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SOAP3-DP.cu
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SOAP3-DP.cu
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/*
*
* SOAP3-DP.cu
* Soap3(gpu)
*
* Copyright (C) 2011, 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.
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <pthread.h>
#include <zlib.h>
#include "Release.h"
#include "DV-Kernel.h"
#include "CPUfunctions.h"
#include "alignment.h"
#include "SAM.h"
#include "samtools-0.1.18/bam.h"
#include "BGS-IO.h"
#include "2bwt-flex/SRAArguments.h"
#include "PEAlgnmt.h"
#include "AlgnResult.h"
#include "OutputDPResult.h"
#include "DV-SemiDP.h"
#include "DV-DPForBothUnalign.h"
#include "DV-DPForSingleReads.h"
#include "aio_thread.h"
int main ( int argc, char ** argv )
{
// ======================================================================================
// | VARIABLE DECLARATION |
// ======================================================================================
// local variables used in main, like BWT indexes and such.
int i;
double startTime, indexLoadTime, readLoadTime;
double lastEventTime;
double totalReadLoadTime = 0.0;
double totalAlignmentTime = 0.0;
double totalTrimAlignmentTime = 0.0;
char * queryFileName = "";
char * queryFileName2 = "";
FILE * outputFile;
FILE * outputDPFile;
FILE * outputDoneFile;
// FILE *queryFile;
// FILE *queryFile2;
//gzFile * gzQueryFile;
//gzFile * gzQueryFile2;
gzFile gzQueryFile;
gzFile gzQueryFile2;
bamFile bamQueryFile;
bam_header_t * bamHeader;
bam1_t * bam;
char isFastq = 0;
// user-specified maximum read length
// and number of words per query
uint maxReadLength;
uint wordPerQuery;
// uint numQueries;
ullint roundUp;
ullint totalQueryLength;
uint * queries;
uint * readLengths;
uint * readIDs;
char * upkdQueryNames;
char * upkdQualities;
uint * queries0;
uint * readLengths0;
uint * readIDs0;
char * upkdQueryNames0;
char * upkdQualities0;
uint * queries1;
uint * readLengths1;
uint * readIDs1;
char * upkdQueryNames1;
char * upkdQualities1;
unsigned int * unAlignedPair;
char queryFileBuffer[INPUT_BUFFER_SIZE];
char queryFileBuffer2[INPUT_BUFFER_SIZE];
unsigned long long numOfAnswer;
unsigned int numOfAlignedRead;
unsigned int numOfUnAlignedPairs;
uint detected_read_length = 0;
// for single-end reads
// it represents the max read length for the first ten reads (i.e. 0, 1, ..., 9)
// for paired-end reads
// the max read length for the first ten reads with even readIDs (i.e. 0,2,...,18)
uint detected_read_length2 = 0;
// for paired-end reads only
// the max read length for the first ten reads with odd readIDs (i.e. 1,3,...,19)
// Declare variables and set up preference for device.
// #ifdef BGS_GPU_CASE_BREAKDOWN_TIME
// cudaEvent_t start, stop;
// float time1, totalDeviceTime;
// #endif
uint * _bwt, *_occ;
uint * _revBwt, *_revOcc;
// Accumulated number of reads aligned and alignments
ullint totalReadsAlignedForInputReads = 0;
ullint totalAnsForInputReads = 0;
// Input parameters
InputOptions input_options;
// Indicate whether the index has been loaded to GPU
uint indexLoadedToGPU = 0;
// The inputs for multi option
MultiInputItem * multiInput = NULL;
int expNum = 0;
int currExp = 0;
// ======================================================================================
// | Configuration on GPU functions |
// ======================================================================================
// not much effect, also this is not supported by old version of cuda library
// like the machines in TJ
// thus these are depreciated
cudaDeviceSetCacheConfig ( cudaFuncCachePreferL1 );
// cudaFuncSetCacheConfig(kernel, cudaFuncCachePreferShared);
// cudaFuncSetCacheConfig(kernel_4mismatch_1, cudaFuncCachePreferShared);
// cudaFuncSetCacheConfig(kernel_4mismatch_2, cudaFuncCachePreferShared);
// ======================================================================================
// | PARSING CONFIGURATION FILE |
// ======================================================================================
char * iniFileName;
iniFileName = ( char * ) malloc ( strlen ( argv[0] ) + 5 );
strcpy ( iniFileName, argv[0] );
strcpy ( iniFileName + strlen ( argv[0] ), ".ini" );
IniParams ini_params;
if ( ParseIniFile ( iniFileName, ini_params ) != 0 )
{
fprintf ( stderr, "Failed to parse config file ... %s\n", iniFileName );
return 1;
}
printf ( "\n[Main] %s v%d.%d.%d (%s)\n", PROJECT_NAME, PROJECT_MAJOR, PROJECT_MINOR, PROJECT_REV, PROJECT_SPECIAL );
// printf("[Main] Finished parsing ini file %s.\n\n", iniFileName);
free ( iniFileName );
// ======================================================================================
// | CHECK THE INPUT ARGUMENTS |
// ======================================================================================
bool inputValid = parseInputArgs ( argc, argv, input_options );
if ( !inputValid )
{ exit ( 1 ); }
// for multi mode
if ( input_options.isReadList == 1 )
{
