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Commits on Sep 30, 2014
  1. markdown-ize README

    Chris Fields committed Sep 30, 2014
Commits on Aug 17, 2009
  1. moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got th…

    …em compiling cleanly. tests not passing yet
    
    svn path=/bioperl-ext/trunk/; revision=15966
    rbuels committed Aug 17, 2009
Commits on Aug 16, 2009
  1. use UPPPER_TOL to catch the case when the expectation maximization step

    appears to be decreasing. This should make it very unlikely to 
    throw exception
    
    svn path=/bioperl-ext/trunk/; revision=15948
    ymc committed Aug 16, 2009
  2. fixed Vitebi typo

    svn path=/bioperl-ext/trunk/; revision=15947
    ymc committed Aug 16, 2009
  3. Fixed the typemap and also a memory bug in viterbi function in HMM.xs

    svn path=/bioperl-ext/trunk/; revision=15942
    ymc committed Aug 16, 2009
Commits on Feb 21, 2009
  1. adding FEEDBACK:Support section to pod

    svn path=/bioperl-ext/trunk/; revision=15553
    maj committed Feb 21, 2009
Commits on Jan 5, 2009
  1. Bump to 1.007 (similar to trunk)

    svn path=/bioperl-ext/trunk/; revision=15297
    cjfields committed Jan 5, 2009
Commits on Nov 26, 2008
  1. ext patches (courtesy Thomas Jahns)

    svn path=/bioperl-ext/trunk/; revision=15030
    cjfields committed Nov 26, 2008
Commits on Sep 1, 2008
  1. get rid of some unended comment warnings from C compiler

    svn path=/bioperl-ext/trunk/; revision=14843
    hyphaltip committed Sep 1, 2008
  2. -fPIC needed for lib construction

    svn path=/bioperl-ext/trunk/; revision=14842
    hyphaltip committed Sep 1, 2008
  3. include errno definition

    svn path=/bioperl-ext/trunk/; revision=14841
    hyphaltip committed Sep 1, 2008
Commits on Aug 2, 2008
  1. removed DEBUG=1

    svn path=/bioperl-ext/trunk/; revision=14781
    ymc committed Aug 2, 2008
  2. IUPAC DNA support

    svn path=/bioperl-ext/trunk/; revision=14779
    ymc committed Aug 2, 2008
  3. IUPAC DNA test case

    svn path=/bioperl-ext/trunk/; revision=14778
    ymc committed Aug 2, 2008
Commits on Feb 5, 2008
  1. Add some helper code and tests to demo evalue oddities (bug 1857); ca…

    …sting issue?
    
    svn path=/bioperl-ext/trunk/; revision=14492
    cjfields committed Feb 5, 2008
Commits on Feb 4, 2008
  1. Add cast to correct pointer type (get rid of warnings)

    svn path=/bioperl-ext/trunk/; revision=14476
    cjfields committed Feb 4, 2008
Commits on Nov 25, 2007
  1. update version to last bioperl release

    svn path=/bioperl-ext/trunk/; revision=682
    cjfields committed Nov 25, 2007
  2. bug 2329

    svn path=/bioperl-ext/trunk/; revision=681
    cjfields committed Nov 25, 2007
Commits on Oct 23, 2007
  1. bug 2074/2329

    svn path=/bioperl-ext/trunk/; revision=680
    cjfields committed Oct 23, 2007
  2. Removed Aaron's old test script (now in t/staden_read.t). Do we modif…

    …y master ext makefile to account for this?
    
    svn path=/bioperl-ext/trunk/; revision=679
    cjfields committed Oct 23, 2007
  3. bug 2074

    svn path=/bioperl-ext/trunk/; revision=678
    cjfields committed Oct 23, 2007
Commits on Aug 30, 2006
  1. added bit about VERSION issues

    svn path=/bioperl-ext/trunk/; revision=677
    cjfields committed Aug 30, 2006
Commits on Aug 29, 2006
  1. Uses io_lib 1.8.11 or 1.8.12; newer versions don't seem to work corre…

    …ctly
    
    svn path=/bioperl-ext/trunk/; revision=676
    cjfields committed Aug 29, 2006
Commits on Jul 4, 2006
  1. Updated bug reporting

    svn path=/bioperl-ext/trunk/; revision=675
    arareko committed Jul 4, 2006
Commits on Jul 2, 2006
  1. Fixed spaces

    svn path=/bioperl-ext/trunk/; revision=674
    arareko committed Jul 2, 2006
Commits on Jul 1, 2006
  1. Fixed spaces and URL's

    svn path=/bioperl-ext/trunk/; revision=673
    arareko committed Jul 1, 2006
  2. Updating mailing lists URL

    svn path=/bioperl-ext/trunk/; revision=672
    arareko committed Jul 1, 2006
Commits on Mar 31, 2006
  1. fixed some memory issues

    svn path=/bioperl-ext/trunk/; revision=671
    ymc committed Mar 31, 2006
Commits on Mar 20, 2006
  1. Now we allocate memory for the emission matrix rows in HMM_new

    svn path=/bioperl-ext/trunk/; revision=670
    ymc committed Mar 20, 2006
Commits on Feb 11, 2006
  1. support for ends-free alignment

    svn path=/bioperl-ext/trunk/; revision=669
    ymc committed Feb 11, 2006
Commits on Dec 23, 2005
  1. Looks like all version numbers must match for 'make'

    svn path=/bioperl-ext/trunk/; revision=668
    bosborne committed Dec 23, 2005
Commits on Dec 8, 2005
  1. also included <string.h> to get rid of warnings when I am calling strlen

    svn path=/bioperl-ext/trunk/; revision=667
    ymc committed Dec 8, 2005
Commits on Nov 7, 2005
  1. Fixed score calculation bugs in some rare cases

    svn path=/bioperl-ext/trunk/; revision=666
    ymc committed Nov 7, 2005
Commits on Oct 9, 2005
  1. Removed all references to submitting bugs using email to the bugs lis…

    …t. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
    
    svn path=/bioperl-ext/trunk/; revision=663
    heikkil committed Oct 9, 2005
Commits on Sep 26, 2005
  1. prep for 1.5.1 release

    svn path=/bioperl-ext/trunk/; revision=657
    hyphaltip committed Sep 26, 2005