Parsing issue

[jeanrjc]

Hello,

I encountered a typo in the doc and a bug in the parser that prevent cosi2 to run properly:

1. The <label> is missing in the doc for selective sweep. One should read (I believe):
   pop_event sweep <label> <pop> <Tend> <selection coefficient> <position of causal allele (0.0-1.0)> <freq at Tend>
   Otherwise it outputs the following error:

   orig seed=239239
   got seed239239
   orig seed=4069885732
   got seed4069885732
   genMap::readFrom - caught UNKNOWN exception of type NSt8ios_base7failureB5cxx11E demangled std::ios_base::failure[abi:cxx11] ; exception is basic_ios::clear: iostream error
   cosi error: ./cosi/file.cc(342): Throw in function int cosi::ParamFileReader::file_get_data(FILE*, FILE*)
   Dynamic exception type: boost::exception_detail::clone_impl<cosi::cosi_param_file_error>
   std::exception::what: std::exception
   [cosi::errinfo_param_name_*] = pop_event
   [cosi::errinfo_param_details_*] = sweep 1 0 0.001 0.5 0.5
   0, "Success"[boost::errinfo_at_line_*] = 9
   [boost::errinfo_file_name_*] = params_bug
   
   

2. the parameter file requires two newlines at the end of the file. The first example will work while the second won't:

   pop_define 1 my_pop
   pop_size 1 10000
   sample_size 1 50
   length 2000000
   
   mutation_rate 0.000000001
   recomb_file model.test
   
   pop_event sweep "sweep1" 1 0 0.001 0.5 0.5
   
   
   

   pop_define 1 my_pop
   pop_size 1 10000
   sample_size 1 50
   length 2000000
   
   mutation_rate 0.000000001
   recomb_file model.test
   
   pop_event sweep "sweep1" 1 0 0.001 0.5 0.5
   

   The latter produces the following error:

   orig seed=239239
   got seed239239
    sim 0 of 1
   orig seed=2451515636
   got seed2451515636
   genMap::readFrom - caught UNKNOWN exception of type NSt8ios_base7failureB5cxx11E demangled std::ios_base::failure[abi:cxx11] ; exception is basic_ios::clear: iostream error
   cosi error: ./cosi/file.cc(342): Throw in function int cosi::ParamFileReader::file_get_data(FILE*, FILE*)
   Dynamic exception type: boost::exception_detail::clone_impl<cosi::cosi_param_file_error>
   std::exception::what: std::exception
   [cosi::errinfo_param_name_*] = pop_event
   [cosi::errinfo_param_details_*] = sweep "sweep1" 1 0 0.001 0.5 0.5
   0, "Success"[boost::errinfo_at_line_*] = 9
   [boost::errinfo_file_name_*] = params_bug
   

Notice the similarity between the 2 error messages. The second error also occurs with other pop_event events.

I believe these are just a typo and a bug in the parser.

Best