Minor changes to AlignmentModels
Unnecessary log statements are removed.
Change to CountScore and ScanStatisticScore: annotationLength is added
to part of the score.
Changes to support single end data while converting to ALignment objects
New program added to get alignment statistics for bam files.
Major change to AddEndRNASeq so that it can trim 3p and 5p data
independent of each other.

Minor commenting out in Scripture

Major change to ScriptureScorer using scoring in transcriptome space.
Paired end writer support for single end data added.
Merging with repository
Merging with repository
Merging with repository
Merging with repository
Merging with repository
Merging with repository. No changes.
Merging with repository. No changes.
Merging with repository. No changes
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	src/java/nextgen/core/annotation/Gene.java
	src/java/nextgen/core/model/AlignmentModel.java
	src/java/nextgen/core/writers/PairedEndWriter.java