FilterPairedReadsByMAQ updated to consider mask
Adding RNA programs
Changed WindowScoreIterator so that initRegion() is only called if the
iterator has windows in that region.
Added function in PairedEndReader to ask if it is reading the file as
our custom format PairedEnd.bam or if it is reading as a standard BAM
file
Added RAP RNA programs
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git