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thread.h
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thread.h
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#ifndef THREAD_H
#define THREAD_H
#include "constants.h"
#include "parameters.h"
#include "tree2.h"
#include "fastq.h"
#include "main.h"
#define THREAD_BYTES_STEP 0x100000
#define THREAD_CELLID_STEP 0x100
/**
* Data which are given to the mapping threads
* tree: the reads tree
* samFile: the name of the output sam file
* firstCellId: the id of the first cell scanned by this thread at depth TREE_BASE_SIZE (included)
* lastCellId: the id of the last cell scanned by this thread at depth TREE_BASE_SIZE (included)
*/
typedef struct {
tree_t *tree;
unsigned int fileId;
char *fastqFileName;
FILE *fastqFile;
pthread_mutex_t *incMutex;
} readingThreadParameters_t;
typedef struct {
tree2_t *tree;
FILE **samFiles;
char threadId;
pthread_mutex_t *incMutex;
pthread_mutex_t *writeMutex;
} mappingThreadParameters_t;
typedef struct {
tree_t *tree1;
tree_t *tree2;
} mergeThreadParameters_t;
typedef struct {
pthread_t *threads;
} thread_t;
unsigned int threadStep;
void createThreads (thread_t *threads) {
threads->threads = (pthread_t *) mallocOrDie((parameters->nThreads-1) * sizeof(pthread_t));
}
void freeThreads (thread_t *threads) {
free(threads->threads);
}
void printProgress () {
unsigned int progress = threadStep * THREAD_CELLID_STEP * 100 / N_TREE_BASE;
if (progress <= 100) {
fprintf(stderr, "Progress: %u%%\r", progress);
}
}
void updateBounds (uint64_t *firstCellId, uint64_t *lastCellId, unsigned long step, pthread_mutex_t *incMutex, bool mappingStep) {
pthread_mutex_lock(incMutex);
*firstCellId = threadStep * step;
*lastCellId = (threadStep + 1) * step - 1;
if (mappingStep) {
printProgress();
}
++threadStep;
pthread_mutex_unlock(incMutex);
}
void *mergingThreadMain (void *parametersVoid) {
mergeThreadParameters_t *parameters = (mergeThreadParameters_t *) parametersVoid;
mergeTree(parameters->tree1, parameters->tree2);
return NULL;
}
void startMergingThreads (thread_t *threads, tree_t *mainTree, tree_t *otherTrees) {
unsigned int nTrees = parameters->nThreads;
unsigned int nMerges = nTrees / 2;
mergeThreadParameters_t *threadParameters = (mergeThreadParameters_t *) mallocOrDie(nMerges * sizeof(mergeThreadParameters_t));
tree_t **allTrees = (tree_t **) mallocOrDie((parameters->nThreads) * sizeof(tree_t *));
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
allTrees[threadId+1] = &otherTrees[threadId];
}
allTrees[0] = mainTree;
while (nTrees != 1) {
for (unsigned int threadId = 0; threadId < nMerges; ++threadId) {
threadParameters[threadId].tree1 = allTrees[threadId*2];
threadParameters[threadId].tree2 = allTrees[threadId*2+1];
if (pthread_create(&threads->threads[threadId], NULL, mergingThreadMain, (void *) &threadParameters[threadId]) != 0) {
fprintf(stderr, "Error! Thread %u cannot be created.\nExiting.\n", threadId);
exit(EXIT_FAILURE);
}
}
for (unsigned int threadId = 0; threadId < nMerges; ++threadId) {
pthread_join(threads->threads[threadId], NULL);
}
nTrees = nMerges + (nTrees & 1);
for (unsigned int threadId = 0; threadId < nTrees; ++threadId) {
allTrees[threadId] = allTrees[2*threadId];
}
nMerges = nTrees / 2;
}
free(allTrees);
free(threadParameters);
}
void *readingThreadMain (void *parametersVoid) {
//printf("Preparing thread...\n"); fflush(stdout);
readingThreadParameters_t *parameters = (readingThreadParameters_t *) parametersVoid;
uint64_t posStart, posEnd;
bool stillData = true;
updateBounds(&posStart, &posEnd, THREAD_BYTES_STEP, parameters->incMutex, false);
while (stillData) {
//printf("Starting thread %" PRIu32 "-%" PRIu32 ": ", firstCellId, lastCellId);
//printSequence(firstCellId, TREE_BASE_SIZE);
//printf("-");
//printSequence(lastCellId, TREE_BASE_SIZE);
//printf("\n");
//fflush(stdout);
stillData = readReadsFile(parameters->fastqFile, parameters->fastqFileName, parameters->tree, parameters->fileId, posStart, posEnd);
//printf("Ending thread %" PRIu32 "-%" PRIu32 " at depth %zu with cell #%" PRIu32 "\n", parameters->firstCellId, parameters->lastCellId, path->nCells, path->cellIds[path->nCells]); fflush(stdout);
updateBounds(&posStart, &posEnd, THREAD_BYTES_STEP, parameters->incMutex, false);
}
return NULL;
}
void startReadingThreads (thread_t *threads, tree_t *tree, FILE **fastqFiles) {
pthread_mutex_t incMutex = PTHREAD_MUTEX_INITIALIZER;
tree_t *trees = (tree_t *) mallocOrDie((parameters->nThreads-1) * sizeof(tree_t));
readingThreadParameters_t *threadParameters = (readingThreadParameters_t *) mallocOrDie(parameters->nThreads * sizeof(readingThreadParameters_t));
if (pthread_mutex_init(&incMutex, NULL) != 0) {
fprintf(stderr, "Error! Cannot initialize mutex.\nExiting.\n");
exit(EXIT_FAILURE);
}
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
createTree(&trees[threadId]);
threadParameters[threadId].tree = &trees[threadId];
