{
"assemblies": [
{
"name": "volvox",
"aliases": ["vvx"],
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_refseq",
"metadata": {
"date": "2020-08-20"
},
"formatAbout": {
"config": "jexl:{extraField:'important data'}"
},
"adapter": {
"type": "TwoBitAdapter",
"twoBitLocation": {
"uri": "volvox.2bit",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearReferenceSequenceDisplay",
"displayId": "volvox_refseq-LinearReferenceSequenceDisplay"
}
]
},
"refNameAliases": {
"adapter": {
"type": "FromConfigAdapter",
"adapterId": "W6DyPGJ0UU",
"features": [
{
"refName": "ctgA",
"uniqueId": "alias1",
"aliases": ["A", "contigA"]
},
{
"refName": "ctgB",
"uniqueId": "alias2",
"aliases": ["B", "contigB"]
}
]
}
}
},
{
"name": "volvox2",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_refseq2",
"adapter": {
"type": "TwoBitAdapter",
"twoBitLocation": {
"uri": "volvox.2bit",
"locationType": "UriLocation"
}
}
}
},
{
"name": "volvox-sample01-anchor",
"displayName": "volvox (sample01 as anchor)",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_sample01_anchor_seq",
"adapter": {
"type": "FromConfigSequenceAdapter",
"adapterId": "volvox-sample01-anchor-seq",
"features": [
{
"uniqueId": "ctgA-sample01",
"refName": "ctgA",
"start": 0,
"end": 45818,
"seq": ""
}
]
}
}
},
{
"name": "volvox404",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_refseq404",
"adapter": {
"type": "TwoBitAdapter",
"twoBitLocation": {
"uri": "volvox.2bit_404",
"locationType": "UriLocation"
}
}
}
},
{
"name": "misc",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "misc_asm",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "misc.fa"
},
"faiLocation": {
"uri": "misc.fa.fai"
}
}
}
},
{
"name": "volvox_del",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_del-ReferenceSequenceTrack",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "volvox_del.fa",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "volvox_del.fa.fai",
"locationType": "UriLocation"
}
}
}
},
{
"name": "volvox_ins",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_ins-ReferenceSequenceTrack",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "volvox_ins.fa",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "volvox_ins.fa.fai",
"locationType": "UriLocation"
}
}
}
},
{
"name": "volvox-rev-del",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox-rev-del-ReferenceSequenceTrack",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "volvox-rev-del.fa",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "volvox-rev-del.fa.fai",
"locationType": "UriLocation"
}
}
}
},
{
"name": "volvox-simple-inv",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox-simple-inv-ReferenceSequenceTrack",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "volvox-simple-inv.fa",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "volvox-simple-inv.fa.fai",
"locationType": "UriLocation"
}
}
}
},
{
"name": "volvox_random_inv",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "volvox_random_inv-ReferenceSequenceTrack",
"adapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "output_prefix3.simseq.genome.fa",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "output_prefix3.simseq.genome.fa.fai",
"locationType": "UriLocation"
}
}
}
}
],
"configuration": {
"LinearGenomeViewPlugin": {
"trackLabels": "offset"
},
"hierarchical": {
"defaultCollapsed": {
"categoryNames": ["Methylation"]
},
"defaultFolderCategories": [
"Integration test,Wiggle,Wiggle Rendering Styles"
]
},
"extraThemes": {
"darkForest": {
"name": "Dark (forest, from config file)",
"palette": {
"primary": {
"main": "#464"
},
"secondary": {
"main": "#376"
},
"tertiary": {
"main": "#253"
},
"quaternary": {
"main": "#6a4"
},
"mode": "dark"
}
}
}
},
"connections": [],
"defaultSession": {
"name": "Integration test example",
"views": [
{
"id": "integration_test",
"type": "LinearGenomeView",
"offsetPx": 2000,
"bpPerPx": 0.05,
"displayedRegions": [
{
"refName": "ctgA",
"start": 0,
"end": 50001,
"assemblyName": "volvox"
}
]
}
],
"widgets": {
"hierarchicalTrackSelector": {
"id": "hierarchicalTrackSelector",
"type": "HierarchicalTrackSelectorWidget",
"filterText": "",
"view": "integration_test"
}
},
"activeWidgets": {
"hierarchicalTrackSelector": "hierarchicalTrackSelector"
}
},
"tracks": [
{
"type": "FeatureTrack",
"trackId": "volvox_mouse_inheritance_painting",
"name": "Mouse inheritance (chromosome painting)",
"category": ["Miscellaneous"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BedTabixAdapter",
"disableGeneHeuristic": true,
"columnNames": [
"chrom",
"chromStart",
"chromEnd",
"name",
"score",
"strand",
"thickStart",
"thickEnd",
"itemRgb",
"sample"
],
"bedGzLocation": {
"uri": "volvox_mouse_inheritance.bed.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox_mouse_inheritance.bed.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearMultiRowFeatureDisplay",
"displayId": "volvox_mouse_inheritance_painting-LinearMultiRowFeatureDisplay",
"rows": "sample",
"rowHeight": 18,
"color": {
"value": "jexl:'rgb('+get(feature,'itemRgb')+')'",
"scale": "identity",
"domain": ["rgb(227,26,28)", "rgb(31,120,180)", "rgb(170,170,170)"],
"labels": ["Maternal", "Paternal", "Unknown"]
}
}
]
},
{
"type": "FeatureTrack",
"trackId": "volvox_mouse_inheritance_rows",
"name": "Mouse inheritance (arranged rows)",
"category": ["Miscellaneous"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BedTabixAdapter",
"disableGeneHeuristic": true,
"columnNames": [
"chrom",
"chromStart",
"chromEnd",
"name",
"score",
"strand",
"thickStart",
"thickEnd",
"rgb",
"sample"
],
"bedGzLocation": {
"uri": "volvox_mouse_inheritance.bed.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox_mouse_inheritance.bed.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearMultiRowFeatureDisplay",
"displayId": "volvox_mouse_inheritance_rows-LinearMultiRowFeatureDisplay",
"rows": {
"field": "sample",
"domain": ["offspring10", "dad"],
"kept": ["offspring10", "dad", "mom", "offspring03", "offspring07"]
},
"rowColor": {
"domain": ["mom", "offspring03"],
"range": ["#222222", "#bbbbbb"]
},
"rowGroups": [{ "match": "^(mom|dad)$", "group": "Parents" }],
"facet": "group",
"rowHeight": 14
}
]
},
{
"type": "GWASTrack",
"trackId": "volvox_gwas",
"name": "Manhattan plot",
"category": ["Variants"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "GWASAdapter",
"scoreColumn": "neg_log_pvalue",
"bedGzLocation": {
"uri": "volvox.gwas.tsv.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.gwas.tsv.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"displayId": "volvox_gwas-LinearManhattanDisplay",
"type": "LinearManhattanDisplay"
}
]
},
{
"type": "GCContentTrack",
"trackId": "volvox_gc",
"assemblyNames": ["volvox"],
"name": "GCContent",
"metadata": {
"description": "GC content track for Volvox mythicus. See Wikipedia: GC content for details.",
"source": "Simulated genome data"
},
"adapter": {
"type": "GCContentAdapter"
}
},
{
"type": "VariantTrack",
"trackId": "volvox_sv_test",
"description": "A uniquely interesting track",
"name": "volvox structural variant test (HTML italic+link)",
"category": ["Variants"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"uri": "volvox.dup.vcf.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.dup.vcf.gz.tbi",
"locationType": "UriLocation"
}
}
}
},
{
"type": "VariantTrack",
"trackId": "volvox_sv_test_renamed",
"name": "volvox structural variant test w/renamed refs",
"category": ["Variants"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"locationType": "UriLocation",
"uri": "volvox.dup.renamed.vcf.gz"
},
"index": {
"location": {
"locationType": "UriLocation",
"uri": "volvox.dup.renamed.vcf.gz.tbi"
}
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_alignments",
"name": "volvox-sorted.cram (contigA, default display)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"uri": "volvox-sorted-altname.cram"
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_pileup",
"name": "volvox-sorted.cram (contigA, LinearPileupDisplay, large height, color mapq)",
"category": ["Integration test"],
"metadata": {
"description": "this is a metadata description",
"name": "this is a metadata name",
"source": "We generated 150bp paired end reads from a Volvox mythicus, an imaginary species, for this jbrowse demo. See Google",
"sub": {
"subkey": "wow"
}
},
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted-altname.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted-altname.cram.crai",
"locationType": "UriLocation"
},
"fetchSizeLimit": 1000
},
"displays": [
{
"type": "LinearPileupDisplay",
"displayId": "volvox_cram_pileup_pileup",
"height": 400,
"color": {
"field": "mapq"
}
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_snpcoverage",
"name": "volvox-sorted.cram (contigA, LinearSNPCoverageDisplay)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted-altname.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted-altname.cram.crai",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearSNPCoverageDisplay",
"displayId": "volvox_cram_snpcoverage_snpcoverage"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_alignments_ctga",
"name": "volvox-sorted.cram (ctgA, default display)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted.cram.crai",
"locationType": "UriLocation"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_pileup_ctga",
"name": "volvox-sorted.cram (ctgA, LinearPileupDisplay)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted.cram.crai",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearPileupDisplay",
