test comment
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git
Modified to allow Transcriptome Space
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	src/java/broad/pda/seq/rap/GenomeCommandLineProgram.java
Modified broad.pda.seq.rap.GenomeCommandLineProgram to work with
TranscriptomeSpace

Added getEntireChromosome method to CoordinateSpace
added getEntireChromosome to MaskedGenomicSpace
Small bug fixes
fixed bug in TranscriptomeSpace WindowIterator hasNext() method
Fixed bug in output BED file score (now prints enrichment, instead of 0)
Changed scope of extendSuperArgsForSample
modified for transcriptome space
class for creating probes from CLIP peaks
fixed bug in getCount iterator
Poisson scoring for ChIP/CLIP/etc
Bug fixed
added flag in MultiSampleScanPeakCaller to print extra bed fields.
temporary bug fix in skip over windows where getCount was failing
updating
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	.classpath
	src/java/broad/core/datastructures/JCSCache.java
	src/java/broad/pda/seq/rap/CollectAnnotationEnrichments.java
	src/java/broad/pda/seq/rap/GenomeCommandLineProgram.java
	src/java/broad/pda/seq/rap/PlotAggregateRegions.java
	src/java/nextgen/core/annotation/Gene.java