////////////////////////////
char iniFilename[MAX_FILENAME_LEN];
sprintf(iniFilename, "%s.ini", argv[0]);
ParseIniFile(iniFilename);
// Command Argument - Override
programInput = ParseInput(argc, argv);
// Parameter Control
ParameterVerification();
////////////////////////////////////////////////////////////
// Initialise the threads information
////////////////////////////////////////////////////////////
int gThreadId = 0;
int micThreadId = 0;
int cpuThreadId = 0;
int maxNumOfThreads = 0;
int numMICActivated = 0;
for (micThreadId = 0; micThreadId < NUM_MIC_EQUIPPED; micThreadId++) {
numMICActivated += InputMICThreads[micThreadId] != 0;
if ( InputMICThreads[micThreadId] > maxNumOfThreads ) {
maxNumOfThreads = InputMICThreads[micThreadId];
}
}
////////////////////////////////////////////////////////////
// Index Handling
////////////////////////////////////////////////////////////
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"Loading index %s ... ", DatabaseName); fflush(stdout);
Idx2BWT * micIdx2BWT = BWTLoad2BWT(DatabaseName,InputSaValueFileName);
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"DONE\n\n");
// Jeanno: The CPUIdx2BWT Index creation here is a bit clumsy.
// Maybe we can work on a module for this later.
Idx2BWT * cpuIdx2BWT = NULL;
if (InputCPULoadSAValue) {
// Only load CPU index if the SA being used is different to the
// one being used by MIC.
cpuIdx2BWT = (Idx2BWT *) MEMManMalloc(sizeof(Idx2BWT), MEMORY_TYPE_CPU);
(*cpuIdx2BWT) = (*micIdx2BWT);
cpuIdx2BWT->bwt = (BWT *) MEMManMalloc(sizeof(BWT), MEMORY_TYPE_CPU);
(*cpuIdx2BWT->bwt) = (*micIdx2BWT->bwt);
// Full Suffix Array for CPU
char saFilename[MAX_INDEX_FILENAME_LENGTH];
strcpy(saFilename, DatabaseName);
strcat(saFilename, InputCPUSaValueFileName);
printf("Loading Full Suffix-Array for CPU %s ... ",saFilename); fflush(stdout);
BWTSALoad(cpuIdx2BWT->mmPool, cpuIdx2BWT->bwt, saFilename,NULL);
printf("DONE\n\n");
} else {
cpuIdx2BWT = micIdx2BWT;
}
// Lookup Table for CPU
char LookupTableFileName[MAX_FILENAME_LEN+1];
char RevLookupTableFileName[MAX_FILENAME_LEN+1];
strcpy(LookupTableFileName,DatabaseName);
strcpy(RevLookupTableFileName,DatabaseName);
strcat(LookupTableFileName,".lkt");
strcat(RevLookupTableFileName,".rev.lkt");
LT * lookup = LTLoad(LookupTableFileName);
LT * revLookup = LTLoad(RevLookupTableFileName);
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"(Elapsed time (Index Loading) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
HSPFillCharMap(charMap);
if (InputSRAInvalidReadHandling == SRA_READ_REPLACE_INVALID) SRAFillCharMap(charMap);
HSPFillComplementMap(complementMap);
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
// Construct the health checker procedure
MICAHealthParm * micaHealth = MICAHealthParmCreate();
#endif
printf("Initialising Read Thread ... "); fflush(stdout);
////////////////////////////////////////////////////////////
// Read Thread
////////////////////////////////////////////////////////////
ListConsumer * listConsumer = LCCreate();
if ( InputFileArgument == MICA_INPUT_FILE_ARG_FILE ) {
LCCreateList(listConsumer,
ReadFileName, MateFileName,
&InputPEInsertionLowerBound, &InputPEInsertionUpperBound,
1, MAX_FILENAME_LEN,MAX_FIELD_LEN);
} else if ( InputFileArgument == MICA_INPUT_FILE_ARG_LIST ) {
LCLoadList(listConsumer,ListFileName,MAX_FILENAME_LEN,MAX_FIELD_LEN);
} else {
printf("[SAFE-GUARD] List consumer not initialised due to unexpected input type.\n");
}
PEReadThread * readThread = PEReadThread_create(charMap,
MIC_MAX_BATCH_SIZE, MAX_SEQ_NAME_LENGTH,
SRA_MAX_READ_LENGTH,
cpuIdx2BWT->hsp, listConsumer, InputOutputFormat, InputOutputNumSamThreads);
PEReadThread_start(readThread);
printf("DONE\n");
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
MICAAddMonitor_ReadThread(micaHealth,readThread);
#endif
MICControllerThread * micThreads[NUM_MIC_EQUIPPED];
CPUControllerThread ** cpuThreads = (CPUControllerThread**) malloc(sizeof(CPUControllerThread*)*InputNumOfCPUThreads);
////////////////////////////////////////////////////////////
// Set up shared arguments and parameters for SRA and PE - CPU
////////////////////////////////////////////////////////////
SRAArguments * cpuSraArgTemplate = SRAARGConstruct();
PEArguments * cpuPeArgTemplate = PEARGConstruct(cpuIdx2BWT->bwt,cpuIdx2BWT->hsp);
// Setting up SRA Indexes
SRAIndexPopulate(cpuSraArgTemplate->AlgnmtIndex, cpuIdx2BWT->bwt, cpuIdx2BWT->rev_bwt,
cpuIdx2BWT->hsp, NULL, lookup, revLookup);
// Setting up SRA Settings
// The Pair-end aligner requires SRA to behave differently in different cases.