threadParameters[threadId].incMutex = &incMutex;
}
// last thread parameter is for the main thread
threadParameters[parameters->nThreads-1].tree = tree;
threadParameters[parameters->nThreads-1].incMutex = &incMutex;
//printf("Got %u threads\n", parameters->nThreads); fflush(stdout);
for (size_t fileId = 0; fileId < parameters->nReadsFiles; ++fileId) {
fprintf(stderr, "Reading file '%s'...\n", parameters->readsFileNames[fileId]);
threadStep = 0;
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
threadParameters[threadId].fastqFileName = parameters->readsFileNames[fileId];
threadParameters[threadId].fastqFile = fopen(parameters->readsFileNames[fileId], "r");
threadParameters[threadId].fileId = fileId;
if (pthread_create(&threads->threads[threadId], NULL, readingThreadMain, (void *) &threadParameters[threadId]) != 0) {
fprintf(stderr, "Error! Thread %u cannot be created.\nExiting.\n", threadId);
exit(EXIT_FAILURE);
}
}
// Use the main thread too
threadParameters[parameters->nThreads-1].fastqFileName = parameters->readsFileNames[fileId];
threadParameters[parameters->nThreads-1].fastqFile = fastqFiles[fileId];
threadParameters[parameters->nThreads-1].fileId = fileId;
readingThreadMain((void *) &threadParameters[parameters->nThreads-1]);
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
pthread_join(threads->threads[threadId], NULL);
fclose(threadParameters[threadId].fastqFile);
}
fprintf(stderr, "... done.\n");
}
// merge all trees to the main tree
if (parameters->nThreads > 1) {
startMergingThreads (threads, tree, trees);
}
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
freeTree(&trees[threadId]);
}
free(trees);
free(threadParameters);
pthread_mutex_destroy(&incMutex);
}
void *mappingThreadMain (void *parametersVoid) {
//printf("Preparing thread...\n"); fflush(stdout);
mappingThreadParameters_t *parameters = (mappingThreadParameters_t *) parametersVoid;
states_t *states = initializeStates(parameters->tree->depth);
path_t *path = initializePath(parameters->tree->depth);
uint64_t firstCellId;
uint64_t lastCellId;
cellVisitor_t cellVisitor;
outputSam_t outputSam;
outputSam.outputFiles = parameters->samFiles;
createOutputSam(&outputSam, parameters->tree->depth, parameters->writeMutex, parameters->threadId);
updateBounds(&firstCellId, &lastCellId, THREAD_CELLID_STEP, parameters->incMutex, true);
clearCellVisitor(&cellVisitor);
while (firstCellId <= N_TREE_BASE) {
//printf("Starting thread %" PRIu32 "-%" PRIu32 ": ", firstCellId, lastCellId);
//printSequence(firstCellId, TREE_BASE_SIZE);
//printf("-");
//printSequence(lastCellId, TREE_BASE_SIZE);
//printf("\n");
//fflush(stdout);
//TODO: Should work without next line
//clearCellVisitor(&cellVisitor, ¶meters->tree->cellInfos);
clearStates(states);
clearPath(path);
_map(parameters->tree, states, path, &cellVisitor, firstCellId, lastCellId, &outputSam);
writeToSam(&outputSam, true);
//printf("Ending thread %" PRIu32 "-%" PRIu32 " at depth %zu with cell #%" PRIu32 "\n", parameters->firstCellId, parameters->lastCellId, path->nCells, path->cellIds[path->nCells]); fflush(stdout);
updateBounds(&firstCellId, &lastCellId, THREAD_CELLID_STEP, parameters->incMutex, true);
}
freeOutputSam(&outputSam);
freeStates(states);
freePath(path);
return NULL;
}
void startMappingThreads (thread_t *threads, tree2_t *tree, FILE **samFiles) {
pthread_mutex_t incMutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_t writeMutex = PTHREAD_MUTEX_INITIALIZER;
mappingThreadParameters_t *threadParameters = (mappingThreadParameters_t *) mallocOrDie(parameters->nThreads * sizeof(mappingThreadParameters_t));
if (pthread_mutex_init(&incMutex, NULL) != 0) {
fprintf(stderr, "Error! Cannot initialize mutex.\nExiting.\n");
exit(EXIT_FAILURE);
}
if (pthread_mutex_init(&writeMutex, NULL) != 0) {
fprintf(stderr, "Error! Cannot initialize mutex.\nExiting.\n");
exit(EXIT_FAILURE);
}
for (unsigned int threadId = 0; threadId < parameters->nThreads; ++threadId) {
threadParameters[threadId].tree = tree;
threadParameters[threadId].samFiles = samFiles;
threadParameters[threadId].incMutex = &incMutex;
threadParameters[threadId].writeMutex = &writeMutex;
threadParameters[threadId].threadId = 'A' + threadId;
}
threadStep = 0;
//printf("Got %u threads\n", parameters->nThreads); fflush(stdout);
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
if (pthread_create(&threads->threads[threadId], NULL, mappingThreadMain, (void *) &threadParameters[threadId]) != 0) {
fprintf(stderr, "Error! Thread %u cannot be created.\nExiting.\n", threadId);
exit(EXIT_FAILURE);
}
}
// Use the main thread too
mappingThreadMain((void *) &threadParameters[parameters->nThreads-1]);
for (unsigned int threadId = 0; threadId < parameters->nThreads-1; ++threadId) {
pthread_join(threads->threads[threadId], NULL);
}
//pthread_exit(NULL);
free(threadParameters);
pthread_mutex_destroy(&incMutex);
pthread_mutex_destroy(&writeMutex);
fprintf(stderr, "\n");
}
#endif