Added option to have matching control files back into pipeline_peakcalling.py, replaced config file option 'tracks_single_control' with option 'tracks_matched_control'
bug fix in previous commit
Fixed bug in assert strict for GTF.flat_gene_iterator, GTF.gene_iterator. Added sort option contig-strand-start-end to GTF.iterator_sorted_chunks
Added option to specify single or multiple inputs to pipeline_peakcalling.py
Major changes to pipeline_rnaseqlncrna.py - added options to retain single exon loci during filtering
returned shebang to farm.py, altered cpc.sh options to run with current blastx version
Merge branch 'master' of ssh://github.com/CGATOxford/cgat