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Final version of two BMC Bioinformatics papers

My two latest BMC Bioinformatics papers are now available in their final form (before they were just there as preliminary PDFs).
The first is on the file format that I’ve blogged about earlier, while the second is an algorithmic paper from APBC’09.
SNPFile – A software library and file format for large scale association mapping and population genetics studies
J. Nielsen and T. Mailund
BMC Bioinformatics 2008, 9:526; doi:10.1186/1471-2105-9-526
A fast algorithm for genome wide haplotype pattern mining
S. Besenbacher, C.N.S. Pedersen and T. Mailund
BMC Bioinformatics, 10(Suppl 1): S74 doi:10.1186/1471-2105-10-S1-S74
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This entry was posted on Saturday, January 31st, 2009 at 6:45 pm and is filed under Research. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

5 Responses to “Final version of two BMC Bioinformatics papers”

  1. Pierre Says:
    April 26th, 2010 at 1:28 pm

    Hi thomas,
    FYI: SNPFile2.0.1 failed to compile under ubuntu 9.
    I had to insert

    #include

    at the top of

    archives.hh

    to make the compilation unit work again

    Best regards,
    Pierre

  2. Thomas Mailund Says:
    April 26th, 2010 at 1:32 pm

    Sorry to hear that. Not that I am surprised, I am not always careful enough to get the right header files included according to the standard, so quite often my code relies on recursive inclusion to compile :-S

  3. Pierre Says:
    April 26th, 2010 at 1:41 pm

    No problem :-)

    Hops, sorry, the HTML was not escaped, the header was boost/cstdint.hpp

    I compiled snpFile with configure –prefix=${HOME}/tmp
    now, I’m trying to compile hapcluster-2.3.0 but it said it cannot find the SNPfile library. (I tried to set the LD_LIBRARY_PATH or LDFLAGS). Do you know how can I fix this ?
    Many thanks

    Pierre

  4. Thomas Mailund Says:
    April 26th, 2010 at 1:45 pm

    I’m not quite sure, but if I recall correctly you want to set LDFLAGS, CPPFLAGS and/or CXXFLAGS to point to the right directories (with -I and -L flags) before running the configure script. Then the script should find it. If you only set LDFLAGS it can probably find the libraries but not the header files, and then that is what it is complaining about…

  5. Pierre Says:
    April 26th, 2010 at 1:50 pm

    Thanks, I’ll try this
    if it still fails I will install it normally in /usr/…
    Thanks again

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