multiInput = loadMultiInputFile ( input_options.queryFileName, ( input_options.readType == PAIR_END_READ ) ? 1 : 0,
input_options.isReadBAM, expNum );
updateInputOption ( ( &input_options ), multiInput, currExp++ );
}
// get the name of the query file (and the second query file for pair-ended reads)
queryFileName = input_options.queryFileName;
if ( input_options.readType == PAIR_END_READ && input_options.isReadBAM == 0 )
{
queryFileName2 = input_options.queryFileName2;
}
maxReadLength = input_options.maxReadLength;
if ( input_options.readType == SINGLE_READ )
{ printf ( "[Main] Loading read file %s\n", queryFileName ); }
else if ( input_options.isReadBAM == 0 )
{ printf ( "[Main] Loading read files %s and %s\n", queryFileName, queryFileName2 ); }
// ======================================================================================
// | Restriction on GPU card with 3G memory |
// ======================================================================================
// restriction on the maxReadLength when using GPU card with 3G memory
if ( ( ini_params.Ini_GPUMemory == 3 ) && ( maxReadLength > 128 ) )
{
printf ( "For GPU card with 3G memory, the program cannot support maximum read length more than 128.\n" );
exit ( 1 );
}
// restriction on the number of hits of each end for pairing
#ifdef NO_CONSTRAINT_SINGLE_READ_NUM_FOR_PAIRING
if ( input_options.readType == PAIR_END_READ )
{ ini_params.Ini_MaxOutputPerRead = 0xFFFFFFFF; }
#endif
// set the maximum number of mismatches allowed for soap3 alignment
// if DP is enabled.
if ( input_options.enableDP == 1 )
{
input_options.numMismatch = ini_params.Ini_Soap3MisMatchAllow;
}
// ======================================================================================
// | Selection of GPU device |
// ======================================================================================
if ( input_options.GPUDeviceID > -1 )
{ cudaSetDevice ( input_options.GPUDeviceID ); }
// ======================================================================================
// | VARIABLES SETTING AND INITIALISATION |
// ======================================================================================
// determine number of words per query. rounded up to power of 2
wordPerQuery = 1;
while ( wordPerQuery < maxReadLength )
{ wordPerQuery *= 2; }
wordPerQuery = wordPerQuery / CHAR_PER_WORD;
uint maxNumQueries = MAX_NUM_BATCH * NUM_BLOCKS * THREADS_PER_BLOCK;
// maxNumQueries has to be divible by 2
maxNumQueries = maxNumQueries / 2 * 2;
// For Output filenames
char * outputFileName[MAX_NUM_CPU_THREADS];
for ( i = 0; i < MAX_NUM_CPU_THREADS; i++ )
{ outputFileName[i] = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 10 ); }
// For Output of the DP results
char * outputDPFileName;
outputDPFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 9 );
// For Output of the unpaired results
char * outputUnpairFileName;
outputUnpairFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 8 );
// For Output the DONE file
char * outputDoneFileName;
outputDoneFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 6 );
for ( i = 0; i < MAX_NUM_CPU_THREADS; i++ )
{
sprintf ( outputFileName[i], "%s.gout.%d", input_options.outputPrefix, i + 1 );
}
sprintf ( outputDPFileName, "%s.dpout.1", input_options.outputPrefix );
sprintf ( outputUnpairFileName, "%s.unpair", input_options.outputPrefix );
sprintf ( outputDoneFileName, "%s.done", input_options.outputPrefix );
// ======================================================================================
// | STRUCTURES FOR SEMI-GLOBAL ALIGNMENT DP |
// ======================================================================================
// Declare the structure for storing the alignment results
// for the pairs of reads with one end has no hit but another has.
// The structure will be used for proceeding semi-global DP
ReadInputForDPArrays readInputForDPall;
readInputForDPall.inputArrays = ( ReadInputForDP ** ) malloc ( MAX_NUM_CPU_THREADS * sizeof ( ReadInputForDP * ) );
readInputForDPall.numArrays = ini_params.Ini_NumOfCpuThreads;
// The following structure will be used for proceeding NEW semi-global DP
ReadInputForDPArrays readInputForNewDPall;
readInputForNewDPall.inputArrays = ( ReadInputForDP ** ) malloc ( MAX_NUM_CPU_THREADS * sizeof ( ReadInputForDP * ) );
readInputForNewDPall.numArrays = ini_params.Ini_NumOfCpuThreads;
// Declare the structure for storing the read IDs of the first end of the pairs
// which both ends cannot be aligned (if the input read is paired-end)
BothUnalignedPairsArrays * bothUnalignedPairsArrays = constructBothUnalignedPairsArrays ( ini_params.Ini_NumOfCpuThreads + 1 );
// OR for single end cannot be aligned (if the input read is single-end)
UnalignedSinglesArrays * unalignedSinglesArrays = bothUnalignedPairsArrays; // same array but just different name
// Declare the structure for storing the alignment results
// for the pairs of reads with both ends have hits but do not have valid insert size or proper strands.
