ssize_t GCFS_ControlControl::write(const char* sBuffer, off_t uiOffset, size_t uiSize)
{
GCFS_Task* pTask = getParentTask();
if(!pTask)
return 0;
std::string value = GCFS_Utils::TrimStr(std::string(sBuffer, uiSize));
GCFS_Utils::keyValueArray_t vValues;
if(!GCFS_Utils::ParseConfigString((char*)value.c_str(), vValues))
return false;
// Check if commands/assignments exists
for(GCFS_Utils::keyValueArray_t::iterator it = vValues.begin(); it != vValues.end(); it++)
{
if(it->second)
{
// It is assignment
if(pTask->getConfigValue(it->first) == NULL)
return false;
}
else
{
bool bFound = false;
for (uint iIndex = 0; iIndex < m_vCommands.size(); iIndex ++)
if (strcasecmp(m_vCommands[iIndex], it->first) == 0)
{
bFound = true;
continue;
}
if(!bFound)
return false;
}
}
// Execute commands/assignments
for(GCFS_Utils::keyValueArray_t::iterator it = vValues.begin(); it != vValues.end(); it++)
{
if(it->second)
{
// It is assignment
if(pTask->getConfigValue(it->first)->write(it->second, 0, 0) <= 0)
return false;
}
else
{
for (uint iIndex = 0; iIndex < m_vCommands.size(); iIndex ++)
if (strcasecmp(m_vCommands[iIndex], it->first) == 0)
if(!executeCommand(pTask, iIndex))
return false;
}
}
return max(0, uiSize - uiOffset);
}
ssize_t GCFS_ControlStatus::read(std::string &sBuffer, off_t uiOffset, size_t uiSize)
{
GCFS_Task* pTask = getParentTask();
if(!pTask)
return 0;
GCFS_Service* pService = g_sConfig.GetService(pTask->m_pConfigDirectory->m_piService->get());
int status = (int)pService->getTaskStatus(pTask);
const std::string id = pService->getTaskId(pTask);
char cbuff[32];
snprintf(cbuff, ARRAYSIZE(cbuff), "%d\t%s", status, statuses[status]);
sBuffer = cbuff;
sBuffer += "\n"+id;
sBuffer += "\n";
return max(0, sBuffer.size() - uiOffset);
}
void ReadShortReadsSubTask::run() {
stateInfo.setProgress(0);
GTIMER(cvar, tvar, "ReadSubTask");
GenomeAlignerTask *parent = static_cast<GenomeAlignerTask*>(getParentTask());
if (!alignContext.bestMode) {
parent->pWriteTask->flush();
}
alignContext.cleanVectors();
dataBunch = new DataBunch();
if (isCanceled()) {
readingFinishedWakeAll();
return;
}
qint64 m = freeMemorySize;
taskLog.details(QString("Memory size is %1").arg(m));
bool alignReversed = settings.getCustomValue(GenomeAlignerTask::OPTION_ALIGN_REVERSED, true).toBool();
int qualityThreshold = settings.getCustomValue(GenomeAlignerTask::OPTION_QUAL_THRESHOLD, 0).toInt();
DNATranslation* transl = AppContext::getDNATranslationRegistry()->
lookupTranslation(BaseDNATranslationIds::NUCL_DNA_DEFAULT_COMPLEMENT);
alignContext.isReadingStarted = true;
bunchSize = 0;
int readNum = 0;
while(!seqReader->isEnd()) {
if (isCanceled()) {
readingFinishedWakeAll();
return;
}
SearchQuery *query = seqReader->read();
if (NULL == query) {
if (!seqReader->isEnd()) {
setError("Short-reads object type must be a sequence, but not a multiple alignment");
readingFinishedWakeAll();
return;
}
break;
}
++bunchSize;
if (!checkDnaQuality(query, qualityThreshold)) {
continue;
}
updateMinMaxReadLengths(alignContext, query->length());
int W = 0, q = 0;
int CMAX = alignContext.nMismatches;
if (!add(CMAX, W, q, readNum, query, parent)) {
delete query;
continue;
}
m -= query->memoryHint();
if (alignReversed) {
SearchQuery *rQu = createRevComplQuery(query, transl);
if (rQu) {
add(CMAX, W, q, readNum, rQu, parent);
m -= rQu->memoryHint();
}
}
qint64 alignContextMemoryHint = dataBunch->memoryHint();
if (m <= alignContextMemoryHint + prevMemoryHint) {
break;
}
SAFE_POINT(NULL != dataBunch, "No dataBunch",);
if (dataBunch->bitValuesV.size() > DROP_BUNCH_DATA_SIZE) {
dropToAlignContext();
readNum = 0;
alignContext.readShortReadsWait.wakeOne();
}
}
dropToAlignContext();
readingFinishedWakeAll();
}
}
}
#define GA_CHECK_BREAK(a) {if (!(a)) {algoLog.trace("Break because of ![" #a "]"); break;}}
#define GA_CHECK_CONTINUE(a) {if (!(a)) {algoLog.trace("Continue because of ![" #a "]"); continue;}}
ShortReadAlignerCPU::ShortReadAlignerCPU(int taskNo, GenomeAlignerIndex *i, AlignContext *s, GenomeAlignerWriteTask *w)
: Task("ShortReadAlignerCPU", TaskFlag_None), taskNo(taskNo), index(i), alignContext(s), writeTask(w)
{
}
void ShortReadAlignerCPU::run() {
SAFE_POINT_EXT (NULL != alignContext, setError("Align context error"),);
assert(!alignContext->openCL);
GenomeAlignerFindTask *parent = static_cast<GenomeAlignerFindTask*>(getParentTask());
SAFE_POINT_EXT(NULL != parent, setError("Aligner parent error"),);
QVector<int> binarySearchResults;
SAFE_POINT_EXT (NULL != index, setError("Aligner index error"),);
for (int part = 0; part < index->getPartCount(); part++) {
if (isCanceled()) {
break;
}
stateInfo.setProgress(100*part/index->getPartCount());
parent->requirePartForAligning(part);
if (parent->hasError()) {
break;
}
