本文整理汇总了C++中KmerCounter::get_kmer_intval方法的典型用法代码示例。如果您正苦于以下问题：C++ KmerCounter::get_kmer_intval方法的具体用法？C++ KmerCounter::get_kmer_intval怎么用？C++ KmerCounter::get_kmer_intval使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类KmerCounter的用法示例。
在下文中一共展示了KmerCounter::get_kmer_intval方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: populate_kmer_counter
void populate_kmer_counter(KmerCounter &kcounter, string &kmers_fasta_file)
{
// code largely copied from IRKE.cpp
int i, myTid;
unsigned long sum,
*record_counter = new unsigned long[omp_get_max_threads()];
unsigned long start, end;
// init record counter
for (int i = 0; i < omp_get_max_threads(); i++) {
record_counter[i] = 0;
}
cerr << "-reading Kmer occurences..." << endl;
start = time(NULL);
Fasta_reader fasta_reader(kmers_fasta_file);
#pragma omp parallel private (myTid)
{
myTid = omp_get_thread_num();
record_counter[myTid] = 0;
while (true) {
Fasta_entry fe = fasta_reader.getNext();
if (fe.get_sequence() == "") break;
record_counter[myTid]++;
if (IRKE_COMMON::MONITOR) {
if (myTid == 0 && record_counter[myTid] % 100000 == 0) {
sum = record_counter[0];
for (i = 1; i < omp_get_num_threads(); i++)
sum += record_counter[i];
cerr << "\r [" << sum / 1000000 << "M] Kmers parsed. ";
}
}
string seq = fe.get_sequence();
if (seq.length() != KMER_SIZE) {
cerr << "ERROR: kmer " << seq << " is not of length: " << KMER_SIZE << endl;
continue;
}
kmer_int_type_t kmer = kcounter.get_kmer_intval(seq);
unsigned int count = atoi(fe.get_header().c_str());
kcounter.add_kmer(kmer, count);
}
}
end = time(NULL);
sum = record_counter[0];
for (i = 1; i < omp_get_max_threads(); i++)
sum += record_counter[i];
delete[] record_counter;
cerr << endl << " done parsing " << sum << " Kmers, " << kcounter.size() << " added, taking " << (end - start)
<< " seconds." << endl;
return;
}