added debug functionality to Pipeline.py
bam2stats - better read pairing
table2table.py - empty table raises error
CGAT/Pipeline.py - debug can work with SGE
split_fasta.py - bugfix
pipeline_mapping - added publication of UCSC hub
runExpression.py - added spike methods
PipelineTracks - added Autosample
bam2geneprofile.py - added control files for normalization
updates to pipelines
Merge branch 'master' of ssh://github.com/CGATOxford/cgat