dev html cleanup

igvteam · Aug 21, 2024 · d0fee36 · d0fee36
1 parent 6e4c739
commit d0fee36
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Showing 12 changed files with 88 additions and 385 deletions.
diff --git a/dev/alignment/bam.html b/dev/alignment/bam.html
@@ -21,26 +21,35 @@ <h2>
 
     const config =
         {
-            "queryParametersSupported": true,
-            "genome": "hg19",
-            "locus": "chr1:155155389",
+            "version": "3.0.2",
+            "showSampleNames": false,
+            "reference": {
+                "id": "mm39",
+                "name": "Mouse (GRCm39/mm39)",
+                "fastaURL": "https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa",
+                "indexURL": "https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.fa.fai",
+                "cytobandURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/cytoBandIdeo.txt.gz",
+                "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chromAlias.txt",
+                "twoBitURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit",
+                "chromSizesURL": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes",
+                "chromosomeOrder": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY"
+            },
+            "locus": "all",
             "roi": [],
             "tracks": [
                 {
-                    "type": "alignment",
-                    "url": "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam",
-                    "indexURL": "gs://genomics-public-data/platinum-genomes/bam/NA12878_S1.bam.bai",
-                    "name": "NA12878",
-                    "format": "bam",
-                    "sort": {
-                        "chr": "chr1",
-                        "position": 155155389,
-                        "option": "BASE",
-                        "direction": "ASC"
-                    },
-                    groupBy: "strand",
-                    height: 800,
-                    filter: {mq: 30}
+                    "type": "sequence",
+                    "order": -9007199254740991
+                },
+,
+                {
+                    "name": "Refseq Genes",
+                    "format": "refgene",
+                    "url": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/ncbiRefSeq.txt.gz",
+                    "indexed": false,
+                    "order": 1000000,
+                    "type": "annotation",
+                    "height": 70
                 }
             ]
         }

diff --git a/dev/wig/bigWigs.html b/dev/wig/bigWigs.html
diff --git a/dev/wig/bigwig.html b/dev/wig/bigwig.html
diff --git a/dev/wig/groupAutoscale-button.html b/dev/wig/groupAutoscale-button.html
diff --git a/dev/wig/issue_1802.html b/dev/wig/issue_1802.html
diff --git a/dev/wig/smallWig.html b/dev/wig/smallWig.html
@@ -9,6 +9,8 @@
 
 <body>
 
+Verify that features are visible in whole genome view.
+
 <div id="myDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto">
 
 </div>

diff --git a/dev/wig/tdf.html b/dev/wig/tdf.html
diff --git a/dev/wig/popover-numbers.html → dev/wig/track_metadata.html b/dev/wig/popover-numbers.html → dev/wig/track_metadata.html