This commit was manufactured by cvs2svn to create branch 'branch-
ensembl-69'.

Sprout from master 2012-10-01 18:55:30 UTC Stephen Searle <searle@sanger.ac.uk> 'Changes from branch68 for BigBedAdaptor setting in AttachedFormat::BIGBED'
Delete:
    modules/Bio/EnsEMBL/GlyphSet/fg_regulatory_features.pm
Methylation track. Branch.
Less mad zooming in methylation zmenu link. Branch.
New strand-paired Methylation tracks. Tweaks to ZMenu creation. Moved
some useful drawing code to more generic position. Branch.
Misc methylation track fixes from various head commits.
TRAC #572: exon ZMenu improvements.
TRAC #537: make karyotype labels clickable.
Use the method get_all_somatic_VariationFeatures_by_source (Slice object)
Strandbump issue of overrunning full track height.
More explicit passing of adaptor.
Add methylation legend track.
Mege multiple commits from head concerning "destranding" methylation data.
Final fix to protein summary exon z-menus pre-relese. Add phases back in.
Typo.
Avoid letter soup from superimposed error messages when empty tracks is turned on and methylation is zoomed out.
fix for when there are no options
This commit was manufactured by cvs2svn to create branch 'branch-
ensembl-69'.

Cherrypick from master 2012-11-05 14:20:25 UTC Simon Brent <sb23@sanger.ac.uk> 'don't unshift undef onto the reg feats array. tidied.':
    modules/Bio/EnsEMBL/GlyphSet/fg_regulatory_features.pm
Steve Wilder's suggested methylation legend improvements.
Fix draw_cigar_features when multiple alignments are shown (#300808).