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
fixmates, bamstreamingmarkduplicates, adddupmarksupport, and calibration_pu added to *PRODUCTION* bwa_mem template
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 pull request #41 from dozy/fixmate_markdups_calibration

Fixmate, streaming markdups, seq error reports, template library