"displayId": "volvox_cram_pileup_ctga_pileup"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_cram_snpcoverage_ctga",
"name": "volvox-sorted.cram (ctgA, LinearSNPCoverageDisplay)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted.cram.crai",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearSNPCoverageDisplay",
"displayId": "volvox_cram_pileup_ctga_snpcoverage"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments",
"name": "volvox-sorted.bam (ctgA, larger default height, color mapq)",
"category": ["Integration test"],
"metadata": {
"description": "Paired-end 150bp reads aligned to Volvox mythicus. Publication: doi:10.1093/bioinformatics/btab817",
"tissue": "leaf tissue"
},
"assemblyNames": ["volvox", "volvox2"],
"adapter": {
"type": "BamAdapter",
"uri": "volvox-sorted.bam"
},
"displays": [
{
"type": "LinearAlignmentsDisplay",
"height": 600,
"displayId": "volvox_alignments_alignments",
"color": {
"field": "mapq"
}
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments_grouped_by_strand",
"name": "volvox-sorted.bam (pre-grouped by strand)",
"category": ["Integration test"],
"assemblyNames": ["volvox", "volvox2"],
"adapter": {
"type": "BamAdapter",
"uri": "volvox-sorted.bam"
},
"displays": [
{
"type": "LinearAlignmentsDisplay",
"height": 600,
"displayId": "volvox_alignments_grouped_by_strand_display",
"facet": "strand"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_bam_snpcoverage",
"name": "volvox-sorted.bam (contigA LinearSNPCoverageDisplay)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted-altname.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted-altname.bam.bai",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearSNPCoverageDisplay",
"displayId": "volvox_bam_snpcoverage_snpcoverage"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_bam_pileup",
"name": "volvox-sorted.bam (contigA LinearPileupDisplay)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted-altname.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted-altname.bam.bai",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearPileupDisplay",
"displayId": "volvox_bam_pileup_pileup"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments_pileup_coverage",
"name": "volvox-sorted.bam (ctgA, canvas)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted.bam.bai",
"locationType": "UriLocation"
}
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_bam_altname",
"name": "volvox-sorted.bam (contigA)",
"assemblyNames": ["volvox"],
"category": ["Integration test"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted-altname.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted-altname.bam.bai",
"locationType": "UriLocation"
}
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_bam_small_max_height",
"name": "volvox-sorted.bam (small max height)",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted.bam.bai",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearAlignmentsDisplay",
"displayId": "volvox_bam_small_max_height_alignments",
"maxHeight": 10
}
]
},
{
"type": "VariantTrack",
"trackId": "volvox_test_vcf",
"formatAbout": {
"hideUris": true
},
"name": "volvox 1000genomes vcf",
"assemblyNames": ["volvox"],
"category": ["Variants"],
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"uri": "volvox.test.vcf.gz",
"locationType": "UriLocation"
},
"samplesTsvLocation": {
"uri": "1000genomes.tsv",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.test.vcf.gz.tbi",
"locationType": "UriLocation"
}
}
}
},
{
"type": "FeatureTrack",
"trackId": "nclist_long_names",
"name": "nclist with long names/descriptions",
"category": ["Integration test"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "NCListAdapter",
"rootUrlTemplate": {
"uri": "volvox_long_names_nclist/{refseq}/trackData.json",
"locationType": "UriLocation"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments_bam_nonexist",
"name": "volvox-sorted.bam (bam nonexist 404)",
"assemblyNames": ["volvox"],
"category": ["Integration test"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted.bam.nonexist",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted.bam.bai",
"locationType": "UriLocation"
}
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox_alignments_bai_nonexist",
"name": "volvox-sorted.bam (bai nonexist 404)",
"assemblyNames": ["volvox"],
"category": ["Integration test"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sorted.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sorted.bam.bai.nonexist",
"locationType": "UriLocation"
}
}
}
},
{
"type": "QuantitativeTrack",
"trackId": "volvox_bigwig_nonexist",
"name": "wiggle_track 404",
"category": ["Integration test", "Wiggle"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "volvox.bw.nonexist",
"locationType": "UriLocation"
}
}
},
{
"type": "MultiQuantitativeTrack",
"trackId": "volvox_microarray_multi2",
"name": "MultiWig no names",
"category": ["MultiWiggle"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "MultiWiggleAdapter",
"subadapters": [
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v1.cram.bw"
}
},
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v2.cram.bw"
}
},
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v3.cram.bw"
}
},
{
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v4.cram.bw"
}
}
]
}
},
{
"type": "MultiQuantitativeTrack",
"trackId": "volvox_microarray_multi",
"name": "MultiWig",
"category": ["MultiWiggle"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "MultiWiggleAdapter",
"subadapters": [
{
"name": "k1",
"source": "j1",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v1.cram.bw"
}
},
{
"name": "k2",
"source": "j2",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v2.cram.bw"
}
},
{
"name": "k3",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v3.cram.bw"
}
},
{
"name": "k4",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v4.cram.bw"
}
}
]
}
},
{
"type": "MultiQuantitativeTrack",
"trackId": "volvox_microarray_multi_multirowxy",
"name": "MultiWig (multirowxy)",
"category": ["MultiWiggle"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "MultiWiggleAdapter",
"subadapters": [
{
"name": "k1",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v1.cram.bw"
}
},
{
"name": "k2",
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "v2.cram.bw"
}
}
]
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{
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"trackId": "wiggle_track_fractional_posneg",
"name": "Volvox microarray with +/- fractional values",
"assemblyNames": ["volvox"],
"category": ["BigWig", "Line"],
"adapter": {
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "volvox_microarray_posneg_frac.bw",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearWiggleDisplay",
"displayId": "wiggle_track_fractional_posneg_line",
"mark": "line"
}
]
},
{
"type": "QuantitativeTrack",
"trackId": "jdYHuGnpAc_",
"name": "Volvox microarray with +/- values",
"assemblyNames": ["volvox"],
"category": ["BigWig", "XYPlot"],
"adapter": {
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "volvox_microarray_posneg.bw",
"locationType": "UriLocation"
}
}
},
{
"type": "QuantitativeTrack",
"trackId": "p7FU-K6WqS_",
"name": "Volvox - BAM coverage",
"assemblyNames": ["volvox"],
"category": ["BigWig", "Line"],
"adapter": {
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "volvox-sorted.bam.coverage.bw",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearWiggleDisplay",
"displayId": "p7FU-K6WqS__line",
"mark": "line"
}
]
},
{
"type": "QuantitativeTrack",
"trackId": "pOOtg9wxcUC",
"name": "Volvox - BAM coverage",
"assemblyNames": ["volvox"],
"category": ["BigWig", "XYPlot"],
"adapter": {
"type": "BigWigAdapter",
"uri": "volvox-sorted.bam.coverage.bw"
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_fake_synteny_alt",
"name": "volvox_fake_synteny_alt",
"assemblyNames": ["volvox", "volvox"],
"adapter": {
"type": "PAFAdapter",
"uri": "volvox_fake_synteny_alt.paf",
"assemblyNames": ["volvox", "volvox"]
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_fake_synteny",
"name": "volvox_fake_synteny",
"assemblyNames": ["volvox", "volvox"],
"adapter": {
"type": "PAFAdapter",
"pafLocation": {
"uri": "volvox_fake_synteny.paf",
"locationType": "UriLocation"
},
"assemblyNames": ["volvox", "volvox"]
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox-rg",
"name": "volvox-rg (read groups, bam)",
"category": ["Alignments"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-rg.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-rg.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "volvox-rg-cram",
"name": "volvox-rg (read groups, cram)",
"category": ["Alignments"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-rg.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-rg.cram.crai",
"locationType": "UriLocation"
}
}
},
{
"type": "QuantitativeTrack",
"trackId": "volvox_wrong_assembly",
"name": "wiggle_track (wrong assembly error)",
"category": ["Integration test"],
"assemblyNames": ["wombat"],
"adapter": {
"type": "BigWigAdapter",
"bigWigLocation": {
"uri": "volvox.bw.nonexist",
"locationType": "UriLocation"
}
}
},
{
"type": "VariantTrack",
"trackId": "variant_colors",
"name": "volvox filtered vcf (green snp, purple indel)",
"category": ["Variants"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"uri": "volvox.filtered.vcf.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.filtered.vcf.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "ChordVariantDisplay",
"displayId": "volvox_filtered_vcf_color-ChordVariantDisplay"
},
{
"type": "LinearVariantDisplay",
"maxFeatureScreenDensity": 0.0006,
"displayId": "volvox_filtered_vcf_color-LinearVariantDisplay",
"color": "jexl:feature.type=='SNV'?'green':'purple'"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "MM-chebi-volvox",
"name": "MM-chebi-volvox",
"category": ["Methylation"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "MM-chebi-volvox.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "MM-chebi-volvox.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "MM-double-volvox",
"name": "MM-double-volvox",
"category": ["Methylation"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "MM-double-volvox.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "MM-double-volvox.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "MM-multi-volvox",
"name": "MM-multi-volvox",
"category": ["Methylation"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "MM-multi-volvox.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "MM-multi-volvox.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "MM-orient-volvox",
"name": "MM-orient-volvox",
"category": ["Methylation"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "MM-orient-volvox.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "MM-orient-volvox.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "FeatureTrack",
"trackId": "single_exon_gene",
"category": ["Miscellaneous"],
"name": "Single exon gene",
"assemblyNames": ["volvox"],
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "single_exon_gene.sorted.gff.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "single_exon_gene.sorted.gff.gz.tbi",
"locationType": "UriLocation"
}
}
}
},
{
"type": "FeatureTrack",
"trackId": "gtf_plain_text_test",
"category": ["Miscellaneous"],
"name": "GTF - volvox.sorted.gtf",
"assemblyNames": ["volvox"],
"metadata": {
"skipTextIndex": true
},
"adapter": {
"type": "GtfAdapter",
"gtfLocation": {
"uri": "volvox.sorted.gtf",
"locationType": "UriLocation"
}
}
},
{
"type": "VariantTrack",
"trackId": "volvox.inv.vcf",
"name": "volvox inversions",
"category": ["Variants"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"uri": "volvox.inv.vcf.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.inv.vcf.gz.tbi",
"locationType": "UriLocation"
},
"indexType": "TBI"
}
}
},
{
"type": "AlignmentsTrack",
"trackId": "Deep sequencing",
"name": "Deep sequencing",
"category": ["Alignments"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "deep_sequencing.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "deep_sequencing.cram.crai",
"locationType": "UriLocation"
}
},
"displays": [
{
"type": "LinearAlignmentsDisplay",
"displayId": "deep_seq_alignments",
"maxHeight": 10000
}
]
},
{
"type": "FeatureTrack",
"trackId": "arc_track",
"name": "FromConfig Track (arcs as link marks)",
"assemblyNames": ["volvox"],
"category": ["Miscellaneous"],
"adapter": {
"type": "FromConfigAdapter",
"adapterId": "Y4yJ6gAC2E",
"features": [
{
"uniqueId": "arc-one",
"refName": "ctgA",
"start": 190,
"end": 200,
"type": "foo",
"score": 2,
"name": "SE_001"
},
{
"uniqueId": "arc-two",
"refName": "ctgA",
"start": 191,
"end": 192,
"type": "bar",
"score": 5,
"name": "SE_002"
},
{
"uniqueId": "arc-three",
"refName": "ctgA",
"start": 210,
"end": 290,
"type": "baz",
"score": 50,
"name": "SE_003"
},
{
"uniqueId": "arc-four",
"refName": "ctgA",
"start": 180,
"end": 189,
"score": 200,
"type": "quux",
"name": "SE_004, and some other characters that make the name extra long"
}
]
},
"displays": [
{
"type": "LinearMarkDisplay",
"displayId": "arc_track_linear",
"marks": [
{
"mark": "link",
"encoding": {
"size": { "field": "score", "scale": "log", "range": [1, 8] }
}
},
{ "mark": "text", "encoding": { "text": "score" } }
]
}
]
},
{
"type": "FeatureTrack",
"trackId": "arc_track_custom_height",
"name": "Arc track (apex at a jexl value)",
"assemblyNames": ["volvox"],
"category": ["Miscellaneous"],
"adapter": {
"type": "FromConfigAdapter",
"adapterId": "arc_custom_height_adapter",
"features": [
{
"uniqueId": "arc-custom-one",
"refName": "ctgA",
"start": 190,
"end": 400,
"type": "foo",
"score": 2,
"name": "SE_001"
},
{
"uniqueId": "arc-custom-two",
"refName": "ctgA",
"start": 191,
"end": 300,
"type": "bar",
"score": 5,
"name": "SE_002"
}
]
},
"displays": [
{
"type": "LinearMarkDisplay",
"displayId": "arc_track_custom_height_linear",
"marks": [
{
"mark": "link",
"encoding": { "y": "jexl:log10(feature.end-feature.start)" }
}
]
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "spliced",
"name": "volvox-rnaseq demo",
"category": ["Alignments"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "spliced.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "spliced.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
}
},
{
"type": "FeatureTrack",
"trackId": "volvox.filtered.lowercase",
"name": "volvox.filtered.lowercase",
