Improved the rst documentation at the beginning of the script.
Updated documentation for bam2wiggle.py and bam_vs_gtf.py
Added new tests to bed2fasta.py and bam2wiggle.py
Fixed bug in bedgraph output from bam2wiggle.py
Removed BED and BIGBED output formats from bam2wiggle.py (use bam2bed.py)
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
standardizing the rst documentation format.
Merge branch 'Scrum-apr-14' of github.com:CGATOxford/cgat into Scrum-apr-14
Updated documentation for bam2wiggle.py, bam_vs_gtf.py. added tests to bed2fasts.py, bam2wiggle.py.

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Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
 pep8 corrections to gff2fasta.py
Added pipelines page to developer section of documentation.
Fixed bug in bam2wiggle tests
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
Fixed --set-gene-to-transcript in gtf2gtf.py and added test
A comprehensive set of tests covering all important options.

If every test is swtiched on, it covers almost all the options.
(they cover 33 out of 34 options)
Merge branch 'Scrum-apr-14' of github.com:CGATOxford/cgat into Scrum-apr-14
standardize the format of documentation at the beginning of the script.
More detailed documentation
Added detailed Options and Usage to doc_string accroding to stardard
format.
A comprehensive set of 10 tests covering all important options.
 updated tests and docs for gff2fasta.py
 futher tests and docs for gff2fasta.py