ReadInputForDPArrays readAnsForNonValidInsert;
readAnsForNonValidInsert.inputArrays = ( ReadInputForDP ** ) malloc ( MAX_NUM_CPU_THREADS * sizeof ( ReadInputForDP * ) );
readAnsForNonValidInsert.numArrays = ini_params.Ini_NumOfCpuThreads;
// Parameters for DP
DPParameters dpParameters;
getParameterForAllDP ( dpParameters, input_options, ini_params );
// ======================================================================================
// | INDEX LOADING |
// ======================================================================================
//Start measuring runtime..
startTime = setStartTime ();
lastEventTime = startTime;
Soap3Index * index = INDEXLoad ( &ini_params, input_options.indexName, ini_params.Ini_shareIndex );
HSP * hsp = index->sraIndex->hsp;
HSPAux * hspaux = index->sraIndex->hspaux;
indexLoadTime = getElapsedTime ( startTime );
printf ( "[Main] Finished loading index into host.\n" );
printf ( "[Main] Loading time : %9.4f seconds\n", indexLoadTime );
printf ( "[Main] Reference sequence length : %u\n\n", index->sraIndex->bwt->textLength );
lastEventTime = indexLoadTime;
roundUp = ( maxNumQueries + 31 ) / 32 * 32;
totalQueryLength = roundUp * wordPerQuery;
// ==============================================================
// | QUALITY CONSTANT and DP MATCH SCORE and alignment type |
// ==============================================================
int quality_constant = DEFAULT_QUAL_CONST;
if ( input_options.isIlluminaQual == 1 )
{ quality_constant = ILLUMINA_QUAL_CONST; }
hspaux->dpMatchScore = ini_params.Ini_MatchScore;
hspaux->dpMisMatchScore = ini_params.Ini_MismatchScore;
hspaux->alignmentType = input_options.alignmentType;
hspaux->readType = input_options.readType;
hspaux->peMaxOutputPerRead = ini_params.Ini_PEMaxOutputPerPair;
if ( input_options.readType == SINGLE_READ )
{ hspaux->ProceedDPForTooManyHits = ini_params.Ini_proceedDPForTooManyHits; }
else
{ hspaux->ProceedDPForTooManyHits = 0; }
// For Mapping Quality Score Calculation
hspaux->x0_array = ( int * ) malloc ( roundUp * sizeof ( int ) );
hspaux->x1_array = ( int * ) malloc ( roundUp * sizeof ( int ) );
hspaux->mismatch_array = ( int * ) malloc ( roundUp * sizeof ( int ) );
hspaux->minMAPQ = ini_params.Ini_minMAPQ;
hspaux->maxMAPQ = ini_params.Ini_maxMAPQ;
hspaux->bwaLikeScore = ini_params.Ini_bwaLikeScore;
hspaux->maxLenReadName = ini_params.Ini_maxReadNameLen;
if ( hspaux->bwaLikeScore )
{ bwase_initialize ( hspaux->g_log_n ); }
// For storing the results of the unpaired reads
hspaux->soap3AnsArray = ( ReadInputForDP ** ) malloc ( roundUp * sizeof ( ReadInputForDP * ) );
hspaux->sa_start = ( unsigned int * ) malloc ( roundUp * sizeof ( unsigned int ) );
hspaux->occ_start = ( unsigned int * ) malloc ( roundUp * sizeof ( unsigned int ) );
hspaux->sa_num = ( unsigned int * ) malloc ( roundUp * sizeof ( unsigned int ) );
hspaux->occ_num = ( unsigned int * ) malloc ( roundUp * sizeof ( unsigned int ) );
// print MD string and NM tag?
hspaux->isPrintMDNM = input_options.isPrintMDNM;
// For the SAM output information
hspaux->readGroup = input_options.readGroup;
if ( strlen ( hspaux->readGroup ) == 0 )
{ hspaux->readGroup = input_options.queryFileName; }
hspaux->sampleName = input_options.sampleName;
if ( strlen ( hspaux->sampleName ) == 0 )
{ hspaux->sampleName = DEFAULT_SAMPLE_NAME; }
hspaux->readGrpOption = input_options.readGrpOption;
// ==================================================================
// | For construction of arrays to store the unaligned read IDs
// | for proceeding single deep-dp on them
// ==================================================================
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
hspaux->readsIDForSingleDP = ( BothUnalignedPairsArrays * ) constructBothUnalignedPairsArrays ( 1 );
hspaux->allHits = ( AllHits * ) constructAllHits (); // for storing the corresponding algnments
#endif
// ======================================================================================
// | ALLOCATE MEMORY FOR THE ARRAYS |
// ======================================================================================
queries0 = ( uint * ) malloc ( totalQueryLength * sizeof ( uint ) ); // a large array to store all queries
readLengths0 = ( uint * ) malloc ( roundUp * sizeof ( uint ) );
readIDs0 = ( uint * ) malloc ( roundUp * sizeof ( uint ) );
upkdQualities0 = ( char * ) malloc ( roundUp * maxReadLength * sizeof ( char ) );
memset ( upkdQualities0, 0, roundUp * maxReadLength );
upkdQueryNames0 = ( char * ) malloc ( roundUp * ini_params.Ini_maxReadNameLen * sizeof ( char ) );
queries1 = ( uint * ) malloc ( totalQueryLength * sizeof ( uint ) ); // a large array to store all queries
readLengths1 = ( uint * ) malloc ( roundUp * sizeof ( uint ) );
readIDs1 = ( uint * ) malloc ( roundUp * sizeof ( uint ) );
upkdQualities1 = ( char * ) malloc ( roundUp * maxReadLength * sizeof ( char ) );
memset ( upkdQualities1, 0, roundUp * maxReadLength );
upkdQueryNames1 = ( char * ) malloc ( roundUp * ini_params.Ini_maxReadNameLen * sizeof ( char ) );
/*
queries = (uint*) malloc(totalQueryLength * sizeof(uint)); // a large array to store all queries
readLengths = (uint*) malloc(roundUp * sizeof(uint));
readIDs = (uint*) malloc(roundUp * sizeof(uint));
upkdQualities = (char*) malloc(roundUp*maxReadLength * sizeof(char));
memset(upkdQualities,0,roundUp*maxReadLength);
upkdQueryNames = (char*) malloc(roundUp*ini_params.Ini_maxReadNameLen * sizeof(char));
*/
unAlignedPair = ( unsigned int * ) malloc ( roundUp * sizeof ( unsigned int ) );
for ( int threadId = 0; threadId < ini_params.Ini_NumOfCpuThreads; ++threadId )
{
readInputForDPall.inputArrays[threadId] = constructReadInputForDP ( ini_params.Ini_NumOfCpuThreads );
readInputForNewDPall.inputArrays[threadId] = constructReadInputForDP ( ini_params.Ini_NumOfCpuThreads );
readAnsForNonValidInsert.inputArrays[threadId] = constructReadInputForDP ( ini_params.Ini_NumOfCpuThreads );
}
uint maxBatchSize = NUM_BLOCKS * THREADS_PER_BLOCK * QUERIES_PER_THREAD; // queries processed in one kernel call
// maxBatchSize has to be divible by 2
maxBatchSize = maxBatchSize / 2 * 2;
// #ifdef BGS_GPU_CASE_BREAKDOWN_TIME
// totalDeviceTime=0;
// #endif
// initialize the output files
bam_header_t samOutputHeader;
samfile_t * samOutputFilePtr[MAX_NUM_CPU_THREADS];
samfile_t * samOutputDPFilePtr;
samfile_t * samOutputUnpairFilePtr;
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
SAMOutputHeaderConstruct ( &samOutputHeader, hsp, hspaux, maxReadLength );
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
if ( input_options.isOutputBinary == 1 )
{ samOutputFilePtr[i] = samopen ( outputFileName[i], "wb", &samOutputHeader ); }
else
{ samOutputFilePtr[i] = samopen ( outputFileName[i], "wh", &samOutputHeader ); }
if ( samOutputFilePtr[i] == NULL )
{
fprintf ( stderr, "Could not open the output file %s\n", outputFileName[i] );
exit ( 1 );
}
}
break;
default:
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
outputFile = ( FILE * ) fopen ( outputFileName[i], "w" );
if ( outputFile == NULL ) { fprintf ( stderr, "Could not open the output file %s\n", outputFileName[i] ); exit ( 1 );}
OCCWriteOutputHeader ( hsp, outputFile, maxReadLength, 1, input_options.outputFormat ); // will modify the number of reads later
fclose ( outputFile );
}
break;
}
// For DP
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
if ( input_options.isOutputBinary == 1 )
{ samOutputDPFilePtr = samopen ( outputDPFileName, "wb", &samOutputHeader ); }
else