"adapter": {
"type": "VcfAdapter",
"vcfLocation": {
"uri": "volvox.filtered.lowercase.vcf",
"locationType": "UriLocation"
}
},
"category": ["Integration test"],
"assemblyNames": ["volvox"]
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_del2.paf",
"name": "volvox_del2.paf",
"assemblyNames": ["volvox", "volvox_del2"],
"adapter": {
"type": "PAFAdapter",
"targetAssembly": "volvox",
"queryAssembly": "volvox_del2",
"pafLocation": {
"uri": "volvox_del.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_del.paf",
"name": "volvox_del.paf",
"assemblyNames": ["volvox", "volvox_del"],
"adapter": {
"type": "PAFAdapter",
"targetAssembly": "volvox",
"queryAssembly": "volvox_del",
"pafLocation": {
"uri": "volvox_del.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_alias_control.paf",
"name": "volvox_alias_control.paf",
"assemblyNames": ["volvox", "volvox_del"],
"adapter": {
"type": "PAFAdapter",
"assemblyNames": ["volvox", "volvox_del"],
"pafLocation": {
"uri": "volvox_alias_control.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_alias_query.paf",
"name": "volvox_alias_query.paf",
"assemblyNames": ["volvox", "volvox_del"],
"adapter": {
"type": "PAFAdapter",
"assemblyNames": ["volvox", "volvox_del"],
"pafLocation": {
"uri": "volvox_alias_query.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_alias_target.paf",
"name": "volvox_alias_target.paf",
"assemblyNames": ["volvox_del", "volvox"],
"adapter": {
"type": "PAFAdapter",
"assemblyNames": ["volvox_del", "volvox"],
"pafLocation": {
"uri": "volvox_alias_target.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_offscreen_alias.paf",
"name": "volvox_offscreen_alias.paf",
"assemblyNames": ["volvox_del", "volvox"],
"adapter": {
"type": "PAFAdapter",
"assemblyNames": ["volvox_del", "volvox"],
"pafLocation": {
"uri": "volvox_offscreen_alias.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_asmalias.paf",
"name": "volvox_asmalias.paf",
"assemblyNames": ["volvox_del", "vvx"],
"adapter": {
"type": "PAFAdapter",
"assemblyNames": ["volvox_del", "vvx"],
"pafLocation": {
"uri": "volvox_asmalias.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_ins.paf",
"name": "volvox_ins.paf",
"assemblyNames": ["volvox", "volvox_ins"],
"adapter": {
"type": "PAFAdapter",
"targetAssembly": "volvox",
"queryAssembly": "volvox_ins",
"pafLocation": {
"uri": "volvox_ins.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_all_vs_all",
"name": "volvox all-vs-all (ins/volvox/del pangenome)",
"assemblyNames": ["volvox_ins", "volvox", "volvox_del"],
"adapter": {
"type": "MultiGenomePAFAdapter",
"assemblyNames": ["volvox_ins", "volvox", "volvox_del"],
"pafLocation": {
"uri": "volvox_all_vs_all.paf"
}
}
},
{
"type": "SyntenyTrack",
"category": ["Synteny"],
"trackId": "volvox_all_vs_all_indexed",
"name": "volvox all-vs-all indexed (ins/volvox/del pangenome)",
"assemblyNames": ["volvox_ins", "volvox", "volvox_del"],
"adapter": {
"type": "MultiGenomeIndexedPAFAdapter",
"assemblyNames": ["volvox_ins", "volvox", "volvox_del"],
"pifGzLocation": {
"uri": "volvox_all_vs_all.pif.gz"
},
"index": {
"indexType": "TBI",
"location": {
"uri": "volvox_all_vs_all.pif.gz.tbi"
}
}
}
},
{
"type": "VariantTrack",
"trackId": "variant_effect_demo_data",
"name": "Ensembl VEP example",
"adapter": {
"type": "VcfAdapter",
"vcfLocation": {
"uri": "variant_effect_demo_data.vcf",
"locationType": "UriLocation"
}
},
"category": ["Variants"],
"assemblyNames": ["volvox"]
},
{
"type": "VariantTrack",
"trackId": "variant_effect_demo_jannovar",
"name": "Jannovar example",
"adapter": {
"type": "VcfAdapter",
"vcfLocation": {
"uri": "volvox_vcf_jannovar.vcf",
"locationType": "UriLocation"
}
},
"category": ["Variants"],
"assemblyNames": ["volvox"]
},
{
"type": "SyntenyTrack",
"trackId": "volvox-rev-del",
"category": ["Synteny"],
"name": "volvox-rev-del",
"adapter": {
"type": "PAFAdapter",
"pafLocation": {
"uri": "volvox-rev-del.paf",
"locationType": "UriLocation"
},
"assemblyNames": ["volvox-rev-del", "volvox"]
},
"assemblyNames": ["volvox-rev-del", "volvox"]
},
{
"type": "FeatureTrack",
"trackId": "volvox-rev-del-annotations",
"name": "volvox-rev-del-annotations",
"adapter": {
"type": "Gff3Adapter",
"gffLocation": {
"uri": "volvox-rev-del.gff",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox-rev-del"]
},
{
"type": "AlignmentsTrack",
"category": ["Alignments"],
"trackId": "volvox-simple-inv.bam",
"name": "volvox-simple-inv.bam",
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-simple-inv.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-simple-inv.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "AlignmentsTrack",
"category": ["Alignments"],
"trackId": "volvox-simple-inv.cram",
"name": "volvox-simple-inv.cram",
