diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp index 57f11c01b9ebbf8802715fc87792ee808fbb9967..a7d496dfa9745acab1436fac765ef9548d783185 100755 --- a/src/ROCKparams.cpp +++ b/src/ROCKparams.cpp @@ -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: