Fixed a bug in AbstractAnnotation.expand()
Some changes to AddEndRNASeqToScripture
Test class to test expanding and trimming in AbstractAnnotation
Gene.overlapsStranded with min overlap is added
Scripture updated and adding end rnaseq updated to use 5' data
correctly. 3' data might be incorrect
Added a correct to getAverageCoverage
Made getOverlappingReadCountsStranded() public
Added NewRatioScore for the ratio count score based on using bed files
as input
Merging
OverlapsStranded added
Remove class files
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	src/java/nextgen/core/model/score/ScanStatisticScore.java
	src/java/nextgen/core/scripture/AddEndRNASeqToScripture.java