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-simple-inv.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-simple-inv.cram.crai",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "AlignmentsTrack",
"category": ["Alignments"],
"trackId": "volvox-simple-inv-paired.cram",
"name": "volvox-simple-inv-paired.cram",
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-simple-inv-paired.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-simple-inv-paired.cram.crai",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "AlignmentsTrack",
"category": ["Alignments"],
"trackId": "volvox-simple-inv-paired.bam",
"name": "volvox-simple-inv-paired.bam",
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-simple-inv-paired.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-simple-inv-paired.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "SyntenyTrack",
"trackId": "volvox_inv_indels",
"name": "volvox_inv_indels",
"category": ["Synteny"],
"adapter": {
"type": "PAFAdapter",
"pafLocation": {
"uri": "volvox_inv_indels.paf",
"locationType": "UriLocation"
},
"assemblyNames": ["volvox_random_inv", "volvox"]
},
"assemblyNames": ["volvox_random_inv", "volvox"]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox-inv-pbsim",
"name": "volvox-inv-pbsim",
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-inv-pbsim.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-inv-pbsim.cram.crai",
"locationType": "UriLocation"
}
},
"category": ["Alignments"],
"assemblyNames": ["volvox"]
},
{
"type": "AlignmentsTrack",
"trackId": "paired_end_stranded_rnaseq",
"name": "volvox-stranded-rnaseq",
"category": ["Alignments"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "paired_end_stranded_rnaseq.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "paired_end_stranded_rnaseq.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "FeatureTrack",
"trackId": "arc_test",
"name": "Arc test track",
"category": ["Miscellaneous"],
"adapter": {
"type": "BedAdapter",
"bedLocation": {
"uri": "arc_test.bed",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "VariantTrack",
"trackId": "volvox_bedpe",
"name": "BEDPE arcs",
"category": ["Variants"],
"adapter": {
"type": "BedpeAdapter",
"bedpeLocation": {
"uri": "volvox.bedpe",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"],
"displays": [
{
"type": "LinearMarkDisplay",
"displayId": "volvox_bedpe-LinearMarkDisplay",
"marks": [
{
"mark": "link",
"encoding": {
"color": { "value": "#a65628" },
"size": 3
},
"transform": [{ "type": "mate" }]
}
]
}
]
},
{
"type": "VariantTrack",
"trackId": "volvox_star_fusion",
"name": "STAR-Fusion fusions",
"category": ["Variants"],
"adapter": {
"type": "StarFusionAdapter",
"starFusionLocation": {
"uri": "volvox.star-fusion.tsv",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"],
"displays": [
{
"type": "LinearMarkDisplay",
"displayId": "volvox_star_fusion-LinearMarkDisplay",
"marks": [
{
"mark": "link",
"encoding": {
"color": { "value": "#a65628" },
"size": 3
},
"transform": [{ "type": "mate" }]
}
]
}
]
},
{
"type": "SyntenyTrack",
"trackId": "volvox_del.pif",
"name": "volvox_del.pif",
"category": ["Synteny"],
"adapter": {
"type": "PairwiseIndexedPAFAdapter",
"pifGzLocation": {
"uri": "volvox_del.pif.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox_del.pif.gz.tbi",
"locationType": "UriLocation"
},
"indexType": "TBI"
},
"assemblyNames": ["volvox_del", "volvox"]
},
"assemblyNames": ["volvox_del", "volvox"]
},
{
"type": "SyntenyTrack",
"trackId": "volvox_ins.pif",
"name": "volvox_ins.pif",
"category": ["Synteny"],
"adapter": {
"type": "PairwiseIndexedPAFAdapter",
"pifGzLocation": {
"uri": "volvox_ins.pif.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox_ins.pif.gz.tbi",
"locationType": "UriLocation"
},
"indexType": "TBI"
},
"assemblyNames": ["volvox_ins", "volvox"]
},
"assemblyNames": ["volvox_ins", "volvox"]
},
{
"type": "FeatureTrack",
"trackId": "test",
"name": "Multi-part feature segments",
"category": ["Integration test"],
"adapter": {
"type": "Gff3Adapter",
"gffLocation": {
"uri": "multipart.gff",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox-sorted.noref.cram",
"name": "volvox-sorted.cram (noref)",
"category": ["Integration test"],
"adapter": {
"type": "CramAdapter",
"cramLocation": {
"uri": "volvox-sorted.noref.cram",
"locationType": "UriLocation"
},
"craiLocation": {
"uri": "volvox-sorted.noref.cram.crai",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "QuantitativeTrack",
"trackId": "volvox_repeats_minus",
"name": "volvox_repeats (minus)",
"assemblyNames": ["volvox"],
"category": ["Integration test", "Wiggle"],
"adapter": {
"type": "BedAdapter",
"bedLocation": {
"locationType": "UriLocation",
"uri": "volvox_repeat_minus.bed"
}
},
"displays": [
{
"type": "LinearWiggleDisplay",
"displayId": "volvox_repeats-minus-LinearWiggleDisplay"
