1. Faheem Mitha
  2. corrmodel_orig2

Commits

Author Commit Message Date Builds
Faheem Mitha
Merge with default
Branches
debian
Faheem Mitha
Fix the facet labels which were going outside the box, by creating stat_labeller function to split labels across two lines with 'atop'.
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
Bugfix for loops in gendatamethod::gendata and gen_dirichlet_fixedprob::gendata (flagged by Clang 3.4).
Faheem Mitha
Compile executables with Clang 3.4 as well.
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
Add MANUAL.
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
Various fixes to sim load functions. * write_config_model_to_db: Raise error none of the following are true: model_id is specified, default_model is True, empty_model is True. * load_all_sim_tables: New function to return simresult for a single pair of rownum, colnum. * Rename load_all_sim_tables to load_simdata_return_simresult. * load_all_sim_tables_parallel: Rename load_all_sim_tables to load_simdata_return_simresult.
Faheem Mitha
Set default for --empty-model in 'all_sim' and 'all_sim_parallel' to be True.
Faheem Mitha
Add some comments.
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
Change 'sequencegroup_id' column in simgroup table to 'id'. Remove comments at bottom.
Faheem Mitha
Fixes to debian/get-orig-source. The script now figures out the revision number by itself, and then the changelog entry is updated.
Branches
debian
Faheem Mitha
Add revision number of default branch tip to version number.
Branches
debian
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
load.py: * load_crossval_dataset: Pass a list of sequences, along with their ids in the motif table to the crossval function instead of an array. * load_allseq_crossval_subgroup: Undo the change made in 7e93155af517 to load_allseq_crossval_subgroup. crossval.py: * crossval: Change samplelst to use the ids in the motif table, instead of integers starting from 0.
Faheem Mitha
Branch merge with default.
Branches
debian
Faheem Mitha
Add override_dh_clean target to remove figures.prv directory.
Branches
debian
Faheem Mitha
Add LaTeX file containing figures from the corrmodel paper. * SConstruct: Set default for 'version' argument to be 2.7. Add 'build' alias. Add figures.pdf target. * setup.py: Call scons with 'build' argument. * figures.tex: LaTeX figures file. * MODEL.tex: TikZ file for model figure.
Faheem Mitha
Merge with default.
Branches
debian
Faheem Mitha
simdata, all_sim, all_sim_parallel: Add mutually exclusive options --model, --empty-model, --default-model.
Faheem Mitha
Fix indentation.
Faheem Mitha
Add 'default_model' config value for use with sim data.
Faheem Mitha
* create_db: The 'default_model' config value is now returned as part of this function. * write_config_model_to_db: Alter function to only do something if default_model or empty_model arguments are True. If default_model, use the 'default_model' config value, which gives the dataset from which to take the default model. * load_file: Correctly handle case when the fasta file is close to the size of the individual sequences. * load_allseq_crossval_subgroup: Correctly handle case wher…
Faheem Mitha
Add debian/clean file for files to clean.
Branches
debian
Faheem Mitha
Switch source format from native to quilt.
Branches
debian
Faheem Mitha
Add get-orig-source target to rules.
Branches
debian
Faheem Mitha
Merge with default.
Branches
debian
Faheem Mitha
load_motif_dataset: Look for motif fasta file in 'datadir' (as defined in the config file).
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