LargeCount VerticesExtractor::getDefaultNumberOfBitsForBloomFilter(){
/*
* This is the product of these values:
*
* * Number of sequences on the rank;
* * K-mer length;
* * Number of strands (2);
* * Number of directions in one dimension (2);
*/
int numberOfErrorsPerRead = 4;
int erroneousKmersPerError = m_parameters->getWordSize() * 2 * 2;
// the formula below is completely arbitrary.
// for serious cases, you should do an initial run
// and then you should modify -bloom-filter-bits
// furthermore, this formula does not consider
// the true kmers in the genome
int numberOfLocalReads = m_myReads->size();
int bits = numberOfErrorsPerRead * erroneousKmersPerError * numberOfLocalReads;
return bits;
}
Solution: add a maximum number of bits (let's say something like 1 GiB).
Link: http://permalink.gmane.org/gmane.science.biology.ray-genome-assembler/619
The code:
Solution: add a maximum number of bits (let's say something like 1 GiB).