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Commit 8bcb0cfe authored by Veronique Legrand's avatar Veronique Legrand
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chose a more explicit name for max cms size class member

parent 5e57df4f
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......@@ -24,7 +24,7 @@ typedef struct {
int lambda;
int kappa;
int kappa_prime;
int filter_size; // max amount of RAM wanted for the CMS.
int max_filter_size; // max amount of RAM wanted for the CMS.
int filter_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).
......
......@@ -60,6 +60,7 @@ class ROCKparams{
vector<PE_files> v_PE_files;
int f_id;
unsigned long cms_size;
//unsigned long total_machine_RAM;
float expected_collision_proba;
......@@ -109,14 +110,17 @@ public:
cms_size=0;
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) throw EXIT_FAILURE;
//total_machine_RAM=getNodePhysMemory();
parms.max_filter_size=getNodePhysMemory()/100.0*90-defaultGRPMAXSize; // Prefer not to use all the machine's memory
if (parms.max_filter_size==0) throw EXIT_FAILURE;
}
void initFromMainOptsArgs(int argc,char ** argv);
CMSparams getCMSparams() const {
return parms;
}
......
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