Added support for counting reads on the reverse strand (native to current illumina pipeline). Also added the ability to count second reads that are either native/flipped. The SamTranscriptomeParser does not flip the strand orientation of the second read by default, so the default settings of the RNASeq and DRDS assume the strand is NOT flipped (native sam). RNASeq and DRDS will run unstranded analysis by default.
