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Commits on Feb 11, 2013
  1. Adding messages to keep track of point in program, fasta read in is f…

    committed Feb 11, 2013
    …ine for 2 sequences
Commits on Oct 11, 2012
  1. Cleaner output

    committed Oct 11, 2012
Commits on Oct 9, 2012
Commits on Oct 5, 2012
  1. Seems to be working in it's entirety.. Need to check that probabiliti…

    committed Oct 5, 2012
    …es are being correctly calculated.
Commits on Oct 4, 2012
  1. Checked and made the order3markov work again. It only works with rese…

    committed Oct 4, 2012
    …t_sequence_indices functional, not set sequence indices that I used to completely rework for HumanDatasimulation (in gillespie)
  2. Perl script to calculate length 15 nucleotide (5 codon... possibly mo…

    committed Oct 4, 2012
    …re) sequences rates away for each possible mutation as well as for the entire sequence, DONE. Using script, discovered an error where the sequence Qi. was not being correctly updated in the forward simulation. Should be fine in the EPC routine. Simulation routine working as it should, but may need to reactivate reset_sequence_indices
Commits on Oct 3, 2012
  1. Fixed issue with stop codons, verified that the indices are correct. …

    committed Oct 3, 2012
    …Need to verify that the values are also correct.
Commits on Oct 2, 2012
  1. run works all the way through, but sequence indices are all reset in …

    committed Oct 2, 2012
    …each round, and the correctness of the results are unverified
  2. Can no calculate the sequence value for the forward routine. Enter in…

    committed Oct 2, 2012
    …to the forward simulation routine, fixing up code along the way
Commits on Sep 26, 2012
  1. set sequence indices (and reset..) needs to be done before successful…

    committed Sep 26, 2012
    …ly getting to TauIJ3
  2. Offsets are now set. Need to set sequence environment, and make sure …

    committed Sep 26, 2012
    …that TauIJ3 comes to the correct conclusion for the offset to be used.
Commits on Sep 25, 2012
Commits on Sep 24, 2012
Commits on Sep 21, 2012
  1. Weekend

    committed Sep 21, 2012
Commits on Sep 20, 2012
Commits on Sep 17, 2012
  1. Working through filling up the selective and neutral lookup tables. R…

    committed Sep 17, 2012
    …emoved lookup_context, since (as far as I can tell) it has no purpose, and was a legacy variable
Commits on Sep 14, 2012
  1. Added neutral_dep to routine. Now have two lookup tables for tauij to…

    committed Sep 14, 2012
    … be calculated with, the dependent and neutral tables
Commits on Sep 13, 2012
  1. Fixed the Markov again to get the expected results to compare against…

    committed Sep 13, 2012
    … the modified version of isg for human data
Commits on Aug 24, 2012
Commits on Aug 22, 2012
Commits on Aug 20, 2012
  1. Added human data folder in the data directory, and copied the counts …

    committed Aug 20, 2012
    …for both CCDS and GRCh37 from ~/iSG/indel-seq-gen/human_data folder
  2. Added human data folder in the data directory, and copied the counts …

    committed Aug 20, 2012
    …for both CCDS and GRCh37 from ~/iSG/indel-seq-gen/human_data folder
Commits on Jul 6, 2012
  1. any changes

    committed Jul 6, 2012
Commits on Jun 11, 2012
  1. assess_paths for mcmc heatmap

    committed Jun 11, 2012
Commits on Jun 8, 2012
  1. Analytical hm is good.

    committed Jun 8, 2012
Commits on Jun 7, 2012
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