Release history
===============

1.1.1.beta (26th May 2016)
--------------------------
- improved lineage treatment
- fixed higher-level taxon assignment in the presence of groups
- fixed feature sample matching when biom HDF5 file is provided
- CoNet can now load adjacency matrices as networks (allows loading SparCC results)

1.1.0.beta (27th January 2016)
----------------------------
- CoNet compiled for Cytoscape 3.X now requires at least Java 7 (previously Java 6), Java 6 compatibility is maintained for CoNet compiled for Cytoscape 2.X
- CoNet compiled for Cytoscape 3.X can now load biom HDF5 files directly using the BiomIO class by Joshua Ladau
- improved handling of missing lineages and lineages with non-unique names
- fix of an irregular bug due to a problem in thread handling in the speed-up part of CoNet

1.0b7 (29th June 2015)
-----------------------
- added cosine correlation (related to the dot product)
- improved table parsing (error messages specify problems better)
- apriori wrapper adjusted to latest version of apriori (6.12), previous apriori versions will no longer work
- bug fix for combining apriori with multiple-testing correction (previously, error message prevented this)
- fixed error when combining groups with feature file
- row groups can now be combined with higher-level taxon assignment
- new help system introduced, fixing the help display problems that occurred previously on some systems
- matrix property display problem for incidence matrices fixed
- removal of all-zero taxa after down-sampling of samples and all-zero samples after down-sampling of taxa
- fixed initial edge selection parameter disappearance after export to settings file or cmd line call generation

1.0b6 (19th August 2014)
------------------------
- change of license (from 22nd May 2014 onwards, CoNet is distributed under the GNU General Public License version 2)
- fixed bug in Kendall implementation
- treatment of ties in Spearman implementation fixed
- fixed problem of setting initial edge selection parameter from settings file
- if groups are provided, the group properties are listed when matrix info is selected
- improved taxonomy parsing from biom files (hit number is parsed if provided)
- fixed rarefaction bug (previously, error message prevented to carry out rarefaction)
- network comment does no longer list removed edges and filtered rows, to reduce size of big networks
- logging level can now be adjusted (defaults to fatal to reduce size of log file)

WARNING: A serious bug was spotted in Jean-Sebastien Lerat's Spearman implementation,
which occurred when missing value treatment was set to pairwise_omit. This bug is now fixed, but 
networks constructed with Spearman and missing value treatment enabled need to be reconstructed. 

1.0b5 (15th April 2014)
-----------------------
- added p-value computation with Fisher's Z-score for correlations
- Lallich routine selection without multiple test correction rejected - bug fixed
- parsing error for sample names starting with E/e and followed by numeric value fixed 
- fixed positive-edges-only filter 
- fixed computation of maximum number of zeros per row (for matrix property display)
- added error message in case automatically obtained lower and upper threshold overlap

1.0b4 (20th December 2013)
--------------------------
- implemented export of positive and negative node degree
- option added to report input matrix properties and suggestion of CoNet settings based on these properties
- fixed settings file bug (disable speedup not set/exported from/to settings file)
- fixed settings file bug (minzeropairs filter not set from settings file)
- fixed settings file bug (copresence/mutual exclusion-only-filter not set back correctly to default)
- fixed command line export bug (--topbottom not exported)
- fixed treatment of feature rows for taxa without lineages in renormalization 
- edges for which methods infer conflicting interaction types are filtered now
- row combination involving summed row are forbidden now

1.0b3.1 (28th October 2013)
----------------------------
- Jean-Sebastien Lerat's library KLD implementation: removed division by number of value pairs
- bug fix for networks merged on the score level
- improved non-SGE parallelization support

1.0b3 (22nd October 2013)
--------------------------
- fixed bug concerning automatic lineage assignment for higher-level taxa with groups
- allow transposing feature matrix
- allow feature/input matrix sample matching to support feature data with samples that have a different order than input matrix samples
- more flexible OTU table from biom file parsing (support parsing lineages from row names)
- better matrix parsing error catching
- too large data menu size fixed
- prevent generation of command line call in the presence of input errors
- removed faulty error message about combining ARACNE with missing values when JSL MI was selected

1.0b2 (12th October 2013)
-------------------------
- support for MI and Jensen-Shannon with Jean-Sebastien Lerat's library
- interface offers 3 MI implementations: minet, aracne and Jean-Sebastien Lerat's library
- fixed bug related to keeping discarded rows as one row per group
- fixed bug concerning group exclusion (betweengroupsonly, withingroupsonly)
- prevent kept summed rows to appear in the network

1.0b1.1 (14th September 2013)
------------------------------
- No Blast hit entry supported in QIIME OTU tables
- execution of R batch scripts in given directory

1.0b1 (10th September 2013)
----------------------------
CoNet beta release.
This release features the re-implementation of the CoNet core by Jean-Sebastien Lerat.
The re-implementation included the renormalization and the measures:

- Pearson
- Spearman
- Kendall
- Hellinger
- Euclid
- Steinhaus
- Bray Curtis
- Kullback-Leibler
- Variance of Log-ratios
- Hilbert-Schmidt independence criterion

All measures were tested to give the same networks from test data as the previous implementations.
This release also adds the following features:

- support of QIIME OTU tables with and without taxonomy
- versioning via CoNet property file, valid for both Cytoscape plugin and command line version 
- added the possibility to filter rows with less than the given number of non-double-zero pairs
- directory of R batch scripts can be specified on command line


0.9 (30th May 2012)
--------------------
CoNet alpha release. 