{ samOutputDPFilePtr = samopen ( outputDPFileName, "wh", &samOutputHeader ); }
if ( samOutputDPFilePtr == NULL )
{
fprintf ( stderr, "Could not open the output file %s\n", outputDPFileName );
exit ( 1 );
}
break;
default:
outputDPFile = ( FILE * ) fopen ( outputDPFileName, "w" );
if ( outputDPFile == NULL ) { fprintf ( stderr, "Could not open the output file %s\n", outputDPFileName ); exit ( 1 );}
OCCWriteOutputHeader ( hsp, outputDPFile, maxReadLength, 1, input_options.outputFormat ); // will modify the number of reads later
fclose ( outputDPFile );
break;
}
// For Unpaired reads
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
if ( input_options.readType == PAIR_END_READ )
{
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
if ( input_options.isOutputBinary == 1 )
{ samOutputUnpairFilePtr = samopen ( outputUnpairFileName, "wb", &samOutputHeader ); }
else
{ samOutputUnpairFilePtr = samopen ( outputUnpairFileName, "wh", &samOutputHeader ); }
if ( samOutputUnpairFilePtr == NULL )
{
fprintf ( stderr, "Could not open the output file %s\n", outputUnpairFileName );
exit ( 1 );
}
break;
}
}
#endif
// ======================================================================================
// | LOADING INPUT SHORT READ FILE |
// ======================================================================================
size_t bufferSize;
uint bufferIndex;
char queryChar;
size_t bufferSize2;
uint bufferIndex2;
char queryChar2;
if ( input_options.isReadBAM )
{
// the query file is in BAM format
bamQueryFile = bam_open ( queryFileName, "r" );
bamHeader = bam_header_init ();
bamHeader = bam_header_read ( bamQueryFile );
bam = bam_init1 ();
}
else
{
//gzQueryFile = ( gzFile * ) gzopen ( queryFileName, "r" );
gzQueryFile = gzopen ( queryFileName, "r" );
if ( gzQueryFile == NULL ) { fprintf ( stderr, "Cannot open queryFile\n" ); exit ( 1 );}
bufferSize = gzread ( gzQueryFile, queryFileBuffer, INPUT_BUFFER_SIZE );
if ( bufferSize < INPUT_BUFFER_SIZE && ( !gzeof ( gzQueryFile ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( gzQueryFile, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex = 0;
queryChar = queryFileBuffer[bufferIndex++];
if ( input_options.readType == PAIR_END_READ )
{
// pair-ended reads
//gzQueryFile2 = ( gzFile * ) gzopen ( queryFileName2, "r" );
gzQueryFile2 = gzopen ( queryFileName2, "r" );
if ( gzQueryFile2 == NULL ) { fprintf ( stderr, "Cannot open queryFile2\n" ); exit ( 1 );}
bufferSize2 = gzread ( gzQueryFile2, queryFileBuffer2, INPUT_BUFFER_SIZE );
if ( bufferSize2 < INPUT_BUFFER_SIZE && ( !gzeof ( gzQueryFile2 ) ) )
{
const char * error_string;
int err;
error_string = gzerror ( gzQueryFile2, & err );
if ( err )
{
fprintf ( stderr, "Error in reading the read file: %s.\n", error_string );
exit ( EXIT_FAILURE );
}
}
bufferIndex2 = 0;
queryChar2 = queryFileBuffer2[bufferIndex2++];
}
}
uint accumReadNum = 0;
uint numQueries;
// create buffers
InputReadsBuffer * buffer0 = InputReadsBufferFullCreate ( maxReadLength,
maxNumQueries, wordPerQuery, quality_constant, queries0,
readLengths0, readIDs0, upkdQualities0, upkdQueryNames0,
isFastq, ini_params.Ini_maxReadNameLen );
InputReadsBuffer * buffer1 = InputReadsBufferFullCreate ( maxReadLength,
maxNumQueries, wordPerQuery, quality_constant, queries1,
readLengths1, readIDs1, upkdQualities1, upkdQueryNames1,
isFastq, ini_params.Ini_maxReadNameLen );
AIOInputBuffer * aiob = AIOInputBufferCreate ( buffer0, buffer1 );
InputFilePointers * ifp = InputFilePointersCreate ();
if ( input_options.isReadBAM )
{
InputFilePointersSetBam ( ifp, bamQueryFile, bamHeader, bam );
}
else if ( input_options.readType == SINGLE_READ )
{
InputFilePointersSetSingle ( ifp, gzQueryFile );
}
else
{
InputFilePointersSetPair ( ifp, gzQueryFile, gzQueryFile2 );
}
aiob->reads = ifp;
InputReadsBuffer * readyReadsBuffer;
//create io thread
AIOInputThreadCreate ( aiob, bufferSize, bufferIndex, index->charMap, queryChar,
queryFileBuffer, bufferSize2, bufferIndex2, queryChar2,
queryFileBuffer2 );
//load reads
readyReadsBuffer = LoadReadsFromAIOBuffer ( aiob );
queries = readyReadsBuffer->queries;
readLengths = readyReadsBuffer->readLengths;
readIDs = readyReadsBuffer->readIDs;
upkdQualities = readyReadsBuffer->upkdQualities;
upkdQueryNames = readyReadsBuffer->upkdQueryNames;
isFastq = readyReadsBuffer->isFastq;
hspaux->isFastq = isFastq;
numQueries = readyReadsBuffer->filledNum;
while ( numQueries > 0 )
{
printf ( "[Main] Loaded %u short reads from the query file.\n", numQueries );
readLoadTime = getElapsedTime ( startTime );
printf ( "[Main] Elapsed time on host : %9.4f seconds\n\n", readLoadTime - lastEventTime );
