Changes to --library type ht-seq-count and BamToWw

-- added support for fr-second strand
-- added -f 3 flag to take properly paired reads in ht-seq-count inputs
-- added ht-seq-count  --strict and --non empty intersection types to
genegcode gene level summaries
-- commented out ht-seq-count transcripts for the moment while
prototyping.
-- added samtools view -f3 tagged bam to tophat out dir.