pipeline_mapping.py - changed view and counting to use fastq counted reads
pipeline_mapping.py - changed view and counting to use fastq counted reads

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