DESCRIPTION:
	- corrected the plotMatrix.R export

scoreMatrix.R:
	- added the BigWig functionality
	- added chr intersection in ScoreMatrix:RleList,GRanges-otherwise
	  it breaks
Split the test files based on the function they test.
ScoreMatrixTest.R:
	- added the ScoreMatrix:bigWig, GRanges test

ScoreMatrix.R:
	- ScoreMatrix - fixed a bug in the if clause when testing for the
	  equality of width of ranges - wrong parentheses
	- added the ability to read bigWig format

ScoreMatrixBin.R:
	- added functionallity to construct from bigWig file

ScoreMatrixList.R:
	- added functionality to read a list of bigWig files
scoreMatrixBin.R:
	- there was a bug in the getViewsBin, line 37 - had -1 after the
	  end coordinate

ScoreMatrixListTests.R:
	- added the test for ScoreMatrixList:bigWig, GRanges with bins
scoreMatrixList.R:
	- renamed the l, granges arguments to target, windows arguments
	- added binMatrix method for ScoreMatrixList

scoreMatrix.R:
	- I can't remember what I did :|
Merge branch 'development' of github.com:al2na/genomation into development

Removed all *.Rd files

DESCRIPTION, NAMESPACE:
	- added the rtracklayer to import and dependency

Conflicts:
	DESCRIPTION
	man/ScoreMatrix-methods.Rd
	man/ScoreMatrixBin-methods.Rd
	man/annotateWithFeature-methods.Rd
	man/annotateWithFeatureFlank-methods.Rd
	man/annotateWithGeneParts-methods.Rd
	man/annotationByGenicParts-methods.Rd
	man/convertBed2Exons-methods.Rd
	man/convertBed2Introns-methods.Rd
	man/convertBedDf-methods.Rd
	man/findFeatureComb-methods.Rd
	man/getFeatsWithTargetsStats-methods.Rd
	man/getFlanks-methods.Rd
	man/getMembers-methods.Rd
	man/getRandomEnrichment-methods.Rd
	man/getTargetAnnotationStats-methods.Rd
	man/heatMatrix-methods.Rd
	man/heatmapProfile-methods.Rd
	man/plotGenicAnnotation-methods.Rd
	man/plotTargetAnnotation-methods.Rd
	man/randomizeFeature-methods.Rd
	man/readFeatureFlank-methods.Rd
	man/readTranscriptFeatures-methods.Rd
	man/scaleScoreMatrix-methods.Rd
	man/scaleScoreMatrixList.Rd
	man/unionScoreMatrixList-methods.Rd
Merge branch 'development' of github.com:al2na/genomation into development

conflicts sorted

pull after push

Conflicts:
	R/scoreMatrix.R
	R/scoreMatrixList.R
	man/ScoreMatrixList-methods.Rd
	man/scaleScoreMatrix-methods.Rd
scoreMatrix.R:
	- added rpm=T

scoreMatrixList.R:
	- added rpm=T

scoreMatrixBin.R:
	- added rpm=T

GenomationManual-knitr.Rnw
	- corrected the ScoreMatrixList code
Merge pull request #36 from frenkiboy/development

Development