2016-07-08  Youri Hoogstrate
	
	* Version 3.0.3: API Changes, only useful for tools depending on FuMa as lib

2016-04-07  Youri Hoogstrate
	
	* Version 3.0.2: Suppresses a warning that occurs in some installations

2016-04-05  Youri Hoogstrate
	
	* Version 3.0.1: Added a simple break statement ensures that the output is
	  in the order of the number of datasets in which a fusion gene is being
	  found.
	  
	  The logging function now does not skip the 100.0% which was caused in some
	  cases occured due to a rounding artefact.

2016-04-01  Youri Hoogstrate
	 
	* Version 3.0.0: The core has been rewritte because it needed to use much
	  less memory for a large number of datasets. Initially the code created
	  sub datasets, because it was expected to export them time-wise and it was
	  very handy for running unit tests and for creating the summary output.
	  This resulted in a very high memory consumption for a large number of
	  experiments (not with respect to the number of total Fusion genes).
	  The rewritten code consumes memory in relation to the total number of
	  Fusion objects. However, for the summary output we still use the legacy
	  code and for the list output we make use of the new code.
	  
	  FuMa now starts with a n*n (num Fusion objects in all experiments)
	  triangular matrix in which it compares all fusions with any other fusion
	  gene. If they are considered identical, a MergedFusion object will be
	  stored for the next iteration. Otherwise, at the end of the iteration,
	  all non matched fusion genes will be exported to file.
	  
	  For the remaining MergedFusion genes, FuMa will create a m (number of
	  MergedFusion objects) * n square matrix and compare whether the Fusion
	  genes matches the Merged fusion genes. Again, if they are identical,
	  they will be kept for the next iteration (these MergedFusion objects
	  will contain 3, 4 or more original Fusion objects each) and those that
	  are not being matched will be exported to file. For those that will be
	  kept for the next iteration, 'duplicates' will be removed. If no matched
	  objects remain, FuMa is finished.
	  
	  Because of this update, for analysis with a low number of samples and a
	  high number of fusion genes, FuMa may have become (quite) a bit slower. 
	  However, we believe the cost of some extra running time is much and much
	  more desired than the exponential memory requirements.
	  
	
		Important:
		We have also found and resolved a small bug. In older versions of FuMa,
		indexing was chromosome-name based. Therefore matching two fusion genes
		only happened when they were annotated upon the same chr name. If you
		would have a fusion gene A-B (both on chr1) and fusion A-B (both on
		chr2), the old versions would consider these distinct whereas the new
		version of FuMa considers these identical.
		
		Important 2:
		We have found another minor bug. In rare situations where no fusion
		gene was matched, the original fusion genes were not reported but
		such that the number of input files did not equal the number of
		output files (test_OverlapComplex 08_b and 09_05 and many in test 10).
		This bug has been resolved in v3.

2016-03-16  Youri Hoogstrate
	
	* Version 2.12.3: Bugfix.

2016-03-16  Youri Hoogstrate
	
	* Version 2.12.2: Removal of unused 'sequence' and 'transition
	  sequence' variables within the Fusion object, to reduce memory.

2016-03-15  Youri Hoogstrate
	
	* Version 2.12.1: Another reuction of memory footprint - from
	  linear scale (as the number of samples increase) to chunk-wise.
	
	* Changed verbosity settings, requires the --verbose argument to get
	  a detailed output.

2016-03-14  Youri Hoogstrate
	
	* Version 2.12.0: Huge reduction of memory footprint - from
	  exponential to linear scale as the number of samples increase.
	  Also the pruning system works very efficient and the memory does
	  not increase too much after a large number of iterations with
	  many samples.

2016-03-14  Youri Hoogstrate
	
	* Version 2.11.8: Reduction of memort footprint

2016-03-14  Youri Hoogstrate
	
	* Version 2.11.7: Reduction of memort footprint

2016-03-11  Youri Hoogstrate
	
	* Version 2.11.6: Added support for JAFFA

2016-03-11  Youri Hoogstrate
	
	* Version 2.11.5: Added utility to create appropriate BED files from GTF files

2016-03-11  Youri Hoogstrate
	
	* Version 2.11.4: Reduces memory footprint for high number of samples

2015-02-08  Youri Hoogstrate
	
	* Version 2.11.3: Fixes support for EricScript
	
	  - Addresses an installation issue with numpy
	  
	  - More convenient way of throwing exceptions if files are being parsed improperly

2015-02-07  Youri Hoogstrate
	
	* Version 2.11.2: Support for SOAPFuse and EricScript

2016-02-05  Youri Hoogstrate

	* Small fix to a utility

2016-02-02  Youri Hoogstrate

	* Small changes to the utilities and the export-to CG function

2015-11-27  Youri Hoogstrate

	* Small change in the __str__ function of Fusion genes to print
	  the genomic strand information

2015-11-20  Youri Hoogstrate
	
	* Version 2.11.0
	
	* Added column to list output to indicate whether long genes are
	  spanning the fusion gene
	
	* Added --long-gene-size argument (default: 200000bp)
	
	* Added --no-strand-specific-matching argument (not default)
	
	* Added --no-acceptor-donor-order-specific-matching (default)
	
	* Updated corresponding test cases

2015-10-13  Youri Hoogstrate
	
	* Version 2.10.1: List output had on tab at each line too much

2015-10-08  Youri Hoogstrate
	
	* Version 2.10.0: Added overlap baded matching
	  - Dropped the --egm argument
	  - Added the -m argument to choose between egm, subset and overlap
	    based matching
	
