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Trying to get rid of some inlining warnings
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@milot-mirdita
milot-mirdita committed Jan 28, 2019
1 parent f17bcd2 commit 74fa1b1
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Showing 3 changed files with 30 additions and 46 deletions.
7 changes: 4 additions & 3 deletions lib/simd/simd.h
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Expand Up @@ -534,9 +534,10 @@ inline F simd_hmin(const F * in, unsigned int n)
inline void *mem_align(size_t boundary, size_t size)
{
void *pointer;
if (posix_memalign(&pointer,boundary,size) != 0)
{
std::cerr<<"Error: Could not allocate memory by memalign. Please report this bug to developers\n";
if (posix_memalign(&pointer, boundary, size) != 0) {
#define MEM_ALIGN_ERROR "mem_align could not allocate memory.\n"
fwrite(MEM_ALIGN_ERROR, sizeof(MEM_ALIGN_ERROR), 1, stderr);
#undef MEM_ALIGN_ERROR
exit(3);
}
return pointer;
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65 changes: 26 additions & 39 deletions src/alignment/Alignment.cpp
View file
Expand Up @@ -276,7 +276,14 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex,
// get the prefiltering list
char *data = prefdbr->getData(id, thread_idx);
unsigned int queryDbKey = prefdbr->getDbKey(id);
setQuerySequence(qSeq, id, queryDbKey, thread_idx);
char *querySeqData = qdbr->getDataByDBKey(queryDbKey, thread_idx);
if (querySeqData == NULL) {
Debug(Debug::ERROR) << "ERROR: Query sequence " << queryDbKey
<< " is required in the prefiltering, but is not contained in the query sequence database.\nPlease check your database.\n";
EXIT(EXIT_FAILURE);
}

qSeq.mapSequence(id, queryDbKey, querySeqData);

matcher.initQuery(&qSeq);
// parse the prefiltering list and calculate a Smith-Waterman alignment for each sequence in the list
Expand All @@ -302,7 +309,12 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex,
diagonal = hit.diagonal;
}

setTargetSequence(dbSeq, dbKey, thread_idx);
char *dbSeqData = tdbr->getDataByDBKey(dbKey, thread_idx);
if (dbSeqData == NULL) {
Debug(Debug::ERROR) << "ERROR: Sequence " << dbKey <<" is required in the prefiltering, but is not contained in the target sequence database!\nPlease check your database.\n";
EXIT(EXIT_FAILURE);
}
dbSeq.mapSequence(static_cast<size_t>(-1), dbKey, dbSeqData);
// check if the sequences could pass the coverage threshold
if(Util::canBeCovered(canCovThr, covMode, static_cast<float>(qSeq.L), static_cast<float>(dbSeq.L)) == false )
{
Expand Down Expand Up @@ -342,7 +354,12 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex,
if (realign == true) {
realigner->initQuery(&qSeq);
for (size_t result = 0; result < swResults.size(); result++) {
setTargetSequence(dbSeq, swResults[result].dbKey, thread_idx);
char *dbSeqData = tdbr->getDataByDBKey(swResults[result].dbKey, thread_idx);
if (dbSeqData == NULL) {
Debug(Debug::ERROR) << "ERROR: Sequence " << swResults[result].dbKey <<" is required in the prefiltering, but is not contained in the target sequence database!\nPlease check your database.\n";
EXIT(EXIT_FAILURE);
}
dbSeq.mapSequence(static_cast<size_t>(-1), swResults[result].dbKey, dbSeqData);
const bool isIdentity = (queryDbKey == swResults[result].dbKey && (includeIdentity || sameQTDB)) ? true : false;
Matcher::result_t res = realigner->getSWResult(&dbSeq, INT_MAX, false, covMode, covThr, FLT_MAX,
Matcher::SCORE_COV_SEQID, seqIdMode, isIdentity);
Expand Down Expand Up @@ -400,41 +417,6 @@ void Alignment::run(const std::string &outDB, const std::string &outDBIndex,
Debug(Debug::INFO) << hits_f << " hits per query sequence.\n";
}

inline void Alignment::setQuerySequence(Sequence &seq, size_t id, unsigned int key, int thread_idx) {

// map the query sequence
char *querySeqData = qdbr->getDataByDBKey(key, thread_idx);
if (querySeqData == NULL) {
#pragma omp critical
{
Debug(Debug::ERROR) << "ERROR: Query sequence " << key
<< " is required in the prefiltering, "
<< "but is not contained in the query sequence database!\n"
<< "Please check your database.\n";
EXIT(EXIT_FAILURE);
}
}

seq.mapSequence(id, key, querySeqData);
}

inline void Alignment::setTargetSequence(Sequence &seq, unsigned int key, int thread_idx) {

char *dbSeqData = tdbr->getDataByDBKey(key, thread_idx);
if (dbSeqData == NULL) {
#pragma omp critical
{
Debug(Debug::ERROR) << "ERROR: Sequence " << key
<< " is required in the prefiltering,"
<< "but is not contained in the target sequence database!\n"
<< "Please check your database.\n";
EXIT(EXIT_FAILURE);
}
}
seq.mapSequence(static_cast<size_t>(-1), key, dbSeqData);
}


size_t Alignment::estimateHDDMemoryConsumption(int dbSize, int maxSeqs) {
return 2 * (dbSize * maxSeqs * 21 * 1.75);
}
Expand Down Expand Up @@ -473,7 +455,12 @@ void Alignment::computeAlternativeAlignment(unsigned int queryDbKey, Sequence &d
if (isIdentity == true) {
continue;
}
setTargetSequence(dbSeq, swResults[i].dbKey, thread_idx);
char *dbSeqData = tdbr->getDataByDBKey(swResults[i].dbKey, thread_idx);
if (dbSeqData == NULL) {
Debug(Debug::ERROR) << "ERROR: Sequence " << swResults[i].dbKey <<" is required in the prefiltering, but is not contained in the target sequence database!\nPlease check your database.\n";
EXIT(EXIT_FAILURE);
}
dbSeq.mapSequence(static_cast<size_t>(-1), swResults[i].dbKey, dbSeqData);
for (int pos = swResults[i].dbStartPos; pos < swResults[i].dbEndPos; ++pos) {
dbSeq.int_sequence[pos] = xIndex;
}
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4 changes: 0 additions & 4 deletions src/alignment/Alignment.h
View file
Expand Up @@ -112,10 +112,6 @@ class Alignment {

void initSWMode(unsigned int alignmentMode);

void setQuerySequence(Sequence &seq, size_t id, unsigned int key, int thread_idx);

void setTargetSequence(Sequence &seq, unsigned int key, int thread_idx);

static size_t estimateHDDMemoryConsumption(int dbSize, int maxSeqs);

void computeAlternativeAlignment(unsigned int queryDbKey, Sequence &dbSeq,
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