totalReadLoadTime += readLoadTime - lastEventTime;
lastEventTime = readLoadTime;
numOfAnswer = 0;
numOfAlignedRead = 0;
numOfUnAlignedPairs = 0;
uint origNumQueries = numQueries;
if ( detected_read_length == 0 )
{
// printParameters(input_options, ini_params);
// ==================================================================
// | DETECT THE READ LENGTH |
// ==================================================================
if ( input_options.readType == PAIR_END_READ )
{
detected_read_length = GetReadLength ( readLengths, numQueries, 2 );
detected_read_length2 = GetReadLength ( readLengths + 1, numQueries, 2 );
// the minimum insert size cannot be smaller than detected_read_length2
if ( input_options.insert_low < detected_read_length2 )
{ input_options.insert_low = detected_read_length2; }
}
else
{
detected_read_length = GetReadLength ( readLengths, numQueries, 1 );
}
// ==================================================================
// | FOR DP IS ENABLED |
// | IF READ LENGTH < MIN_READ_LEN_FOR_DP (i.e. 30) |
// | THEN DP IS DISABLE., |
// | IF READ LENGTH > 150, SKIP SOAP3 MODULE. |
// | IF READ LENGTH <= 50, ONLY ALLOW 1 MISMATCH IN SOAP3 |
// ==================================================================
if ( input_options.readType == SINGLE_READ && detected_read_length < MIN_READ_LEN_FOR_DP && input_options.enableDP == 1 )
{
input_options.enableDP = 0;
printf ( "Dynamic programming is disabled because read length < %i\n", MIN_READ_LEN_FOR_DP );
}
else if ( input_options.readType == PAIR_END_READ && ( detected_read_length < MIN_READ_LEN_FOR_DP || detected_read_length2 < MIN_READ_LEN_FOR_DP ) && input_options.enableDP == 1 )
{
input_options.enableDP = 0;
printf ( "Dynamic programming is disabled because read length < %i\n", MIN_READ_LEN_FOR_DP );
}
else if ( input_options.readType == PAIR_END_READ && ( detected_read_length > 150 || detected_read_length2 > 150 ) && input_options.enableDP == 1 )
{
ini_params.Ini_skipSOAP3Alignment = 1;
printf ( "All reads are directly processed by DP, because the read length > 150\n" );
}
else if ( input_options.readType == PAIR_END_READ && ( detected_read_length <= 50 || detected_read_length2 <= 50 ) && input_options.enableDP == 1 )
{
input_options.numMismatch = 1;
}
// ==================================================================
// | IF DP IS DISABLE AND USER DOES NOT SPECIFY # OF MISMATCHES |
// | THEN SET THE DEFAULT # OF MISMATCHES AS: |
// | - IF READ LENGTH < 50, DEFAULT_NUM_MISMATCH_FOR_SHORT_READ |
// | - IF READ LENGTH >= 50, DEFAULT_NUM_MISMATCH_FOR_NORMAL_READ |
// ==================================================================
if ( input_options.enableDP == 0 && input_options.numMismatch == -1 )
{
// user does not specify # of mismatches
input_options.numMismatch = getDefaultMismatchNum ( detected_read_length );
printf ( "Maximum number of mismatches allowed: %i\n", input_options.numMismatch );
}
// get the max hit # for default DP
if ( input_options.enableDP == 1 && input_options.readType == PAIR_END_READ )
{
input_options.maxHitNum = getMaxHitNumForDefaultDP ( detected_read_length );
input_options.maxHitNum2 = getMaxHitNumForDefaultDP ( detected_read_length2 );
}
}
// Reset the array for mapping quality score calculation
memset ( hspaux->x0_array, 0, roundUp * sizeof ( int ) );
memset ( hspaux->x1_array, 0, roundUp * sizeof ( int ) );
memset ( hspaux->mismatch_array, 0, roundUp * sizeof ( int ) );
memset ( hspaux->sa_start, 0, roundUp * sizeof ( unsigned int ) );
memset ( hspaux->occ_start, 0, roundUp * sizeof ( unsigned int ) );
memset ( hspaux->sa_num, 0, roundUp * sizeof ( unsigned int ) );
memset ( hspaux->occ_num, 0, roundUp * sizeof ( unsigned int ) );
memset ( ( ( ReadInputForDP ** ) hspaux->soap3AnsArray ), 0, roundUp * sizeof ( ReadInputForDP * ) );
// Reset the array for storing the single alignment for those unaligned paired-end reads
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
resetAllHits ( ( AllHits * ) hspaux->allHits );
#endif
// =====================================================================
// | Reset the arrays for storing alignment results for semi-global DP |
// =====================================================================
if ( input_options.enableDP == 1 )
{
if ( input_options.readType == PAIR_END_READ )
for ( int threadId = 0; threadId < ini_params.Ini_NumOfCpuThreads; ++threadId )
{
resetReadInputForDP ( readInputForDPall.inputArrays[threadId] );
resetReadInputForDP ( readInputForNewDPall.inputArrays[threadId] );
