Fixed rap.SlideAndCalculate
Reformated the AnnotationFactory and refactored the AnnotationFileReader
to a more generic tabbed file reader (nextgen.core.general.TabbedReader)
Added program to filter a list of reads out of a FASTQ file
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	src/java/broad/pda/seq/rap/GenomeScoringProgramFromBed.java [deleted]
	src/java/nextgen/core/annotation/AnnotationFileReader.java

AnnotationFileReader was refactored to TabbedReader, which now includes
the IOExceptions that Manuel added in the last commit to
AnnotationFileReader.