Changes to pipeline_mapping to move files (including optionaly input files) into subdirectories
Merge branch 'master' of ssh://github.com/CGATOxford/cgat

Conflicts:
	CGATPipelines/pipeline_mapping.py
Merge branch 'master' of ssh://github.com/CGATOxford/cgat
fastqs2fastqs.py: add option to allow output of unpaired reads
PipelineUCSC.py: fix SQL syntax for repeat classes
Work to modularise pipeline_mapping.py. Change pipeline_mapping.py to collect duplication/complexity stats (MarkDuplicates) by default. Add work around for running MarkDuplicates on gsnap bam files with split alignments (by filtering out XT flagged alignments).
Merge branch 'master' of ssh://github.com/CGATOxford/cgat

Conflicts:
	CGATPipelines/pipeline_mapping.py