2014-01-22 Camille Marchet <camille.marchet@inria.fr>
	* 2.0.0 -> 2.1.0
	Pipeline features : 
		- Bug fixed :  
			-Error removal step erased random edges. Now fixed : discards edges according to C value.
		- "N" nucleotides are now ignored by the pipeline during graph building.
		- Now working with Minia r6025 and Minigraph r5097.
		- Now using 4 Bloom filters by default.

	Options and parameters :
		- New option --mismatches makes possible to allow some mismatches while KissReads' reads alignment on results.
		- Option -u has changed:	=1 to store unfinished bcc (default)
						=0 to discard unfinished bcc
		- Default parameters have changed : k moves from 25 to 41 and M from 1000 to 10000. 

	Outputs :
		- The command line is returned in the output (.o) file.
		- Type_0 results file now presents two types of variants : 
			Type_0a where only one single nucleotide change is returned in the upper path
			Type_0b where several single nucleotide changes are returned in the upper path

	For developpers :
		- 3 Functional tests added : test each module (ks_error_removal, ks_run_module, ks_bubble_enumeration).
		- A test on debruijn graph construction added	
		- It is possible to perfom profiling on KisSplice using gprof



2013-11-13 Alice Julien-Laferriere <alice.julien-laferriere@inria.fr>
	* 1.8.3 -> 2.0
	-New kissreads version following developments of symbiose project: specific counts for kissplice. 4 counts are made now : ASB, AS, SB ,S, AB (for events: ASB, AB). parallel version by default
	-Coherence is made based on reads covering nt not on reads covering kmer. min_overlap parameters is added. A read is count only if it overlap the variable part if the events by min_overlap nt. eg: if the read overlap by min_overlap S it is count in S, by min_overlap the junction AS, etc.
	-New counting option for junction are therefore in kissplice.py scripts: options --counts : 0 (counts are reported as CX), 1 (  ASX, SBX, ASSBX, ABX), 2 ( ASX, SBX, SX, ASSB, ABX). See user_guide for full information.
	-There are k nucleotide sequences on both sides of the variations (instead of k-1 in previous version)
	- New options : --output-context and --output-path
	--output-context : if is possible, KisSplice will output the longest sequences possible before and after the events, the outputted context is in lower case
	--output-path: kissplice output in all_path_k{k value} file the nodes ids of the cycles
	-The counts are made for the SNPs with a seed of k + 1 because of the k nt context
	- It is now forbidden to pick an even value for k
	-Changes the results, they are more numerous due to distinction of switching node enable by the k nt context. Counts can be modified a little bit, because of the seed of k+1 nt for nt and the min_overlap parameters. 
	-Efficient internal use of disk capacities. Suitable for a large range of systems from laptops to clusters. Implemented by Gunter Roeth (Bull HPC Extreme Computing <gunter.roeth@bull.net>)
	
2013-08-02 David Parsons <david.parsons@inria.fr>
	* 1.8.2 -> 1.8.3
	New build organization: main binary kissplice remains in the bin directory, all the secondary binaries now go to lib/kissplice

2013-06-03 Vincent Miele <vincent.miele@univ-lyon1.fr>
	* 1.8.1 -> 1.8.2
	New kissreads version, more stable
	compressed reads are now valid input
	
2013-04-04 Alice Julien-Laferriere <alice.julien-laferriere@inria.fr>
	* 1.8.0 -> 1.8.1
	Patch: it is now possible to compile and use k-mer > 31
	(use cmake . -DKMERS_OVER_32=ON)
	-C option: default to  0.02
	
2013-03-28  Alice Julien-Laferriere <alice.julien-laferriere@inria.fr>
	* 1.7.1 -> 1.8.0
	De Bruijn Graph construction use new Minia version (v4) much more memory efficient
	Dynamic error removal: a pre-processing step to remove edges with low relative coverage, which are likely sequencing errors.
	Uniform criteria to stop the enumeration: if a bcc reached the timeout OR the maximum number of cycles, nothing is output. This should change the results.

2012-09-01 Gustavo Sacomoto <sacomoto@gmail.com>
	* 1.6.3 -> 1.7
	Python script kissplice replaces shell script kissplice.sh

2012-04-04 Gustavo Sacomoto <sacomoto@gmail.com>
	* 1.6.2 -> 1.6.3
	Bug related to mac OS fixed

2012-03-29 Gustavo Sacomoto <sacomoto@gmail.com>
	* 1.6 -> 1.6.2
    Large k (k>32) bug fixed
    Proper installation using cmake / done by Vincent Miele
	
2012-02-14 Pierre Peterlongo <pierre.peterlongo@inria.fr>
	* 1.5.1 -> 1.6
  	Possibility to chose the output directory (-o)
    Possibility to run kissplice from any directory
    Possibility to avoid the computation of SNPs and sequencing errors (-s)
    Updated manual
    
2012-02-03 Gustavo Sacomoto <sacomoto@gmail.com>
	* 1.5 -> 1.5.1
	Small bug fixed
	
2012-01-23 Pierre Peterongo <pierre.peterlongo@inria.fr>
	* 1.4 -> 1.5
    ranking and sorting results on read coverage and not k-mer coverage
    provides 5 files:
    	uncoherent (a bit useless)
        Type 0: SNPS / sequencing errors
        Type 1: splicing events
        Type 2: Tandem repeats
        Type 3: Short indels
        
2012-01-17 Pierre Peterlongo <pierre.peterlongo@inria.fr>
 	* 1.2 -> 1.4
 	Possibility to use k larger than 32 nt (slower) or smaller than 32 (faster)

2012-01-16 Pierre Peterlongo <pierre.peterlongo@inria.fr>
	* 1.1 -> 1.2
  	Better de-bruijn graph creation
    Read length unlimited
    Checks the read coherency and provides read coverage on results
    
2011-10-28 Gustavo Sacomoto <sacomoto@gmail.com>
	* 1.0 -> 1.1
	Fixed small bugs
	Improved the user guide
    
2011-10-24 Pierre Peterlongo <pierre.peterlongo@inria.fr>
 	* 1.0
 	Initial release

