add fixmate and adddupmarksupport to the coordinate bamsort command in final_output_prep
upgrade bammarkduplicates command to bammarkstreamingmarkduplicates
made parameter names consistent between alignment and realignment templates (vtlib)
correct template names in README.vtlib
remove superfluous file
Merge remote-tracking branch 'kl2-remote/fixmate_markdups_calibration' into devel
fixmates, bamstreamingmarkduplicates, adddupmarksupport, and calibration_pu added to *PRODUCTION* bwa_mem template
Merge remote-tracking branch 'kl2-remote/fixmate_markdups_calibration' into devel
added fixmates, calibrartion_pu, adddupmarksupport and bamstreamingmarkduplicates to current production tophat2 template
removed tophat2 realignment template - should now use the subgraph version (under vtlib)
Merge remote-tracking branch 'kl2-remote/fixmate_markdups_calibration' into devel
Merge pull request #41 from dozy/fixmate_markdups_calibration

Fixmate, streaming markdups, seq error reports, template library
Merge branch 'devel' of github.com:wtsi-npg/p4 into devel