restore bam dev file

igvteam · Sep 5, 2024 · 9c717d2 · 9c717d2
1 parent 87b3652
commit 9c717d2
Showing 1 changed file with 17 additions and 26 deletions.
diff --git a/dev/alignment/bam.html b/dev/alignment/bam.html
@@ -21,35 +21,26 @@ <h2>
 
     const config =
         {
-            "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",
+            "queryParametersSupported": true,
+            "genome": "hg19",
+            "locus": "chr1:155155389",
             "roi": [],
             "tracks": [
                 {
-                    "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
+                    "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}
                 }
             ]
         }