New flag UPDATE_ALIGNMENT added.
Added update_alignment control. If it is an update alignment it needs to change database insertion method UPDATE/INSERT.
New capacity levels, in order to avoid max number of connection errors.
Add a new scape branch for copy_trees_from_previous_release.
Add new analysis: hmm_annot_table_reuse
Add raxml_update clusterset_id
Correct an error in the clustering mode condition.
Change the resource class of some analysis which were previously running on the default class.
Correct the module name for copy_trees_from_previous_release.
Change in the minimize tree call, minimize_tree returns a new root_id that the prunned tree needs to point to.
Added features to deal with addeed or deleted genes.
Added logic to disavow list the leaves that need to be removed since the current tree has a different species set, potentially producing trees that have fewer leaves.
Added logic to cope with the differences in ids to update, delete && add.
New hashes to store the ids that need action.
Store needs_update tag in the gene_tree_root_tag table.
Some indentation corrections.
Added control for the target_tree which needs to be different if the raxml_update flag is active.
Correcting some identation issues.
Added a param for storing the copy_gene_tree.
We should obtail all the alignment related data from the copy_gene_tree, so the change off all the objects refering current_gene_tree to copy_gene_tree.
Added param_defaults function, so that we can undef 'aln_update'
Added control for 'aln_update', so that:
1 - we use the get_GeneAlignAdaptor correctly
2 - we run load_cigars_from_file with the correct parameters.
Change in fetch_input, making the tree adaptor fetch the correct tree (copy_tree), and dump the correct alignment (copy_tree) to the working dir.
Fetch the tags from gene_tree_root_tag for: current_gene_tree && current_gene_tree, and use them to creat the file conatining the "new" sequences to be added.
Remove unnecessary dependency.
Added a few parameters to the param_defaults
Change in the command line 'cmd'. We had a 'sed' call in order to filter the outputs. But that is not necessary since the raxml
command we are using does not include any characters in the resulting trees.
Added papio_anubis
Species trees containing only mammals+baboon