// For example, when we are performing all-valid PE we don't need SRA to be staged
// by different number of mismatch; Thus in that case we merely need to perform a
// SRA_REPORT_ALL. In cases like all-best alignment, it's a requirement to have it
// set toe SRA_REPORT_ALL_SORTED to allow the pair-end alignment to early terminate.
if ( InputReportType == PE_REPORT_ALL_BEST ) {
cpuSraArgTemplate->AlgnmtSetting->OutputType = SRA_REPORT_ALL_SORTED;
} else {
cpuSraArgTemplate->AlgnmtSetting->OutputType = SRA_REPORT_ALL;
}
cpuSraArgTemplate->AlgnmtSetting->ErrorType = InputErrorType;
cpuSraArgTemplate->AlgnmtSetting->MaxError = InputMaxError;
cpuSraArgTemplate->AlgnmtSetting->MaxNBMismatch = InputMaxNBMismatch;
// Setting up SRA Output Settings
cpuSraArgTemplate->AlgnmtSetting->OutputFormat = InputOutputFormat;
// Setting up PE Settings
cpuPeArgTemplate->PEAlgnmtInput->OutputType = InputReportType;
cpuPeArgTemplate->PEAlgnmtInput->maxResult = InputMaxNumOfAlignment;
cpuPeArgTemplate->PEAlgnmtInput->insertLbound = InputPEInsertionLowerBound;
cpuPeArgTemplate->PEAlgnmtInput->insertUbound = InputPEInsertionUpperBound;
cpuPeArgTemplate->PEAlgnmtInput->strandLeftLeg = InputPEStrandLeftLeg;
cpuPeArgTemplate->PEAlgnmtInput->strandRightLeg = InputPEStrandRightLeg;
// Setting up PE-DP Settings
cpuPeArgTemplate->pedpSetting->SGAScoreTF = InputSGAScoreTF;
cpuPeArgTemplate->pedpSetting->SGASoftHeadClipLength = InputSGASoftHeadClipLength;
cpuPeArgTemplate->pedpSetting->SGASoftTailClipLength = InputSGASoftTailClipLength;
cpuPeArgTemplate->pedpSetting->SGASoftTotalClipLength = InputSGASoftTotalClipLength;
cpuPeArgTemplate->pedpSetting->SGAOrphanEnhancement = InputSGAOrphanEnhancement;
cpuPeArgTemplate->pedpSetting->SGAOrphanTriggerTF = InputSGAOrphanTriggerTF;
cpuPeArgTemplate->pedpSetting->SGAOrphanExtendEnhancement = InputSGAOrphanExtendEnhancement;
cpuPeArgTemplate->pedpSetting->SGAOrphanExtendTriggerTF = InputSGAOrphanExtendTriggerTF;
cpuPeArgTemplate->dpArguments->dpScores->dpMatch = InputSGAScoreMatch;
cpuPeArgTemplate->dpArguments->dpScores->dpMismatch = InputSGAScoreMismatch;
cpuPeArgTemplate->dpArguments->dpScores->dpGapOpen = InputSGAScoreGapOpen;
cpuPeArgTemplate->dpArguments->dpScores->dpGapExtend = InputSGAScoreGapExtend;
cpuPeArgTemplate->pedpSetting->SGASeedEnhancement = InputSGASeedEnhancement;
cpuPeArgTemplate->pedpSetting->SGASeedLength = InputSGASeedLength;
cpuPeArgTemplate->pedpSetting->SGASeedLengthOverlap = InputSGASeedLengthOverlap;
cpuPeArgTemplate->pedpSetting->SGASeedLooseCriteria = InputSGASeedLooseCriteria;
cpuPeArgTemplate->pedpSetting->SGASeedOccLimitation = InputSGASeedOccLimitation;
cpuPeArgTemplate->pedpSetting->SGASeedEnhancement_1 = InputSGASeedEnhancement_1;
cpuPeArgTemplate->pedpSetting->SGASeedLength_1 = InputSGASeedLength_1;
cpuPeArgTemplate->pedpSetting->SGASeedLengthOverlap_1 = InputSGASeedLengthOverlap_1;
cpuPeArgTemplate->pedpSetting->SGASeedLooseCriteria_1 = InputSGASeedLooseCriteria_1;
cpuPeArgTemplate->pedpSetting->SGASeedOccLimitation_1 = InputSGASeedOccLimitation_1;
//Printing Settings
if ( InputFileArgument == MICA_INPUT_FILE_ARG_FILE ) {
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"Input = %s / %s\n",ReadFileName,MateFileName);
} else if ( InputFileArgument == MICA_INPUT_FILE_ARG_LIST ) {
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"Input = %s\n",ListFileName);
} else if ( InputFileArgument == MICA_INPUT_FILE_ARG_LIST ) {
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"Input = Unknown\n");
}
PrintAlignmentSettings(logger,cpuSraArgTemplate,cpuPeArgTemplate);
////////////////////////////////////////////////////////////
// Write Thread
////////////////////////////////////////////////////////////
printf("Initialising Write Thread ... "); fflush(stdout);
unsigned int maxNumReadPerCore = (MIC_MAX_BATCH_SIZE + maxNumOfThreads - 1) / maxNumOfThreads;
PEWriteThread * gWriteThread = PEWTCreate(maxNumReadPerCore, maxNumOfThreads,
