Skip to content

Commit

Permalink
Revert to original test config in index.html
Browse files Browse the repository at this point in the history
  • Loading branch information
@pkerpedjiev
pkerpedjiev committed Nov 30, 2024
1 parent 244e82d commit cda350b
Showing 1 changed file with 147 additions and 40 deletions.
187 changes: 147 additions & 40 deletions src/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -66,24 +66,82 @@
"exportViewUrl": "/api/v1/viewconfs",
"views": [
{
"initialXDomain": [
1853645535.4582071,
1853645704.8611746
],
//"initialXDomain": [1069795,1070508],

// Variant + Soft Clipping (left)
"initialXDomain": [1558492965,1558493030],

// Insertions + Soft Clipping both sides
//"initialXDomain": [105706,105906],

// Hard Clipping (left and both sides)
//"initialXDomain": [145009,145409],

// Deletions
//"initialXDomain": [128870,129070],

"initialYDomain": [
-406323904.4626087,
-406323832.0176704
180520.26598912096,
180863.4346387336
],
"tracks": {
"top": [
// {
// "type": "pileup",
// "uid": "WBTUIwm0SB2gcas7wzwztA",
// "tilesetUid": "NLxWZTCoSzei1lkH4yVJmg",
// "server": "https://resgen.io/api/v1",
// "options": {
// "axisPositionHorizontal": "right",
// "axisLabelFormatting": "normal",
// "outlineReadOnHover": false,
// "showMousePosition": false,
// "name": "HG002 Illumina (60x)",
// "labelPosition": "bottomLeft",
// "groupBy": null,
// "colorScale": [
// "#08519c",
// "#6baed6",
// "#993404",
// "#fe9929",
// "#808080",
// "#DCDCDC"
// ]
// },
// "width": 651,
// "height": 362
// },
{
"type": "pileup",
"uid": "NgvIT-sdTf2M6eeh3WlJlw",
"tilesetUid": "OAQ516H3SfWvyutsR07oYg",
"server": "http://localhost:8000/api/v1",
"uid": "AdlJsUYFRzuJRZyYeKDX2A",
"type": "chromosome-labels",
"width": 811,
"height": 30,
"server": "//higlass.io/api/v1",
"options": {
"axisPositionHorizontal": "right",
"axisLabelFormatting": "normal",
"color": "#808080",
"stroke": "#ffffff",
"fontSize": 12,
"fontIsLeftAligned": false,
"showMousePosition": false,
"mousePositionColor": "#000000"
},
"filetype": "chromsizes-tsv",
"tilesetUid": "NyITQvZsS_mOFNlz5C2LJg"
},
{
"uid": "fastaex",
"data": {
"type": "fasta",
"faiUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa.fai",
"fastaUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.fa",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes"
},
"type": "horizontal-sequence",
"width": 768,
"height": 25,
"options": {
"name": "hg38",
"barBorder": true,
"colorScale": [
"#08519c",
"#6baed6",
Expand All @@ -92,34 +150,83 @@
"#808080",
"#DCDCDC"
],
"outlineReadOnHover": false,
"showMousePosition": false,
"showCoverage": false,
"coverageHeight": 10,
"name": "https://genomeark.s3.amazonaws.com/species/Gorilla_gorilla/mGorGor1/assembly_curated/mapping/bwa.analysis-dip.illumina.bam",
"outlineMateOnHover": true,
"maxTileWidth": 200000,
"collapseWhenMaxTileWidthReached": false,
"minMappingQuality": 0,
"highlightReadsBy": [],
"largeInsertSizeThreshold": 1000,
"viewAsPairs": false
},
"width": 774,
"height": 317
"labelColor": "black",
"valueScaling": "linear",
"labelPosition": "topLeft",
"barBorderColor": "white",
"backgroundColor": "white",
"labelTextOpacity": 0.4,
"sortLargestOnTop": true,
"trackBorderColor": "white",
"trackBorderWidth": 0,
"extendedPreloading": false,
"colorAggregationMode": "none",
"notificationText": "Zoom in to see nucleotides...",
"fontSize": 16,
"fontFamily": "Arial",
"fontColor": "white",
"textOption": {
"fontSize": "32px",
"fontFamily": "Arial",
"fill": 16777215,
"fontWeight": "bold"
}
}
},
{
"type": "top-axis",
"local": true,
"orientation": "1d-horizontal",
"thumbnail": {},
"defaultOptions": {},
"server": "",
"tilesetUid": "JYQIW1hmQAWH-K0APqZq-A",
"uid": "HHTqfZfqQF-FjCdGTESZ9A",
"options": {},
"width": 461,
"height": 20
"type": "pileup",
"options": {
"axisPositionHorizontal": "right",
"axisLabelFormatting": "normal",
"outlineReadOnHover": "yes",
"groupBy": "strand",
"minusStrandColor": "#ffd1d4",
"plusStrandColor": "#cfd0ff",
"showCoverage": true,
"colorScale": [
// A T G C N Other
"#08519c",
"#6baed6",
"#993404",
"#fe9929",
"#808080",
"#DCDCDC"
]
},
"height": 500,
"uid": "FylkvVBTSumoJ959HT4-5B",
"data": {
"type": "bam",

// Caution: Example does not fit to the sequence track above.
// "url": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam",
// "chromSizesUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes",

// Variant + Soft Clipping (left)
"bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr9_22004085.bam",
"baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr9_22004085.bam.bai",
"chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes",

// Insertions + Soft Clipping both sides
// "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_105806_S_I.bam",
// "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_105806_S_I.bam.bai",
// "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes",

// Hard Clipping (left and both sides)
// "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_145209_H.bam",
// "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_145209_H.bam.bai",
// "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes",

// Deletions
// "bamUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_128970_D.bam",
// "baiUrl": "https://aveit.s3.amazonaws.com/higlass/bam/example_chr1_128970_D.bam.bai",
// "chromSizesUrl": "https://aveit.s3.amazonaws.com/higlass/data/sequence/hg38.mod.chrom.sizes",

"options": {
"maxTileWidth": 30000
}
},
"width": 470
}
],
"left": [],
Expand All @@ -131,11 +238,11 @@
},
"layout": {
"w": 12,
"h": 12,
"h": 6,
"x": 0,
"y": 0
},
"uid": "cz2sOeJgRIWJ5J0wYZu4fw"
"uid": "WdlA7F8aTY2gXQzPGiBlwQ"
}
],
"zoomLocks": {
Expand Down

0 comments on commit cda350b

Please sign in to comment.