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GenABEL-Project / ProbABEL

Tool for genome-wide association analysis of imputed genetic data.
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Problem with reading gzipped dosage files #44

Open Sodbo opened 7 years ago

Sodbo commented 7 years ago

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

lckarssen commented 7 years ago

Thanks for reporting this! Excellent bug report!
I noticed you are running v1.58 of the Boost libraries. The most recent version in v1.64. Could you try and see if the bug is still present in that version?

lckarssen commented 7 years ago

Hi @Sodbo, hav eyou had time to see whether the issue persists after using a more recent version of the Boost libs?

odedor commented 5 years ago

Hi, I'm seeing the same issue, was it fixed? If so, from which version is it fixed?

lckarssen commented 5 years ago

@odedor I don't think this was fixed anywhere.

Unfortunately, we have not managed to secure any funding for ProbABEL maintenance and/or development, so we have had to stop working on it. Feel free to submit a patch or pull request with a fix if you manage to find a solution.