3.21	2008/08/27
	* Removed flag -y (replaced with -P, different meaning)
	* Added flag -P phrapScore
	* Added flag -C config-file
	* Added flag -U version
	* Added internal 1-channel quality encoding
	* Added actual computation of the best score possible for the read
	* Fixed output for paired reads - some hits did not have "target" columns set

3.22    2008/09/03
    * Added flag -R (mutual orientation)
    * Added development version of di-nucleotide colorspace mapping

3.23	2008/09/17
	* Now -A1 -n1 allows one ambiguity per hash word on subject side - it gets considered as miamatch
	* Option -W is added, now window may be longer then 15 bases (may be up to 24).

3.28	2008/11/12
	* A lot of chages:
	 -w window/word    sets window size and word size (window may include two words)
	 -H bits           now sets index part of hash, rest is hashed as sorted list
	 -S stride         sets stride size
	 -N count          sets maximal number of consecutive windows to hash
	 -e 0|1            may allow indels to be hashed
	 -k pos[,...]      allows to force certain positions of all reads to be skipped
	 -x cnt            allows to reuse guide file hits having mismatches
	 -R type           allows only four mutual orientations now
	 -D min[-max]      now sets paired read range (instead of -z -Z)
	 -m value          sets fuzz for -D values
	 -a count          sets maximal number of ambiguities in window on read side now
	 -A count          sets maximal number of ambiguities in window on subject side now
	 -y seqid [-y ...] add seqid to the list of allowed subject ids to scan
	 --pass0, --pass1  allow to select pass for which -w, -H, -S, -N, -e, -n will be applied
	 -f                removed
	 -z				   removed
	 -Z                removed

3.32	2008/11/24
	* Added multiple windows option -N (affected by --pass?)
	* Added --NaHSO3=+|- to process sodium bisulfite treated data
	* Fixed some errors

3.91	2009/02/20
	* New way to align using adopted Smith-Waterman, and a lot of changes connected to it.
	* No colorspace, bisulfite curation of quality scores are allowed yet
	* Going towards 4.0

3.99    2009/06/15
    * SAM 1.2 hsould be used as guide file format

3.101	2009/11/03
	* SAM 1.2 is default format for output. 
	* FASTA and FASTAq are supported as input
	* Feature files (limit search to the given loci) are added
	* Colorspace and bisulfite curation are back
	* A number of small improvements, optimizations and bugfixes
	* Improved SAM output for colorspace
	* FASTA Seq-ids are not parsed anymore by default
	* bmfilter added