MIC_CONTROL_WRITE_THREAD_BUFFER_COUNT,
InputNumOfCPUThreads + NUM_MIC_EQUIPPED,
0);
PEWTRegisterArguments(gWriteThread, cpuSraArgTemplate, cpuPeArgTemplate,
InputAlignmentModel,
charMap);
PEWTRoll(gWriteThread);
printf("DONE\n");
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
MICAAddMonitor_WriteThread(micaHealth,gWriteThread);
#endif
////////////////////////////////////////////////////////////
// Create multiple MIC Threads
////////////////////////////////////////////////////////////
printf("Initialising MIC Controller (%u) ... ", numMICActivated); fflush(stdout);
for (micThreadId = 0; micThreadId < NUM_MIC_EQUIPPED; micThreadId++) {
if (InputMICThreads[micThreadId] == 0) {
continue;
}
micThreads[micThreadId] = MICCTCreate(gThreadId, micIdx2BWT, charMap,
MIC_MAX_BATCH_SIZE, micThreadId, InputMICThreads[micThreadId]);
MICControllerThread * micThread = micThreads[micThreadId];
MICCTSetSRA(micThread, InputAlignmentModel, cpuSraArgTemplate);
MICCTSetPE(micThread, cpuPeArgTemplate);
MICCTSetReadThread(micThread, readThread);
MICCTSetWriteThread(micThread, gWriteThread);
MICCTStart(micThread);
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
MICAAddMonitor_MICControl(micaHealth,micThread);
#endif
gThreadId++;
}
printf("DONE\n");
////////////////////////////////////////////////////////////
// Create multiple CPU Threads
////////////////////////////////////////////////////////////
printf("Initialising CPU Controller (%u) ... ",InputNumOfCPUThreads); fflush(stdout);
for (cpuThreadId = 0; cpuThreadId < InputNumOfCPUThreads; cpuThreadId++) {
cpuThreads[cpuThreadId] = CPUCTCreate(gThreadId, charMap, MIC_MAX_BATCH_SIZE);
CPUControllerThread * cpuThread = cpuThreads[cpuThreadId];
CPUCTSetSRA(cpuThread, InputAlignmentModel, cpuSraArgTemplate);
CPUCTSetPE(cpuThread, cpuPeArgTemplate);
CPUCTSetReadThread(cpuThread, readThread);
CPUCTSetWriteThread(cpuThread, gWriteThread);
CPUCTStart(cpuThread);
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
MICAAddMonitor_CPUControl(micaHealth,cpuThread);
#endif
gThreadId++;
}
printf("DONE\n");
printf("\n");
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
MICAHealthParmRoll(micaHealth);
#endif
// Join and Free micThreads
for (micThreadId = 0; micThreadId < NUM_MIC_EQUIPPED; micThreadId++) {
if (InputMICThreads[micThreadId] == 0) {
continue;
}
MICCTJoin(micThreads[micThreadId]);
}
// Join and Free cpuThreads
for (cpuThreadId = 0; cpuThreadId < InputNumOfCPUThreads; cpuThreadId++) {
CPUCTJoin(cpuThreads[cpuThreadId]);
}
// Join and Free micThreads
for (micThreadId = 0; micThreadId < NUM_MIC_EQUIPPED; micThreadId++) {
if (InputMICThreads[micThreadId] == 0) {
continue;
}
MICCTPrintStats(micThreads[micThreadId],logger);
MICCTFree(micThreads[micThreadId]);
}
// Join and Free cpuThreads
for (cpuThreadId = 0; cpuThreadId < InputNumOfCPUThreads; cpuThreadId++) {
CPUCTPrintStats(cpuThreads[cpuThreadId],logger);
CPUCTFree(cpuThreads[cpuThreadId]);
}
free(cpuThreads);
#ifdef MICA_PE_ENABLE_HEALTH_CHECK
// Free the health checker
MICAHealthParmJoin(micaHealth);
MICAHealthParmFree(micaHealth);
#endif
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"[INFO] Total Shared Working Memory allocated = %9.2f Mbytes\n",MEMManGetUsage(MEMORY_TYPE_SHARED)/1024.0/1024.0);
if (InputMemoryMICMaxUsageMBytes!=-1 && MEMManGetUsage(MEMORY_TYPE_SHARED)>(unsigned long long) InputMemoryMICMaxUsageMBytes*1024*1024) {
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"[ERROR] Exceeded defined MIC limitation of %u MBytes\n",InputMemoryMICMaxUsageMBytes);
}
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"[INFO] Total CPU Working Memory allocated = %9.2f Mbytes\n",MEMManGetUsage(MEMORY_TYPE_CPU)/1024.0/1024.0);
if (InputMemoryCPUMaxUsageMBytes!=-1 && MEMManGetUsage(MEMORY_TYPE_CPU)>(unsigned long long) InputMemoryCPUMaxUsageMBytes*1024*1024) {
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"[ERROR] Exceeded defined CPU limitation of %u MBytes\n",InputMemoryMICMaxUsageMBytes);
}