	* Added --overlap-based-matching argument
	
	* Added --strand-specific-matching argument
	
	* Added many test cases
	
	* Updated manual 
	
	* Many code cleanups (args passed through op many places as
	configuration variable)
	  - Fixes a bug such that FuMa now uses consistently the same
	    settings for duplication removal as well as matching
	
	* Added support for STAR Fusion format
	
	* Added support for TopHat Fusions HTML output format

2015-08-26  Youri Hoogstrate
	
	* Version 2.9.2: Support for StarFusion

2015-08-12  Youri Hoogstrate
	
	* Version 2.9.1: Support for Chimera prettyPrint format
	
	* Test case for parsing Chimera prettyPrint file
	
	* Added FusionDetectionExperiment::__getitem__

2015-08-07  Youri Hoogstrate
	
	* Version 2.9.0: Support for strand-specific-matching
	
	* Test case for strand specific matching
	
	* Code cleanup

2015-07-13  Youri Hoogstrate
	
	* Small fix in parsing empty fusioncatcher output files

2015-06-19  Youri Hoogstrate
	
	* List output is sorted, to ensure consistent output.
	
	* Updated the test framework and README and travis-ci.

2015-05-05  Youri Hoogstrate
	
	* Version 2.8.0: Added "Exact Gene-list Matching" (EGM).

2015-04-08  Youri Hoogstrate
	
	* Version 2.7.3: Fixed loggin issue in "fusioncatcher-to-CG".
	
	* More correct format description in error handling.

2015-04-08  Youri Hoogstrate
	
	* Version 2.7.2: Fixed a column issue in the ChimeraScan parser that
	  affects conversion with "chimerascan-relative-bedpe-to-CG".

2015-04-02  Youri Hoogstrate
	
	* Version 2.7.1: Added "fuma-list-to-boolean-list" binary to convert
	  the output format.

2015-04-01  Youri Hoogstrate
	
	* Version 2.7.0: Added the "--formats" argument.
	
	* Added a new logging scheme.
	
	* Updated README.
	
	* Separated CLI code from the executable.
	
	* Added ChimeraScan conversion executable to installer

2015-03-16  Youri Hoogstate
	
	* Version 2.6.6 (beta): Several fixed in 
	  "chimerascan-relative-bedpe-to-CG".

2015-03-16  Youri Hoogstate
	
	* Version 2.6.5 (beta): Fixed "defuse-clusters-to-CG" and
	  "fusioncatcher-to-CG".

2015-03-16  Youri Hoogstate
	
	* Version 2.6.4 (beta): Fixed "defuse-clusters-to-CG" by using
	  correct class reference.

2015-03-05  Youri Hoogstate
	
	* Version 2.6.3 (beta): Added exception handling.

2015-03-05  Youri Hoogstate
	
	* Version 2.6.2 (beta): Fixed issue that crashes the exoport type
	  summary, introduced after exporting 'list' type output.
	
	* Changed expectation of unit tests to the subset matching behaviour
	  introduced since version 2.5.0.
	
	* Added two functional tests to the test unit.

2015-03-02  Youri Hoogstate
	
	* Version 2.6.1 (beta): Fixed some settings in the Fusion object
	  that allows 'list' type output.

2015-03-02  Youri Hoogstate
	
	* Version 2.6.0 (beta): Added the 'list' output type which seems to
	  be the most natural way of representing the results.

2015-02-19  Youri Hoogstate
	
	* Version 2.5.2 (beta): Added Reader for 1-2-3-SV.

2015-01-22  Youri Hoogstate
	
	* Version 2.5.1 (beta): Added code that supports different types of
	  matching, used for benchmarking.

2015-01-19  Youri Hoogstate
	
	* Version 2.5.0 (beta): The match function returns only the subset 
	  of the matching gene lists to avoid 'gene set growing'.

2015-01-14  Youri Hoogstate
	
	* Version 2.4.2 (beta): Changed defuse output parser from 1 based to
	  0 based.

2015-01-14  Youri Hoogstate
	
	* Version 2.4.1 (beta): Support for the 'RelatedJunctions'-column in
	  the output for the "-f extensive" argument.

2015-01-09  Youri Hoogstate
	
	* Version 2.4.0 (beta): Fixed the "-f extensive" argument.

2015-01-09  Youri Hoogstate
	
	* Version 2.3.3 (beta): Added code to read files from FusionMap.

2014-12-01  Youri Hoogstrate
	
	*  Version 2.3.2 (beta): Added code to read files from OncoFuse.

2014-11-11  Youri Hoogstrate
	
	*  Version 2.3.1 (beta): Added indexing code for FusionCatcher
	   reference files and added conversion scripts for interim files
	   that describe fusions relative to gene-ids.
	
	*  Exporting a FusionDetectionExperiment to CompleteGenomics format
	   now accepts "-" for stdout.

2014-11-05  Youri Hoogstrate
	
	*  Version 2.3.0 (beta): Added support for the FusionCatcher
	   "final-list_candidate-fusion-genes.txt" files.

2014-09-30  Youri Hoogstrate
	
	*  Version 2.2.0 (beta): Added support for the RNA-STAR
	   "Chimeric.out.junction" files.

2014-09-22  Youri Hoogstrate
	
	*  Version 2.1.0 (beta): many bugfixes to the fuma binary (to make it
	   compatible with all 2.* changes.
	*  Added a parser for Tophat Fusion post's "result.txt"

2014-09-21  Youri Hoogstrate
	
	*  Version 2.0.0 (beta) got released. Rewrote many code and added unit
	   tests.
