rename MultiSNPScan --> SNPScan
rename PrecalculateThresholdLists --> PrecalculateThresholds
BioUML API removed
Progressions extracted from inner class to a subpackage
small refactor of PrecalculateThresholds
fix examples of MultiSNPScan usage: it used API
--background synonym for -b
--discretization synonym for -d
--pvalue synonym for -p; progression mode is now case-insensitive
--first-ppm|-first-pcm; effective-count-first --> first-effective-count
--[query-|collection-] effective-count, pcm, ppm
remove obsolete --silent option
document full-names of options
ScanCollection --precise now has an optional argument
ScanCollection results sorting
fix a bug which loaded motifs before specifing motif loading format
--silence --> --silent