printf("\n");
PEWTSignal(gWriteThread, MICA_PE_WRITE_THREAD_HEALTH_DEPLETED);
PEWTThreadJoin(gWriteThread);
PEWTPrintStats(gWriteThread,logger);
PEReadThread_quit(readThread);
PEReadThread_join(readThread);
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
LOGWriteLine(logger, LOGGING_MSG_TYPE_ALL,
"Elapsed time (Total MIC and CPU Processing) : %9.4f seconds\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
////////////////////////////////////////////////////////////
// Free Memory Allocated
////////////////////////////////////////////////////////////
printf("Free index ... ");
fflush(stdout);
PEARGFree(cpuPeArgTemplate);
SRAARGFree(cpuSraArgTemplate);
LTFree(lookup);
LTFree(revLookup);
if (InputCPULoadSAValue) {
// Free up CPU memory only if it's branched off from MIC Index.
BWTSAFree(cpuIdx2BWT->mmPool, cpuIdx2BWT->bwt);
free(cpuIdx2BWT->bwt);
free(cpuIdx2BWT);
}
BWTFree2BWT(micIdx2BWT);
printf("DONE\n");
printf("Free Read/Write Thead ... ");
fflush(stdout);
PEReadThread_free(readThread);
PEWTFree(gWriteThread);
LCFree(listConsumer);
printf("DONE\n");
LOGFree(logger);
iniparser_freedict(programInput);
return 0;
}
void PrintAlignmentSettings(Logging * logger, SRAArguments * sArgs, PEArguments * peArgs) {
SRASetting * sraSettings = sArgs->AlgnmtSetting;
SRAIndex * sraIndex = sArgs->AlgnmtIndex;
switch (peArgs->PEAlgnmtInput->OutputType) {
case PE_REPORT_ALL_BEST:
if (peArgs->PEAlgnmtInput->maxResult==-1) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Report = All Best Alignment (All).\n");
} else {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Report = All Best Alignment (#<=%d).\n",peArgs->PEAlgnmtInput->maxResult);
}
break;
case PE_REPORT_ALL:
if (peArgs->PEAlgnmtInput->maxResult==-1) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Report = All Alignment (All).\n");
} else {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Report = All Alignment (#<=%d).\n",peArgs->PEAlgnmtInput->maxResult);
}
break;
}
if (sraSettings->ErrorType==SRA_TYPE_MISMATCH_ONLY) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Max #Mismatch = %d\n",sraSettings->MaxError);
} else if (sraSettings->ErrorType==SRA_TYPE_EDIT_DISTANCE) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Max #Edit = %d\n",sraSettings->MaxError);
}
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Max #NBMism = %d\n",sraSettings->MaxNBMismatch);
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Ref.Seq Length = %u\n",sraIndex->bwt->textLength);
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Strand = ");
switch (sraSettings->ReadStrand) {
case QUERY_POS_STRAND:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Positive\n");
break;
case QUERY_NEG_STRAND:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Negative\n");
break;
case QUERY_BOTH_STRAND:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Both\n");
break;
}
char tmp[4] = "?+-";
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Pair strand = %c/%c\n",tmp[InputPEStrandLeftLeg],tmp[InputPEStrandRightLeg]);
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"CPU Threads = %d\n",InputNumOfCPUThreads);
if (InputSGAOrphanEnhancement || InputSGAOrphanExtendEnhancement || InputSGASeedEnhancement) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA Soft-clip = %.2f / %.2f / %.2f \n", InputSGASoftHeadClipLength, InputSGASoftTailClipLength, InputSGASoftTotalClipLength);
}
if (InputSGAOrphanEnhancement) LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA Orphan Rvy = %.2f / %.2f \n", InputSGAOrphanTriggerTF, InputSGAScoreTF);
if (InputSGAOrphanExtendEnhancement) LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA OrpExt Rvy = %.2f / %.2f \n", InputSGAOrphanExtendTriggerTF, InputSGAScoreTF);
//if (InputSGAOrphanEnhancement) LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA Orphan Rvy = %.2f / %.2f\n",InputSGAOrphanTriggerTF, InputSGAScoreTF);
/*
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Pre-Align Trim = ");
