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Commits on Jun 1, 2014
  1. Update to work with GHC 7.8.

    BurntSushi committed Apr 15, 2014
    Also, fix HMM parser so that it shows a helpful error message.
    
    Finally, add a few header entries so that SMURFLite templates don't
    cause MRFy to barf.
Commits on May 26, 2013
  1. Control the number of times viterbi runs. (For the Oracle.)

    BurntSushi committed May 26, 2013
    Conflicts:
    	FileOps.hs
  2. added ViterbiPlusX to the Oracle

    nrnrnr committed with BurntSushi May 25, 2013
Commits on May 22, 2013
  1. andrew is stooopid

    BurntSushi committed May 22, 2013
Commits on May 17, 2013
  1. AG is lazy.

    BurntSushi committed May 17, 2013
Commits on May 6, 2013
Commits on May 2, 2013
  1. ignore mrfy-bench directory

    BurntSushi committed May 2, 2013
Commits on Apr 29, 2013
  1. consistent indentation pleez

    BurntSushi committed Apr 29, 2013
  2. vim-fu

    BurntSushi committed Apr 29, 2013
  3. Run bench shortcut.

    BurntSushi committed Apr 29, 2013
  4. optimize

    BurntSushi committed Apr 29, 2013
Commits on Apr 24, 2013
Commits on Apr 21, 2013
  1. The `Bio` package is deprecated; use biofasta.

    BurntSushi committed Apr 21, 2013
    The `Bio` folks are splitting up the package into smaller chunks.
    Adjust `mrfy` to use the new `biofasta` package, which has the
    advantage of working with GHC 7.6.
Commits on Mar 30, 2013
Commits on Jul 10, 2012
  1. sandwich.hmm+ works

    BurntSushi committed Jul 10, 2012
Commits on Jul 9, 2012
  1. higher-order Viterbi produces any of three outputs:

    nrnrnr committed Jul 9, 2012
      - score only
      - scored path
      - search tree for A-star
  2. more on local alignments

    ndaniels committed Jul 9, 2012
Commits on Jul 8, 2012
Commits on Jul 7, 2012
Commits on Jul 5, 2012
  1. Fix a div-by-zero error

    ndaniels committed Jul 5, 2012
  2. export approxEq

    ndaniels committed Jul 5, 2012
  3. adding sandwich mrf that addIndexInfo barfs on

    Noah Daniels committed Jul 5, 2012
Commits on Jul 4, 2012
  1. consistent-scoring passes!

    ndaniels committed Jul 4, 2012
Commits on Jul 3, 2012
  1. Prohibit empty HMMs. Fixed a bug in Viterbi thanks to QuickCheck

    ndaniels committed Jul 3, 2012
    One bug was that we were missing the begin-to-Ins transition in
    scoreHMM.
    Bug in Viterbi was that we were forgetting to reverse the state list.
    Remember, we're consing, not snacking, so we have to reverse. We had
    this right at one point.