Skip to content
Snippets Groups Projects
Commit 59f1d08c authored by Veronique Legrand's avatar Veronique Legrand
Browse files

fixed compilation issue

parent 68a5e8ef
No related branches found
No related tags found
No related merge requests found
......@@ -258,6 +258,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
std::vector<string> v_input_lines;
std::vector<string> v_output_lines;
static int PE_separately=1;
float proba=k_max_collision_proba;
while((i = getopt(argc, argv, "i:o:l:k:c:C:n:vq:m:f:")) != -1) {
switch(i) {
......@@ -268,7 +269,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
case 'c':
parms.kappa_prime=atoi(optarg);break;
case 'f':
float proba=atof(optarg);
proba=atof(optarg);
if ((proba<=0.0) or (proba>=1.0)) {
cout<<"maximum for collision probability in the CMS must be > 0.0 and <1.0."<<endl;
usage(EXIT_FAILURE);
......@@ -319,7 +320,6 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
cout<<"minimum number of valid k-mer for keeping a read must be an integer >=1"<<endl;
usage(EXIT_FAILURE);
}
qual_thres.min_correct_k_mers_in_read=atoi(optarg);
break;
default:
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment