[DAS2] DAS intro

[Ed Erwin]

Andrew Dalke wrote:
> 
> I believe I understand this.  There really is only one reference frame for
> the entire genome sequence, for a given assembly, and all other coordinate
> systems are a fixed and definite offset of that single reference frame.

No.  The coordinate transformations are often more complicated than 
simple offsets.  The coordinate space for features on one contig can be 
'backwards' with respect to a different contig, and the coordinate space 
for a gene may skip over one or more gaps with respect to the genomic 
sequence.

Also, the term 'reference frame' bugs me a bit because 'frame' always 
makes me think of 'reading frame', which is not what you intend.