static SearchQuery* createRevComplQuery(SearchQuery* query, DNATranslation* transl) {
SAFE_POINT(query != NULL, "Query is null", NULL);
SAFE_POINT(transl != NULL, "Transl is null", NULL);
QByteArray reversed(query->constSequence());
TextUtils::reverse(reversed.data(), reversed.count());
DNASequence dnaSeq(QString("%1_rev").arg(query->getName()), reversed, NULL);
SearchQuery *rQu = new SearchQuery(&dnaSeq, query);
transl->translate(const_cast<char*>(rQu->constData()), rQu->length());
if (rQu->constSequence() == query->constSequence()) {
delete rQu; rQu = NULL;
return NULL;
}
query->setRevCompl(rQu);
return rQu;
}
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();
}