I ran ProbABEL using palinear (which was compiled from read-gzipped-genotypes branch) to conduct GWAS using gzipped DOSAGE file. (please find attached gaussian_probabel_error.txt)
While reading gunzipped DOSAGE file, ProbABEL terminated with following error log:
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::iostreams::gzip_error> >' what(): gzip error: iostream error Aborted (core dumped)
I wrote simple code read_gz.cpp (attached) which reproduces what ProbABEL's gendata.cpp does. This script ends up with same error on same DOSAGE gzipped. Moreover, I found, that error pops up after reading last line of DOSAGE file.
My suggestion is that this error can be referred to the known bug in C++ Boost library
https://svn.boost.org/trac/boost/ticket/6994
Users have provided patch for zlib.cpp from BOOST library which solve the problem.
Thus, usage of ProbABEL-read-gzipped-files is limited due to the bug in BOOST library.
I was able to patch zlib.cpp after which read_gz.cpp started work well om DOSAGE gzipped file.
But it takes too much efforts from my side to try to compile ProbABEL with patched boost library, as ProbABEL uses automake (or whatever).
read_gz.cpp.txt
gaussian_probabel_error.txt
I ran ProbABEL using palinear (which was compiled from read-gzipped-genotypes branch) to conduct GWAS using gzipped DOSAGE file. (please find attached gaussian_probabel_error.txt)
While reading gunzipped DOSAGE file, ProbABEL terminated with following error log:
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::iostreams::gzip_error> >' what(): gzip error: iostream error Aborted (core dumped)I wrote simple code read_gz.cpp (attached) which reproduces what ProbABEL's gendata.cpp does. This script ends up with same error on same DOSAGE gzipped. Moreover, I found, that error pops up after reading last line of DOSAGE file.
My suggestion is that this error can be referred to the known bug in C++ Boost library
https://svn.boost.org/trac/boost/ticket/6994
Users have provided patch for zlib.cpp from BOOST library which solve the problem.
Thus, usage of ProbABEL-read-gzipped-files is limited due to the bug in BOOST library.
I was able to patch zlib.cpp after which read_gz.cpp started work well om DOSAGE gzipped file.
But it takes too much efforts from my side to try to compile ProbABEL with patched boost library, as ProbABEL uses automake (or whatever).
read_gz.cpp.txt
gaussian_probabel_error.txt