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v2.0.6 - Bugfix: Using STAR parameter --outSAMheaderHD to add SO tag into header line

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@amatchan amatchan released this 07 Mar 16:08
· 331 commits to dev since this release

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.