v2.0.6 - Bugfix: Using STAR parameter --outSAMheaderHD to add SO tag into header line
The final stage in the star mapping code is to coordinate sort the aligned BAM file using biobambam bamsort.
This should update the @hd header line with the following tag SO:coordinate but this was not happening becuase STAR does not add the SO tag by default. It should be adding SO:unsorted to the output mapped BAM.
Now the STAR parameter --outSAMheaderHD is used to ensure the SO tag is present prior to sorting with bamsort.