if (TrimPrealignRead>0) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Enabled (trimming=%u%c)\n",TrimPrealignRead ,'%');
} else {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Disabled\n");
}
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"2-Pass = ");
if (SRASecondPassEnabled) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Enabled (trimming=%u%c loosen=%d forceIndel=%d)\n",TrimUnalignRead,'%',LooseCriteriaUnalignRead,ForceIndelUnalignedRead);
} else {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Disabled\n");
}
*/
if (InputSGASeedEnhancement) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA Seed Rvy = %.2f / %.2f\n",InputSGASeedLength, InputSGASeedLengthOverlap);
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL," = loosen=%d\n",InputSGASeedLooseCriteria);
if (InputSGASeedOccLimitation!=-1)
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL," = limit'd=%d\n",InputSGASeedOccLimitation);
}
if (InputSGASeedEnhancement_1) {
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"SGA Seed Rvy-2 = %.2f / %.2f\n",InputSGASeedLength_1, InputSGASeedLengthOverlap_1);
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL," = loosen=%d\n",InputSGASeedLooseCriteria_1);
if (InputSGASeedOccLimitation_1!=-1)
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL," = limit'd=%d\n",InputSGASeedOccLimitation_1);
}
switch (sraSettings->OutputFormat) {
case SRA_OUTPUT_FORMAT_PLAIN:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Output Format = Succinct (Plain).\n");
break;
case SRA_OUTPUT_FORMAT_SAM:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Output Format = SAM v1.4 (Plain).\n");
break;
case SRA_OUTPUT_FORMAT_BAM:
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"Output Format = BAM v1.4 (Binary).\n");
break;
}
LOGWriteLine(logger,LOGGING_MSG_TYPE_ALL,"\n");
}
void ParseIniFile(char *iniFileName) {
dictionary *ini;
char tmp[10];
printf("Loading %s ..", iniFileName);
ini = iniparser_load(iniFileName, FALSE);
if (ini == NULL) {
printf("not found.\n");
return;
}
printf("done.\n");
// Memory parameters
InputMemoryMICMaxUsageMBytes = iniparser_getuint(ini, "Memory:MemoryMICMaxUsageMBytes", InputMemoryMICMaxUsageMBytes);
InputMemoryCPUMaxUsageMBytes = iniparser_getuint(ini, "Memory:MemoryCPUMaxUsageMBytes", InputMemoryCPUMaxUsageMBytes);
// Database parameters
iniparser_copystring(ini, "Database:SaValueFileName", InputSaValueFileName, InputSaValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:CPUSaValueFileName", InputCPUSaValueFileName, InputCPUSaValueFileName, MAX_FILENAME_LEN);
if (strcmp(InputSaValueFileName,InputCPUSaValueFileName)==0) {
InputCPULoadSAValue = 0;
} else {
InputCPULoadSAValue = 1;
}
//Query Parameters
InputNumOfCPUThreads = iniparser_getuint(ini, "MultipleThreading:NumOfCPUThreads", InputNumOfCPUThreads );
//Output Format Parameters
InputOutputNumSamThreads = iniparser_getuint(ini, "BAMSpecific:NumOfCompressionThreads", InputOutputNumSamThreads );
// Short Read Alignement Parameters
iniparser_copystring(ini, "AlignmentModel:AlignmentModel", tmp, tmp, 4);
if (strcmp(tmp,"16G")==0) {
InputAlignmentModel = SRA_MODEL_16G;
} else {
InputAlignmentModel = SRA_MODEL_8G;
}
// Read input handling
iniparser_copystring(ini, "AlignmentModel:InvalidReadHandling", tmp, tmp, 8);
if (strcmp(tmp,"REPLACE")==0) {
InputSRAInvalidReadHandling = SRA_READ_REPLACE_INVALID;
} else {
InputSRAInvalidReadHandling = SRA_READ_SKIP_INVALID;
}
InputMaxNumOfAlignment = iniparser_getdouble(ini, "PairEnd:MaxNumOfAlignment", InputMaxNumOfAlignment );
iniparser_copystring(ini, "PairEnd:StrandArrangement", tmp, tmp, 10);
if (strcmp(tmp,"+/+")==0) {
InputPEStrandLeftLeg = QUERY_POS_STRAND;
InputPEStrandRightLeg = QUERY_POS_STRAND;
} else if (strcmp(tmp,"-/+")==0) {
InputPEStrandLeftLeg = QUERY_NEG_STRAND;
InputPEStrandRightLeg = QUERY_POS_STRAND;
} else if (strcmp(tmp,"-/-")==0) {
InputPEStrandLeftLeg = QUERY_NEG_STRAND;
InputPEStrandRightLeg = QUERY_NEG_STRAND;
} else {