resetReadInputForDP ( readAnsForNonValidInsert.inputArrays[threadId] );
}
resetBothUnalignedPairsArrays ( bothUnalignedPairsArrays );
}
// =======================================
// | BATCH PROCESS READ (GPU/GPU/CPU) |
// =======================================
char ** currOutputFileName = outputFileName;
samfile_t ** currSamOutputFilePtr = samOutputFilePtr;
// ========================================
// | IF THE INDEX IS NOT IN DEVICE, THEN |
// | COPY INDEX TO DEVICE MEMORY |
// ========================================
if ( indexLoadedToGPU == 0 )
{
GPUINDEXUpload ( index, &_bwt, &_occ,
&_revBwt, &_revOcc );
double copyTime = getElapsedTime ( startTime );
printf ( "[Main] Finished copying index into device (GPU).\n" );
printf ( "[Main] Loading time : %9.4f seconds\n\n", copyTime - lastEventTime );
lastEventTime = copyTime;
indexLoadedToGPU = 1;
}
//*******************************//
// Perform Alignment //
//*******************************//
if ( input_options.readType == PAIR_END_READ )
{
soap3_dp_pair_align ( queries, readLengths, input_options.numMismatch, wordPerQuery,
maxBatchSize, numQueries, accumReadNum,
index,
_bwt, _revBwt,
_occ, _revOcc,
ini_params, input_options,
maxReadLength, detected_read_length, detected_read_length2,
upkdQualities,
unAlignedPair, numOfUnAlignedPairs,
readIDs, upkdQueryNames,
currOutputFileName, currSamOutputFilePtr,
outputDPFileName, samOutputDPFilePtr,
samOutputUnpairFilePtr,
numOfAnswer, numOfAlignedRead,
&readInputForDPall, &readInputForNewDPall,
&readAnsForNonValidInsert,
bothUnalignedPairsArrays,
startTime, lastEventTime, totalAlignmentTime,
indexLoadedToGPU );
}
else
{
soap3_dp_single_align ( queries, readLengths, input_options.numMismatch, wordPerQuery,
maxBatchSize, numQueries, accumReadNum,
index, _bwt, _revBwt,
_occ, _revOcc,
ini_params, input_options,
maxReadLength, detected_read_length,
upkdQualities,
unAlignedPair, numOfUnAlignedPairs,
readIDs, upkdQueryNames,
currOutputFileName, currSamOutputFilePtr,
outputDPFileName, samOutputDPFilePtr,
numOfAnswer, numOfAlignedRead,
&readInputForDPall,
unalignedSinglesArrays,
startTime, lastEventTime, totalAlignmentTime,
indexLoadedToGPU );
}
// ========================================
// | GET NEXT BATCH OF READ |
// ========================================
totalReadsAlignedForInputReads += numOfAlignedRead;
totalAnsForInputReads += numOfAnswer;
accumReadNum += origNumQueries;
ResetBufferStatusToUnfilled ( aiob );
readyReadsBuffer = LoadReadsFromAIOBuffer ( aiob );
queries = readyReadsBuffer->queries;
readLengths = readyReadsBuffer->readLengths;
readIDs = readyReadsBuffer->readIDs;
upkdQualities = readyReadsBuffer->upkdQualities;
upkdQueryNames = readyReadsBuffer->upkdQueryNames;
isFastq = readyReadsBuffer->isFastq;
numQueries = readyReadsBuffer->filledNum;
// If the current opened file still have queries returned
// skip the code to process the result / open next file; and continue
if ( numQueries > 0 )
{
// Skip
continue;
}
// show the summary of the result and then load another pair of read files
// ======================================================================================
// | SHOW THE SUMMARY |
// ======================================================================================
if ( input_options.readType == PAIR_END_READ )
{
// printf("[Main] Overall number of pairs of reads aligned: %llu (number of alignments: %llu)\n", totalReadsAlignedForInputReads/2, totalAnsForInputReads);
printf ( "[Main] Overall number of pairs of reads aligned: %llu\n", totalReadsAlignedForInputReads / 2 );
}
else
{
// printf("[Main] Overall number of reads aligned: %llu (number of alignments: %llu)\n", totalReadsAlignedForInputReads, totalAnsForInputReads);
// printf("[Main] Overall number of unaligned reads: %llu\n", accumReadNum-totalReadsAlignedForInputReads);
printf ( "[Main] Overall number of reads aligned: %llu\n", totalReadsAlignedForInputReads );
printf ( "[Main] Overall number of unaligned reads: %llu\n", accumReadNum - totalReadsAlignedForInputReads );
}
printf ( "[Main] Overall read load time : %9.4f seconds\n", totalReadLoadTime );
printf ( "[Main] Overall alignment time (excl. read loading) : %9.4f seconds\n", totalAlignmentTime + totalTrimAlignmentTime );
// ======================================================================================
// | SHOW THE COMMAND FOR MERGING THE OUTPUT FILES INTO ONE |
// ======================================================================================
// update the output files
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_DEFAULT:
