@title("silk locus format")

= Silk Locus Format (draft)

== Example
<code>
%silk(version:1.0)
# coordinate specifies the target sequence
-track(name:pairdReads, description:Clone Paired Reads)

-coordinate(group:utgb, species:human, revision:hg18)
 -locus(coordinate.name, start, end, name, strand, block(start, end, color)*, color, _[json])|
chr22 1000 5000 cloneA + [[1,567, "red"], [3513, 4000]] #00FFFF {"score":960}
chr22 2000 6000 cloneB - [[1,433], [3602, 4000, "blue"]]         {"score":900}
</code>



<code>

class Locus
{
  String name = "locus";
  long start = -1;
  long end = -1;
  String strand = "+";
  String color = "#00FFFF";
}
</code>



corresponding BED format:
<code>
track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601
</code>

<pre>
BED: start:1000 end:5000 
Silk: [1001, 5000]
</pre>


<code>
%silk(version:1.0)
# coordinate specifies the target sequence
-track(name:pairdReads, description:Clone Paired Reads)

-coordinate(group:utgb, species:human, revision:hg18)
 -gene(coordinate.name, start, end, name, strand, cds(start, end), exon(start, end)*, color, _[json])|
chr22 1000 5000 cloneA + [1000, 5000] [[1,567], [3513, 4000]] #00FFFF {"score":960}
chr22 2000 6000 cloneB - [2000, 6000] [[1,433], [3602, 4000]]         {"score":900}
</code>


<code>

class Gene extends Locus
{
  List<Exon> exon;
  CDS cds;
}

class Exon extends Locus
{
}

class CDS extends Locus
{

} 
</code>


<code>
-coordinate(name:chr22)
 -gene(start:1, end:5000, color:"#00FFFF")
  -cds(start:1000, end:5000)
  -exon(start:1, end:567)
  -exon(start:3513, end:4000)
 -gene(start:2000, end:6000)
  -cds(start:2000, end:6000)
  -exon(start, end)|
   1    433
   3602 4000
 -gene(start:1, end:5000, color:"#00FFFF")
..
</code>