InputPEStrandLeftLeg = QUERY_POS_STRAND;
InputPEStrandRightLeg = QUERY_NEG_STRAND;
}
// DP Common
InputSGAScoreTF = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGAScoreTF", InputSGAScoreTF );
InputSGAScoreMatch = iniparser_getint(ini, "PairEndSGAEnhancement:SGAScoreMatch", InputSGAScoreMatch );
InputSGAScoreMismatch = iniparser_getint(ini, "PairEndSGAEnhancement:SGAScoreMismatch", InputSGAScoreMismatch );
InputSGAScoreGapOpen = iniparser_getint(ini, "PairEndSGAEnhancement:SGAScoreGapOpen", InputSGAScoreGapOpen );
InputSGAScoreGapExtend = iniparser_getint(ini, "PairEndSGAEnhancement:SGAScoreGapExtend", InputSGAScoreGapExtend );
InputSGASoftHeadClipLength = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASoftHeadClipLength", InputSGASoftHeadClipLength );
InputSGASoftTailClipLength = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASoftTailClipLength", InputSGASoftTailClipLength );
InputSGASoftTotalClipLength = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASoftTotalClipLength", InputSGASoftTotalClipLength );
// Orhpan Recovery
iniparser_copystring(ini, "PairEndSGAEnhancement:SGAOrphanEnhancement", tmp, tmp, 6);
if (strcmp(tmp,"TRUE")==0) {
InputSGAOrphanEnhancement = 1;
} else {
InputSGAOrphanEnhancement = 0;
}
InputSGAOrphanTriggerTF = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGAOrphanTriggerTF", InputSGAOrphanTriggerTF );
iniparser_copystring(ini, "PairEndSGAEnhancement:SGAOrphanExtendEnhancement", tmp, tmp, 6);
if (strcmp(tmp,"TRUE")==0) {
InputSGAOrphanExtendEnhancement = 1;
} else {
InputSGAOrphanExtendEnhancement = 0;
}
InputSGAOrphanExtendTriggerTF = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGAOrphanExtendTriggerTF", InputSGAOrphanExtendTriggerTF );
// Seed Enhancement
iniparser_copystring(ini, "PairEndSGAEnhancement:SGASeedEnhancement", tmp, tmp, 6);
if (strcmp(tmp,"TRUE")==0) {
InputSGASeedEnhancement = 1;
} else {
InputSGASeedEnhancement = 0;
}
InputSGASeedLength = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASeedLength", InputSGASeedLength );
InputSGASeedLengthOverlap = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASeedLengthOverlap", InputSGASeedLengthOverlap );
InputSGASeedLooseCriteria = iniparser_getint(ini, "PairEndSGAEnhancement:SGASeedLooseCriteria", InputSGASeedLooseCriteria );
InputSGASeedOccLimitation = iniparser_getint(ini, "PairEndSGAEnhancement:SGASeedOccLimitation", InputSGASeedOccLimitation );
// Seed Enhancement (2nd-level)
iniparser_copystring(ini, "PairEndSGAEnhancement:SGASeedEnhancement_1", tmp, tmp, 6);
if (strcmp(tmp,"TRUE")==0) {
InputSGASeedEnhancement_1 = 1;
} else {
InputSGASeedEnhancement_1 = 0;
}
InputSGASeedLength_1 = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASeedLength_1", InputSGASeedLength_1 );
InputSGASeedLengthOverlap_1 = iniparser_getdouble(ini, "PairEndSGAEnhancement:SGASeedLengthOverlap_1", InputSGASeedLengthOverlap_1 );
InputSGASeedLooseCriteria_1 = iniparser_getint(ini, "PairEndSGAEnhancement:SGASeedLooseCriteria_1", InputSGASeedLooseCriteria_1 );
InputSGASeedOccLimitation_1 = iniparser_getint(ini, "PairEndSGAEnhancement:SGASeedOccLimitation_1", InputSGASeedOccLimitation_1 );
// MIC threads parameters
InputMICThreads[0] = iniparser_getuint(ini, "MultipleThreading:NumOfMICThreads", 0);
InputMICThreads[1] = iniparser_getuint(ini, "MultipleThreading:NumOfMICThreads_1", 0);
InputMICThreads[2] = iniparser_getuint(ini, "MultipleThreading:NumOfMICThreads_2", 0);
iniparser_freedict(ini);
}
dictionary *ParseInput(int argc, char** argv) {
dictionary *programInput;
char t1[3] = "-c"; // specify that this is a boolean type parameter; no following argument
char t2[3] = "-U"; // specify that this is a boolean type parameter; no following argument
char t3[3] = "-A"; // specify that this is a boolean type parameter; no following argument
char *d[3];
char *tempString;
int len;
int i;
d[0] = t1;
d[1] = t2;
d[2] = t3;
programInput = paraparser_load(argc, argv, 3, d); // 4 parameters are boolean type
if (argc<5) {
PrintHelp();
exit(1);
}
if (strcmp(argv[1],"pair")!=0) {
PrintHelp();
exit(1);
}
// Get database, query name and output file name
if (!iniparser_find_entry(programInput, "argument:2")) {
PrintHelp();
exit(1);
}
iniparser_copystring(programInput, "argument:2", DatabaseName, DatabaseName, MAX_FILENAME_LEN);
if (iniparser_find_entry(programInput, "parameter:-i")) {
// User input is a list of reads
InputFileArgument = MICA_INPUT_FILE_ARG_LIST;
iniparser_copystring(programInput, "parameter:-i", ListFileName, ListFileName, MAX_FILENAME_LEN);
} else {
// User input is a pair of file
InputFileArgument = MICA_INPUT_FILE_ARG_FILE;
if (!iniparser_find_entry(programInput, "argument:3")) {
PrintHelp();
exit(1);
}
iniparser_copystring(programInput, "argument:3", ReadFileName, ReadFileName, MAX_FILENAME_LEN);
iniparser_copystring(programInput, "argument:4", MateFileName, MateFileName, MAX_FILENAME_LEN);
InputPEInsertionLowerBound = iniparser_getint(programInput,"parameter:-v", InputPEInsertionLowerBound);
InputPEInsertionUpperBound = iniparser_getint(programInput,"parameter:-u", InputPEInsertionUpperBound);
}
InputQueryStrand = iniparser_getint(programInput, "parameter:-S", InputQueryStrand);
if (iniparser_find_entry(programInput, "parameter:-m")) {
tempString = iniparser_getstr(programInput, "parameter:-m");
len = (int)strlen(tempString);
InputErrorType = SRA_TYPE_MISMATCH_ONLY;
if ( len > 0 && strncmp(tempString + len - 1, "e", 1) == 0) {
len--;
tempString[len] = '\0';
InputErrorType = SRA_TYPE_EDIT_DISTANCE;
}
if ( len > 0 ) {
for (i=0;i<len;i++) {
if (tempString[i]<'0' || tempString[i]>'9') {
PrintHelp();
exit(1);
}
}
InputMaxError = atoi(tempString);
}
}
InputMaxNBMismatch = iniparser_getint(programInput,"parameter:-n", InputMaxNBMismatch);
InputReportType = iniparser_getint(programInput,"parameter:-h", InputReportType);
InputOutputFileName = iniparser_find_entry(programInput, "parameter:-o");
if (InputOutputFileName) {
iniparser_copystring(programInput, "parameter:-o", OutputFileName, OutputFileName, MAX_FILENAME_LEN);
} else {
InputOutputFileName=MIC_MAIN_NON_INPUT_VALUE;
}
InputOutputFormat = iniparser_getint(programInput, "parameter:-b", InputOutputFormat);
return programInput;
}
void PrintHelp() {
printf("Syntax:\n");
printf("Pair End Alignment Syntax:\n");
printf(" %s pair <2bwt index> <read file 1> <read file 2> -v <l-insert> -u <u-insert> [Options]\n",PROJECT_ALIGNER_BINARY);
printf(" %s pair <2bwt index> -i <input list file> [Options]\n", PROJECT_ALIGNER_BINARY);
printf("\n");
printf(" [Mandatory]\n");
printf(" -v: Lower bound;\n");
printf(" -u: Upper bound of the insertion size between a pair.\n");
printf(" A pair will be reported if the insertion size falls\n");
printf(" between [v,u] and their strands match.\n");
printf("\n");
printf(" [Options]\n");
printf(" -m: Maximum #errors allowed. [Def=2]\n");
printf(" Expect value in this format \"-m <intNum>\".\n");
printf(" <intNum> is the maximum number of errors\n");
printf(" allowed. Valid values are 0,..,%d\n", MAX_NUM_OF_MISMATCH);
printf(" -h: Alignment type. [Def=%d]\n",SRA_REPORT_ALL_BEST);
printf(" %d : All Valid Alignment\n", SRA_REPORT_ALL);
printf(" %d : All Best Alignment\n", SRA_REPORT_ALL_BEST);
//printf(" %d : Unique Best Alignment\n", SRA_REPORT_UNIQUE_BEST);
//printf(" %d : Random Best Alignment\n", SRA_REPORT_RANDOM_BEST);
//printf(" %d : Best Quality Alignment\n", SRA_REPORT_BEST_QUALITY);
printf(" -b: Output format. [Def=%d]\n",SRA_OUTPUT_FORMAT_SAM);
//printf(" %d : Succinct (Plain)\n", SRA_OUTPUT_FORMAT_PLAIN);
printf(" %d : SAM 1.4 (Plain)\n", SRA_OUTPUT_FORMAT_SAM);
printf(" %d : BAM 1.4 (Compress)\n", SRA_OUTPUT_FORMAT_BAM);
printf("\n");
}
void ParameterVerification() {
// Internal Checking
if (InputSGASeedOccLimitation==-1 || InputSGASeedOccLimitation>MIC_SRA_OUTPUT_MAX_ALIGNMENT) {
printf("Potential Configuration Error:\n");
printf("Seed alignment expects boundary %u which cannot be satisfied \n",InputSGASeedOccLimitation);
