chapmanb/bcbb — pull request #60 by roryk (2012-11-02 18:04:57+00:00)
Title: Sorry for the messy multiple issue pull

Two minor commits to update Tophat alignments. The other updates PicardMetricsParser to handle the output from CollectRnaSeqMetrics from Picard and introduces a subclass of PicardMetrics specifically for collecting Picard metrics from RNASeq data. I left PicardMetrics alone.

Both PicardMetrics and RNASeqPicardMetrics work fine after the update.