modified code to reflect changes in samtools sort
modified code to reflect changes in samtools sort

AntonioJBT/CGATPipeline_core,AntonioJBT/CGATPipeline_core,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,CGATOxford/CGATPipelines,AntonioJBT/CGATPipeline_core,CGATOxford/CGATPipelines