2016-10-24  Youri Hoogstrate
	* (v2.3.3) 
	  - Fixes a parallelization bug in pysam (#17) by opening as many pysam wrappers
	    as the number of regions. This should have been a pysam.fetch() object for
	    each region, but this fails when the results are yielded

2016-10-24  Youri Hoogstrate
	* (v2.3.2) 
	  - Catches pysam Exception in rare alignment conditions #2

2016-10-24  Youri Hoogstrate
	* (v2.3.1) 
	  - Catches pysam Exception in rare alignment conditions

2016-10-24  Youri Hoogstrate
	* (v2.3.0) 
	  - Fixed behaviour that on multiple optima the result could be randomly one of each
	  - Fixed issue that increased the memory consumption the further in the genome 
	    aligned reads were analysed

2016-10-20  Youri Hoogstrate
	* (v2.2.0) Many extra cleanups, reorganization of classes to get rid of a linear
	  increase of memory usage with respect to the number of output entities.

2016-10-20  Youri Hoogstrate
	* (v2.1.5) Cleanups and large reduction of memory footprint

2016-10-19  Youri Hoogstrate
	* (v2.1.4) Cleanups and minor memory improvements

2016-10-19  Youri Hoogstrate
	* (v2.1.1-v2.1.3) Getting the pkg_resource data into pip
	  Thanks xref: http://stackoverflow.com/questions/7522250/how-to-include-package-data-with-setuptools-distribute
	  - Solved bug where FlaiMapper crashed on reads that have no aligned blocks 

2016-10-19  Youri Hoogstrate
	* (v2.1.0) Reduction of memory footprint
	  - Uses a different data structure and new method that estimates the median
	    values in a much sparser way.

2016-10-11  Youri Hoogstrate
	* (v2.0.0) Large rewrite
	  - Enable TravisCI for unit testing during further development
	  - Written several tests (both unit as functional) including all parameters.
	  - Refactored a lot of code, removed a lot of unused code
	  - Removed SSLM binaries
	  - Removed binary used to generate MASK files
	  - Removed --mask argument
	  - Wrote algorithm that replaces the MASK functionality
	  - Added --parameters argument, allowing to customize the filter
	  - Included data in pkg_resources that allow to grap default parameter file from there
	  - Improved GTF output; two lines per detected fragment of which one (type=exon) can be used by expression estimation tools, new way of generating gene_id's
	  - Added optional arguments `--offset5p` and `--offset3p`.
	  - Dropped samtools dependency and rely completely on pysam
	  - Replacement of tabs with spaces (s/\t/ /g)
	  - Use a logging system to be able to get a verbose output, also for testing
	  - Better way of trowining exceptions which shall cause more appropriate stack traces
	  - Disabled possibility to use multiple BAM files - concatenation should be done with samtools merge
	  - Made FlaiMapper available in pip and bioconda
	  - Many cleanups, removal of unused properties, imports, functions and classes

2015-09-02  Youri Hoogstrate
	* (v1.2.2) Added GTF/GFF as output format.
	
2015-06-03  Youri Hoogstrate
	* (v1.2.1) Output files are sorted on chromosome names. This ensures
	  that lines in the output file always appear in the same order.
	  Deriving GTF/GFF files from FASTA files has now the correct
	  1-based offset.
	
	* (v1.2.0) Fixed a bug that didn't allow reads larger than 35bp.
	  The 0-based and 1-based coordinates are now consistent. some out
	  commented code has been removed. Improved output format 1 "table;
	  per fragment". This includes that the file format has changed to
	  0-based (both start- and end positions). Also columns have been
	  added: positions relative to the gene annotation(s) for the "Full
	  genome alignment"-type analysis. The GTF/GFF parser now supports
	  "gene_id" column parsing. The mask file
	  share/annotations/ncRNA_annotation/ncrnadb09.gtf was using 0-based
	  cooridnates while the GTF/GFF format requires 1-based coordinates.
	  The fixed file is provided at:
	  share/annotations/ncRNA_annotation/ncrnadb09_v2.0.gtf
	
2015-06-01  Youri Hoogstrate
	* (v1.1.6) Fixed a GFF/GTF parsing error - FlaiMapper only supported
	  annotations with the score value set.
	
2015-03-20  Youri Hoogstrate
	* (v1.1.5) Removed warning written to stderr that should be reported
	  to stdout.
	
	* (v1.1.4) Tabix libraries from the pysam library have been replaced
	  with flaimapper libraries because of multiple incompatibility
	  issues.
	
	* (v1.1.3) Pysam 0.8.2.1 shows different behavior with the
	  TabixFile.fetch() function when no arguments are given. Flaimapper
	  has been made compatible also with the latest version of pysam.

2015-01-19  Youri Hoogstrate
	* (v1.1.2) Found and disabled an unnecessairy double exectution of a
	  'run' function which caused double calculation time.

2014-11-14  Youri Hoogstrate
	* (v1.1.1) Added "src/bin/gtf-from-fasta" and added the file to the
	  installer. This file makes it posible to create a mask file that
	  corresponds to a reference fasta file (only if mature ncRNAs are
	  given in the fasta file).