root@max:/data/images/proton/DKlab/mr/parclip/bmix/nlopt-2.4.2# ./configure --enable-shared
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ LD_LIBRARY_PATH=/usr/local/lib
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ export LD_LIBRARY_PATH
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix$ R CMD INSTALL nloptr_1.0.4.tar.gz 
reczko@max:/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/source_R$ ./BMix ../test/CONFIG.txt 
../test/BMix_output/  created
Constructing mpileup file ...
Extracting mismatch information ...
../test/BMix_output/MismSummaries/  created
Output mismatch summary files opened in ../test/BMix_output/MismSummaries/
Classifying mismatches
../test/BMix_output/TC_Results/  created
Executing Rscript
[1] "../test/BMix_output/MismSummaries/" "../test/BMix_output/TC_Results/"   
[3] "5"                                  "0.95"                              
[5] "1"                                 
[1] "Estimated parameters:"
[1] "epsilon 0.001"
[1] "gamma 0.106025018001361"
[1] "nu 0.0080474838480915"
[1] "psi 0.422296623309176"
[1] "Estimated parameters:"
[1] "epsilon 0.0029154908599324"
[1] "gamma 0.145269909966978"
[1] "nu 0.00804172058596477"
[1] "psi 0.291050863933724"
Forming read groups ...
Reporting binding sites ...
../test/BMix_output/BindingSites/  created