printf("by MIC-SRA alignment model (capped at %u). \n",MIC_SRA_OUTPUT_MAX_ALIGNMENT);
printf("Seed alignment with more than %u results will be passed to CPU\n",InputSGASeedOccLimitation);
printf("for Seed alignment which might degrade performance\n");
}
// Internal Checking
if (MIC_DP_OUTPUT_MAX_ALIGNMENT>MIC_PE_MAX_RESULT) {
printf("Potential Configuration Error:\n");
printf("DP Enhancement could reporting occurrences through PE output buffer.\n");
printf("The number of output per read is configured as:\n");
printf("SRA-PE <= %u and DP <= %u, which could result in overflow.\n",MIC_PE_MAX_RESULT,MIC_DP_OUTPUT_MAX_ALIGNMENT);
}
if ( InputMaxNumOfAlignment < -1 || InputMaxNumOfAlignment == 0 ) {
printf("MaxNumOfAlignment can only be set to -1; or any positive integer.\n");
exit(1);
}
if ( InputMaxNumOfAlignment > MIC_PE_MAX_RESULT ) {
printf("Potential Configuration Error:\n");
printf("MaxNumOfAlignment(%d) exceeded the capacity of MIC allocated buffer(%d)\n",InputMaxNumOfAlignment,MIC_PE_MAX_RESULT);
printf("Any read pairs have number of output exceeding the MIC capacity are handled by CPU.\n");
printf("That could potentially affect alignment performance.\n");
}
if (InputReportType!=MIC_MAIN_NON_INPUT_VALUE &&
InputReportType!=PE_REPORT_ALL &&
InputReportType!=PE_REPORT_ALL_BEST ) {
fprintf(stderr, "Report mode must be %d=All-Valid %d=All-Best.\n", PE_REPORT_ALL, PE_REPORT_ALL_BEST);
exit(1);
}
/* ATTENTION : AWAITING IMPLEMENTATION OF ALL-BEST ALIGNMENT
if (InputReportType!=MIC_MAIN_NON_INPUT_VALUE &&
InputReportType!=PE_REPORT_ALL &&
InputReportType!=REPORT_ALL_BEST ) {
fprintf(stderr, "Report mode must be either %d=All-Valid, %d=All-Best.\n", PE_REPORT_ALL, PE_REPORT_ALL_BEST);
exit(1);
}
*/
if (InputErrorType == SRA_TYPE_MISMATCH_ONLY) {
if (InputMaxError!=MIC_MAIN_NON_INPUT_VALUE && (InputMaxError<0 || InputMaxError>MAX_NUM_OF_MISMATCH)) {
fprintf(stderr, "Maximum mismatches must be within the range [0-%d].\n",MAX_NUM_OF_MISMATCH);
exit(1);
}
} else if (InputErrorType == SRA_TYPE_EDIT_DISTANCE) {
if (InputMaxError!=MIC_MAIN_NON_INPUT_VALUE && (InputMaxError<0 || InputMaxError>MAX_NUM_OF_INDEL)) {
fprintf(stderr, "Maximum edit distance must be within the range [0-%d].\n",MAX_NUM_OF_INDEL);
exit(1);
}
}
/* ATTENTION : AWAITING IMPLEMENTATION OF NBM
if (InputMaxNBMismatch!=MIC_MAIN_NON_INPUT_VALUE && (InputMaxNBMismatch < 0 || InputMaxNBMismatch > MAX_NUM_OF_NBM_ERROR)) {
fprintf(stderr, "Maximum Non-Branching error must be within the range [0-%d].\n",MAX_NUM_OF_NBM_ERROR);
exit(1);
}
*/
if (InputOutputFormat != SRA_OUTPUT_FORMAT_SAM && InputOutputFormat != SRA_OUTPUT_FORMAT_BAM) {
fprintf(stderr, "Output format must be %d=SAM or %d=BAM.\n", SRA_OUTPUT_FORMAT_SAM, SRA_OUTPUT_FORMAT_BAM);
exit(1);
}
if (InputOutputFormat==SRA_OUTPUT_FORMAT_BAM && InputOutputNumSamThreads < 1) {
fprintf(stderr, "Number of output compression threads must be at least 1\n");
exit(1);
}
if ( InputFileArgument == MICA_INPUT_FILE_ARG_FILE) {
if (InputPEInsertionUpperBound==MIC_MAIN_NON_INPUT_VALUE || InputPEInsertionLowerBound==MIC_MAIN_NON_INPUT_VALUE) {
fprintf(stderr, "Lower and upper bound of the insertion must be supplied!\n");
exit(1);
} else if (InputPEInsertionUpperBound < InputPEInsertionLowerBound) {
fprintf(stderr, "Supplied upper bound is smaller than lower bound!\n");
exit(1);
}
}
// Dynamics Program Parameters
if ( !InputSGASeedEnhancement && InputSGASeedEnhancement_1 ) {
fprintf(stderr, "Second level SRA Seed Enhancement is enabled but the first level is disabled.\n");
exit(1);
}
}
void SRAFillCharMap(unsigned char * charMap) {
int i;
memset(charMap,2,256);
for (i=0;i<ALPHABET_SIZE;i++) {
charMap[dnaChar[i]] = i;
}
}
void SRAGetFileSuffix(int threadId, char * suffixStr) {
if (threadId<0 || threadId>=1000) {
threadId=0;
}
suffixStr[0]='.';
suffixStr[1]='0'+threadId / 100;
suffixStr[2]='0'+(threadId % 100) / 10;
suffixStr[3]='0'+(threadId % 10);
suffixStr[4]='\0';
}