Setting up repository with copies of the UCSC schemas.
Adding documentation describing the design of the schema, which is an optimized version of the scheme we detail in the paper.
Updating comments, shortening length fields
Simplifying away the two different ways of refering to endpoints.
Update and rename referenceHierarchy.avdl to referenceAlignments.avdl

Sorry to hijack this file, I'm proposing to generalise it to represent alignments, with two possible constructs - the alignment block and a cigar alignment. The alignment block is a pairwise structure that matches intervals between two blocks, and can be placed in an array to describe a pairwise alignment. The second alignment structure is a CIGAR based alignment that apes the basic CIGAR format, with the difference that the alignment is between to paths in two sequence graphs.
Update referenceAlignments.avdl

Fixing typos.
Update referenceAlignments.avdl

Simplifying to just represent cigars
Update referenceAlignments.avdl

Adding in alignment from sequence to sequence graph.
change endOffset to be one beyond the last base

change definition of endOffset so that endOffset-startOffset is length (if all within one block)
and you can iterate while (i < endOffset).  This is natural in 0-based coordinate systems, 
avoiding +1 or -1 calculations on lengths.
Merge branch 'master' of ../RefVariationTaskTeam
Merging referenceVariation schema files into repo
Update referenceAlignments.avdl

Fixing documentation style, updating reference names.
Update referenceStructure.avdl

Fixing coding style and renaming to be consistent with merged schemas repository.
Update referenceAlignments.avdl
Update referenceStructure.avdl
Update referenceAlignments.avdl

Fixing file.
Update referenceAlignments.avdl
Merge pull request #46 from benedictpaten/master

Merging in RefVar .avdl schemas
added GARun object
add /runs/search method