New Writer and Translator modules, plus Writer-related additions to parsers


Former-commit-id: 25bca28cc8bf51aa9486626c1cf8f6066c55c0f8
Removed warn


Former-commit-id: 488fd9f374895ded7e90d72c5ca4e25783443c56
Extended tests to incorporate more data types and output fields


Former-commit-id: 1373bfe11fc61d71a913cc32fdbb38c82685b686
Added variation features and track colours (latter still needs work!)


Former-commit-id: 998436fea849709c1cd86993ba6b9fc409848cf2
Added overriding of create_record method in child parsers


Former-commit-id: ca449988bfbd398f853f0109269c3b7ed30cb9d1
Made it possible to pass existing SpeciesDefs object into Writer (potentially useful in webcode)


Former-commit-id: e545e8a35abada1a4d3999816b38cb86aac24adb
Added code needed to handle bedgraph format


Former-commit-id: b76cea20f3f72632511aa1d52301b1d0f025fc83
Parsers for VEP input and output formats, along with unit tests


Former-commit-id: 0cdf5899cbab9b0141ea4f1b3e3d8306094e9b2b
New parser for simple lists of strings, e.g. feature IDs


Former-commit-id: b1cb6098f62e766b717edcafd53b4cc107ae8ee6
Some more parsers for formats used on the web


Former-commit-id: 59eb3981e5e955cda0af58f7170c0a20292d8f5b
Tidied up some whitespace


Former-commit-id: ecf9c34795cfa9bb526f2f6e10ae5fbc0a80cea1
Added note about current "under development" status


Former-commit-id: b7731ae78f50a712d4931fb5db8f60724b3dea97
Factored out common accessors into a parent class


Former-commit-id: aee91fd1e5b535223ee2eacd6478c86f5e7dfc9d
Added 'or die' to print method!


Former-commit-id: 882732c605e0e50c519eb7a7ef65ae3a09204619
Factored out code that writes metadata and features into separate methods that can be called directly by an iterator, for greater efficiency (e.g. dumping large datasets)


Former-commit-id: 7420c3f6567330e78fbafa090c3c4ac6444f6628
First pass at using Utils::IO instead of raw filehandles


Former-commit-id: 6d737e24452e3cefa2ebe0177e1896fdcbd5f362
Updated test to be independent of database, and fixed bugs arising from test re-run


Former-commit-id: 107941a456a655ea995e9d605f2ce2e58b63ca61
Shortening name of child classes of Parser, removing -Parser suffix


Former-commit-id: 32e2edbfa36f7f7c30f5fb58fc0512fb698fd9b2
Removed Camel-case from Bigfile parsers


Former-commit-id: d21187738e8884dbde97cef325c26e3edce89f07
Merge branch 'feature/writer'

Conflicts:
	modules/Bio/EnsEMBL/IO/Parser.pm

Former-commit-id: 5a982a04242c97dc865a671898b98d4d1af1f2f1