intfilter_size;// max amount of RAM wanted for the CMS.
intmax_filter_size;// max amount of RAM wanted for the CMS.
intfilter_PE_separately;// indicates whether PE reads must be treated as single by the cms. Indeed it may appear that 1 end contains useful k-mer but that other end contains k-mer such that "global" median is below threshold.
// In this case, read is rejected by the CMS (default behavior). We want to do an experimentation to see if keeping such reads wold lead to better results in assembling.
// Values can be 0 (process PE as single),1 (process PE separately with strict implementation for kappa_prime) or 2 (process PE separately with lenient implementation for kappa prime).
expected_collision_proba=0.0;//! collision probability that is computed at the beginning of ROCK from the expected number of distinct k-mers provided by the user.
//min_correct_k_mers_in_read=0;
parms.filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize;// Prefer not to use all the machine's memory
if(parms.filter_size==0)throwEXIT_FAILURE;
//total_machine_RAM=getNodePhysMemory();
parms.max_filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize;// Prefer not to use all the machine's memory