// update the header of the output files
outputDPFile = ( FILE * ) fopen ( outputDPFileName, "r+" );
if ( outputDPFile == NULL ) { fprintf ( stderr, "Cannot open outputFile %s\n", outputDPFileName ); exit ( 1 );}
fseek ( outputDPFile , 0 , SEEK_SET );
OCCWriteOutputHeader ( hsp, outputDPFile, maxReadLength, accumReadNum, input_options.outputFormat ); // update the number of reads
fclose ( outputDPFile );
break;
case SRA_OUTPUT_FORMAT_SAM_API:
samclose ( samOutputDPFilePtr );
break;
}
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_DEFAULT:
// update the header of the output files
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
outputFile = ( FILE * ) fopen ( outputFileName[i], "r+" );
if ( outputFile == NULL ) { fprintf ( stderr, "Cannot open outputFile %s\n", outputFileName[i] ); exit ( 1 );}
fseek ( outputFile , 0 , SEEK_SET );
OCCWriteOutputHeader ( hsp, outputFile, maxReadLength, accumReadNum, input_options.outputFormat ); // update the number of reads
fclose ( outputFile );
}
break;
case SRA_OUTPUT_FORMAT_SAM_API:
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
samclose ( samOutputFilePtr[i] );
}
break;
}
// For Unpaired reads
if ( input_options.readType == PAIR_END_READ )
{
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
samclose ( samOutputUnpairFilePtr );
break;
}
}
// create the done file
outputDoneFile = ( FILE * ) fopen ( outputDoneFileName, "w" );
if ( outputDoneFile == NULL )
{
fprintf ( stderr, "Could not create the output file %s\n",
outputDoneFileName );
}
fclose ( outputDoneFile );
free ( outputDoneFileName );
// release memory and close files
for ( i = 0; i < MAX_NUM_CPU_THREADS; i++ )
{ free ( outputFileName[i] ); }
free ( outputDPFileName );
free ( outputUnpairFileName );
if ( input_options.isReadBAM )
{
bam_close ( bamQueryFile );
bam_destroy1 ( bam );
}
else
{
gzclose ( gzQueryFile );
if ( input_options.readType == PAIR_END_READ )
{
gzclose ( gzQueryFile2 );
}
}
// ======================================================================================
// | Load the next set of files |
// ======================================================================================
if ( input_options.isReadList == 1 && currExp < expNum )
{
printf ( "\n[Main] Load the next set of files\n" );
updateInputOption ( ( &input_options ), multiInput, currExp++ );
queryFileName = input_options.queryFileName;
if ( input_options.readType == PAIR_END_READ && input_options.isReadBAM == 0 )
{
queryFileName2 = input_options.queryFileName2;
}
// Update the HSP information
hspaux->readGroup = input_options.readGroup;
if ( strlen ( hspaux->readGroup ) == 0 )
{ hspaux->readGroup = input_options.queryFileName; }
hspaux->sampleName = input_options.sampleName;
if ( strlen ( hspaux->sampleName ) == 0 )
{ hspaux->sampleName = DEFAULT_SAMPLE_NAME; }
hspaux->readGrpOption = input_options.readGrpOption;
// update the output files
for ( i = 0; i < MAX_NUM_CPU_THREADS; i++ )
{ outputFileName[i] = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 10 ); }
outputDPFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 9 );
outputUnpairFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 8 );
for ( i = 0; i < MAX_NUM_CPU_THREADS; i++ )
{
sprintf ( outputFileName[i], "%s.gout.%d", input_options.outputPrefix, i + 1 );
}
sprintf ( outputDPFileName, "%s.dpout.1", input_options.outputPrefix );
sprintf ( outputUnpairFileName, "%s.unpair", input_options.outputPrefix );
outputDoneFileName = ( char * ) malloc ( strlen ( input_options.outputPrefix ) + 6 );
sprintf ( outputDoneFileName, "%s.done", input_options.outputPrefix );
// initialize the output files
switch ( input_options.outputFormat )
{
case SRA_OUTPUT_FORMAT_SAM_API:
SAMOutputHeaderConstruct ( &samOutputHeader, hsp, hspaux, maxReadLength );
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
if ( input_options.isOutputBinary == 1 )
{ samOutputFilePtr[i] = samopen ( outputFileName[i], "wb", &samOutputHeader ); }
else
{ samOutputFilePtr[i] = samopen ( outputFileName[i], "wh", &samOutputHeader ); }
if ( samOutputFilePtr[i] == NULL )
{
fprintf ( stderr, "Could not open the output file %s\n", outputFileName[i] );
exit ( 1 );
}
}
break;
default:
for ( int i = 0; i < ini_params.Ini_NumOfCpuThreads; i++ )
{
outputFile = ( FILE * ) fopen ( outputFileName[i], "w" );
if ( outputFile == NULL ) { fprintf ( stderr, "Cannot open outputFile %s\n", outputFileName[i] ); exit ( 1 );}
OCCWriteOutputHeader ( hsp, outputFile, maxReadLength, 1, input_options.outputFormat ); // will modify the number of reads later