Merge pull request #16 from xzhuo/patch-1

Add genome comparison track in the annotation tracks, and use chromos…

docs/add.rst

@@ -84,16 +84,27 @@ In the mm10 folder, create a file called ``annotationTracks.json`` with followin
                     "height": 30
                 }
             ]
-        }
+        },
+        "Genome Comparison": [
+            {
+                "name": "hg38tomm10",
+                "label": "Human hg38 to mm10 blastz",
+                "querygenome": "hg38",
+                "filetype": "genomealign",
+                "url": "https://vizhub.wustl.edu/public/mm10/weaver/mm10_hg38_axt.gz"
+            }
+        ]
     }
 
 Get chromosome sizes
 ~~~~~~~~~~~~~~~~~~~~
 
 Download the file from http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes,
-you can following awk command to get the input as below::
+you can following awk command to create the ``chromSize.json`` file::
 
-    awk '{ print "new Chromosome(\""$1"\", "$2"),"}' <( sort -V mm10.chrom.sizes | grep -v '_')
+    sort -V myoLuc2.chrom.sizes | awk 'BEGIN{print "["}{ print "\t{\"chr\": \""$1"\", \"size\": "$2"},"}END{print "]"}' > chromSize.json
+
+Move the ``chromSize.json`` file into the mm10 folder.
 
 Create genome configuration file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -105,31 +116,10 @@ Create a file called ``mm10.js``, filling the following contents::
     import TrackModel from '../../TrackModel';
     import cytobands from './cytoBand.json';
     import annotationTracks from "./annotationTracks.json";
-
-    const genome = new Genome("mm10", [
-        new Chromosome("chr1", 195471971),
-        new Chromosome("chr2", 182113224),
-        new Chromosome("chr3", 160039680),
-        new Chromosome("chr4", 156508116),
-        new Chromosome("chr5", 151834684),
-        new Chromosome("chr6", 149736546),
-        new Chromosome("chr7", 145441459),
-        new Chromosome("chr8", 129401213),
-        new Chromosome("chr9", 124595110),
-        new Chromosome("chr10", 130694993),
-        new Chromosome("chr11", 122082543),
-        new Chromosome("chr12", 120129022),
-        new Chromosome("chr13", 120421639),
-        new Chromosome("chr14", 124902244),
-        new Chromosome("chr15", 104043685),
-        new Chromosome("chr16", 98207768),
-        new Chromosome("chr17", 94987271),
-        new Chromosome("chr18", 90702639),
-        new Chromosome("chr19", 61431566),
-        new Chromosome("chrX", 171031299),
-        new Chromosome("chrY", 91744698),
-        new Chromosome("chrM", 16299),
-    ]);
+    import chromSize from "./chromSize.json";
+    
+    const allSize = chromSize.map(genom => new Chromosome(genom.chr, genom.size));
+    const genome = new Genome("myoLuc2", allSize);
 
     const navContext = genome.makeNavContext();
     const defaultRegion = navContext.parse("chr6:52425276-52425961");