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Commit ac660f2f authored by Veronique Legrand's avatar Veronique Legrand
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fixed compilation issue

parent c67a3dde
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...@@ -258,6 +258,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) { ...@@ -258,6 +258,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
std::vector<string> v_input_lines; std::vector<string> v_input_lines;
std::vector<string> v_output_lines; std::vector<string> v_output_lines;
static int PE_separately=1; 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) { while((i = getopt(argc, argv, "i:o:l:k:c:C:n:vq:m:f:")) != -1) {
switch(i) { switch(i) {
...@@ -268,7 +269,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) { ...@@ -268,7 +269,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
case 'c': case 'c':
parms.kappa_prime=atoi(optarg);break; parms.kappa_prime=atoi(optarg);break;
case 'f': case 'f':
float proba=atof(optarg); proba=atof(optarg);
if ((proba<=0.0) or (proba>=1.0)) { if ((proba<=0.0) or (proba>=1.0)) {
cout<<"maximum for collision probability in the CMS must be > 0.0 and <1.0."<<endl; cout<<"maximum for collision probability in the CMS must be > 0.0 and <1.0."<<endl;
usage(EXIT_FAILURE); usage(EXIT_FAILURE);
...@@ -319,7 +320,6 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) { ...@@ -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; cout<<"minimum number of valid k-mer for keeping a read must be an integer >=1"<<endl;
usage(EXIT_FAILURE); usage(EXIT_FAILURE);
} }
qual_thres.min_correct_k_mers_in_read=atoi(optarg); qual_thres.min_correct_k_mers_in_read=atoi(optarg);
break; break;
default: default:
......
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