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changelog
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2016-11-25 Emil Hägglund <[email protected]> & Andreas Sjödin <[email protected]>
CanSNPer version 1.0.8
* bug fix release
Minor release to fix rumtime bug introduced in 1.0.7
2016-11-25 Emil Hägglund <[email protected]> & Andreas Sjödin <[email protected]>
CanSNPer version 1.0.7
* setup.py
Major rearrangement of of the code to allow installation using setup.py.
* Francisella
Added B.44-B-80 describing the Iberian, Orebro, Bulgarian and Finish isolates.
* Brucella
First version of Brucella CanSNPer support.
2016-06-01 Adrian Lärkeryd & Andreas Sjödin <[email protected]>
CanSNPer version 1.06
* (draw_ete2_tree)
Improve the coloring by making missing SNPs due to gaps to by colored grey .
* (align)
Print percent similarity between sequences for verbose mode.
2015-01-19 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.05
* (multi_tree_walker)
Many developer printouts were added to debug the walking algorithm.
* (multi_tree_walker)
Changed the name of cont_flag to force_flag to better describe what it
stands for
* (multi_tree_walker)
Changed how forcing a node works. Now handles leaves when forcing and
fixed a bug that caused sequences to be classified as non-derived nodes,
even though CanSNPer at the same time warned that this node was not
derived.
* (align)
Changed multiprocessing operations to subprocess Popens. This was done to
get rid of some waiting time where the previous implementation had to wait
for all processes in a batch to end before starting the next batch. Now
new processes start immediately when one is done, keeping the number at
batch size.
* (align)
Removed verbose output that said which references were being aligned. This
must now be seen in the dev printout that lists Mauve commands if the
information is needed.
2014-02-14 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.04
* GALAXY TOOL, added CanSNPer.xml
* (parse_arguments, read_config)
Added a --galaxy argument that will cause behaviour apropriate for when
running the Galaxy tool that was just created.
* (draw_ete2_tree)
Changed file_name to tree_file_name for clarity and added a DEV printout
* (align)
Added a DEV printout for progressiveMauve commands
Added a check for the --galaxy argument that determines where to put the
tree pdf file. In case of galaxy it is put in the working directory,
otherwise works like before (ie in the query file directory)
2013-12-06 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.03
* (import_sequence)
Fixed a bug where if the same strain name was used in multiple organisms
loading the sequence to the second organism only updated the "old" one
because it only checked for strain name. Now checks organism as well.
2013-10-17 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.02
* (import_to_db)
Changed the strings imported to the db with the --import_snp_file to be
unicode strings.
* (import_tree)
Fixed a bug where the same node name in several trees caused errors in
newick creation.
2013-10-14 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.01
* (parse_arguments)
Print help if no arguments were sent to CanSNPer.
* (purge_organism)
Make sure the user wants to delete organism by asking.
2013-10-10 Adrian Lärkeryd <[email protected]>
CanSNPer version 1.00