void MPHFAlgorithm<span,Abundance_t,NodeState_t>::execute ()
{
/** We check whether we can use such a type. */
if (_buildOrLoad == true)
{
/** We need a progress object. */
tools::dp::IteratorListener* delegate = createIteratorListener(0,""); LOCAL (delegate);
setProgress (new ProgressCustom(delegate));
//if MPHF_BOOPHF and verbose 0, give a null progress to the builder, make it understand the internal progress bar of boophf needs to be removed
if((typeid(*delegate) == typeid(tools::dp::IteratorListener)))
setProgress (0);
// get number of threads from dispatcher
unsigned int nbThreads = this->getDispatcher()->getExecutionUnitsNumber();
/** We build the hash. */
{ TIME_INFO (getTimeInfo(), "build");
_abundanceMap->build (*_solidKmers, nbThreads, _progress);
}
/** We save the hash object in the dedicated storage group. */
{ TIME_INFO (getTimeInfo(), "save");
_dataSize = _abundanceMap->save (_group, _name);
}
/** We populate the hash table. */
populate ();
/** init a clean node state map */
initNodeStates ();
}
}
int main(int argc, char* argv[]) {
Option opt;
GetParameter(argc, argv, opt);
CReference refGenome;
CHashTable hashTable;
TIME_INFO(BuildIndex(opt, &refGenome, &hashTable), "Build index");
/* release memory*/
free(refGenome.refSeq);
free(hashTable.counter);
free(hashTable.index);
return 0;
}
MPHFAlgorithm<span,Abundance_t,NodeState_t>::MPHFAlgorithm (
Group& group,
const std::string& name,
Iterable<Count>* solidCounts,
Iterable<Type>* solidKmers,
unsigned int nbCores,
bool buildOrLoad,
IProperties* options
)
: Algorithm("mphf", nbCores, options), _group(group), _name(name), _buildOrLoad(buildOrLoad),
_dataSize(0), _nb_abundances_above_precision(0), _solidCounts(0), _solidKmers(0), _abundanceMap(0), _nodeStateMap(0), _adjacencyMap(0), _progress(0)
{
/** We keep a reference on the solid kmers. */
setSolidCounts (solidCounts);
/** We keep a reference on the solid kmers. */
setSolidKmers (solidKmers);
/** We build the hash object. */
setAbundanceMap (new AbundanceMap());
setNodeStateMap (new NodeStateMap());
setAdjacencyMap (new AdjacencyMap());
/** In case of load, we load the mphf and populate right now. */
if (buildOrLoad == false)
{
/** We load the hash object from the dedicated storage group. */
{ TIME_INFO (getTimeInfo(), "load");
_abundanceMap->load (_group, _name);
}
/** We populate the abundance hash table. */
populate ();
/** init a clean node state map */
initNodeStates ();
}
}
void ReadReads(const Option & opt, const CReference * refGenome,
const CHashTable * hashTable) {
FILE * fout = fopen(opt.outputFile.c_str(), "wb");
CRead * reads, *reads_rev;
CRegion * region;
char * strReads;
MEMORY_ALLOCATE_CHECK(
reads = (CRead *) malloc(MAX_MAPPING_READS * sizeof(CRead)));
MEMORY_ALLOCATE_CHECK(
reads_rev = (CRead *) malloc(MAX_MAPPING_READS * sizeof(CRead)));
MEMORY_ALLOCATE_CHECK(
region = (CRegion *) malloc(
MAX_MAPPING_READS * TOTAL_SHIFT_rev * sizeof(CRegion)));
/* read reads from the file*/
INFO("read reads from", opt.readsFile);
SIZE_T readsLen = ReadWholeFile(opt.readsFile, &strReads);
char strRead[MAX_LINE_LEN];
SIZE_T nReadsNum = 0;
SIZE_T readID = 0;
map < SIZE_T, SIZE_T > mapPosCount;
for (SIZE_T i = 0; i < readsLen; i++) {
SIZE_T len = GetLineFromString(&strReads[i], strRead);
i += len;
if (strRead[0] != '>' && len != 0) {
CHECK_READ_LEN(len, nReadsNum);
strcpy(reads[nReadsNum].readInStr, strRead);
reads[nReadsNum].readLen = len;
nReadsNum++;
}
if (nReadsNum == MAX_MAPPING_READS
|| (nReadsNum > 0 && i >= readsLen - 1)) {
Reverse_Kernel(reads, reads_rev, nReadsNum);
SIZE_T NUM = TOTAL_SHIFT_rev * nReadsNum;
TIME_INFO(
Match_Kernel(refGenome, hashTable, reads, reads_rev, region, NUM),
"match time");
for (SIZE_T i = 0; i < NUM; i++) {
for (SIZE_T j = region[i].lower; j <= region[i].upper; j++) {
mapPosCount[hashTable->index[j] - i % TOTAL_SHIFT]++;
}
if ((i + 1) % TOTAL_SHIFT == 0) {
for (map<SIZE_T, SIZE_T>::iterator it = mapPosCount.begin();
it != mapPosCount.end(); it++) {
if (it->second > 1) {
fprintf(fout, "read %d: %d %d\n", i / TOTAL_SHIFT_rev, it->first,
it->second);
}
}
mapPosCount.clear();
}
}
readID += nReadsNum;
nReadsNum = 0;
}
}
fclose(fout);
free(strReads);
free(reads);
free(region);
}
static void migrate_exit(void)
{
hrtimer_cancel(&migrate_hrtimer);
TIME_INFO();
}