}
]
},
{
"type": "QuantitativeTrack",
"trackId": "volvox_repeats_plus",
"name": "volvox_repeats (plus)",
"assemblyNames": ["volvox"],
"category": ["Integration test", "Wiggle"],
"adapter": {
"type": "BedAdapter",
"bedLocation": {
"locationType": "UriLocation",
"uri": "volvox_repeat_plus.bed"
}
},
"displays": [
{
"type": "LinearWiggleDisplay",
"displayId": "volvox_repeat-plus-LinearWiggleDisplay"
}
]
},
{
"type": "AlignmentsTrack",
"trackId": "volvox-sv.renamed",
"name": "volvox-sv.renamed",
"category": ["Alignments"],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "volvox-sv.renamed.bam",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox-sv.renamed.bam.bai",
"locationType": "UriLocation"
},
"indexType": "BAI"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "FeatureTrack",
"trackId": "gff3_custom_tooltips",
"assemblyNames": ["volvox"],
"name": "Custom Tooltips (mouseover callback)",
"category": ["Label Positioning Examples"],
"metadata": {
"skipTextIndex": true
},
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "volvox.sort.gff3.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.sort.gff3.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"mouseover": "jexl:`${feature.name} [${feature.type}] at ${feature.start} - ${feature.end} (strand: ${(feature.strand == 1 ? '+' : feature.strand == -1 ? '-' : 'none'})`",
"labels": {
"name": "jexl:feature.name || feature.id",
"description": "jexl:feature.note || feature.description || ''"
},
"showLabels": "auto",
"subfeatureLabels": "below",
"type": "LinearBasicDisplay",
"displayId": "gff3_custom_tooltips_linear"
}
]
},
{
"type": "FeatureTrack",
"trackId": "gff3_mouseover_attr",
"assemblyNames": ["volvox"],
"name": "_mouseOver Attributes",
"category": ["Label Positioning Examples"],
"metadata": {
"skipTextIndex": true
},
"adapter": {
"type": "Gff3Adapter",
"gffLocation": {
"uri": "volvox_mouseover.sorted.gff3",
"locationType": "UriLocation"
}
},
"displays": [
{
"labels": {
"name": "jexl:feature.name || feature.id",
"description": "jexl:feature.note || feature.description || ''"
},
"showLabels": "auto",
"subfeatureLabels": "below",
"type": "LinearBasicDisplay",
"displayId": "gff3_mouseover_attr_linear"
}
]
},
{
"type": "VariantTrack",
"trackId": "volvox_del_sv",
"name": "Volvox DEL SV",
"category": ["Variants"],
"adapter": {
"type": "VcfAdapter",
"vcfLocation": {
"uri": "volvox.del.vcf",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "LDTrack",
"trackId": "volvox_ld",
"name": "volvox LD (PLINK --r2)",
"category": ["Variants"],
"adapter": {
"type": "PlinkLDAdapter",
"ldLocation": {
"uri": "volvox.ld",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"]
},
{
"type": "VariantTrack",
"trackId": "volvox multi-sample sv",
"name": "volvox multi-sample sv",
"category": ["Variants"],
"adapter": {
"type": "VcfTabixAdapter",
"uri": "volvox.sv.vcf.gz",
"samplesTsvLocation": {
"uri": "volvox.sv.samples.tsv",
"locationType": "UriLocation"
}
},
"assemblyNames": ["volvox"],
"displays": [
{
"type": "LinearMultiSampleVariantDisplay",
"displayId": "volvox multi-sample sv-LinearMultiSampleVariantDisplay",
"referenceDrawingMode": "draw",
"rowColor": "population"
}
]
},
{
"type": "VariantTrack",
"trackId": "volvox_test_vcf_jexl",
"name": "volvox 1000genomes vcf (JEXL filters + coloring)",
"assemblyNames": ["volvox"],
"category": ["Variants"],
"adapter": {
"type": "VcfTabixAdapter",
"uri": "volvox.test.vcf.gz"
},
"displays": [
{
"type": "LinearVariantDisplay",
"displayId": "volvox_test_vcf_jexl-LinearVariantDisplay",
"filter": ["jexl:feature.start<8000"],
"color": "jexl:feature.start>5000?'darkgreen':'red'"
}
]
},
{
"type": "VariantTrack",
"trackId": "volvox_variants_vcf",
"name": "volvox variants (vg deconstruct -a -u)",
"category": ["Synteny"],
"assemblyNames": ["volvox"],
"metadata": {
"skipTextIndex": true
},
"adapter": {
"type": "VcfTabixAdapter",
"vcfGzLocation": {
"uri": "volvox.variants.vcf.gz",
"locationType": "UriLocation"
},
"index": {
"location": {
"uri": "volvox.variants.vcf.gz.tbi",
"locationType": "UriLocation"
}
}
}
},
{
"type": "MafTrack",
"trackId": "volvox_maf",
"name": "MAF multiple alignment (tabix)",
"category": ["Multiple alignment"],
"assemblyNames": ["volvox"],
"adapter": {
"type": "MafTabixAdapter",
"samples": [
"volvox",
"simvolvox",
"minivolvox",
"microvolvox",
"nanovolvox",
"megavolvox",
"ultravolvox",
"picovolvox",
"hypervolvox",
"metavolvox"
],
"bedGzLocation": {
"uri": "volvox.maf.bed.gz",
"locationType": "UriLocation"
},
"nhLocation": {
"uri": "volvox.maf.nh",
"locationType": "UriLocation"
},
"index": {
"indexType": "TBI",
"location": {
"uri": "volvox.maf.bed.gz.tbi",
"locationType": "UriLocation"
}
}
},
"displays": [
{
"type": "LinearMafDisplay",
"displayId": "volvox_maf-LinearMafDisplay"
}
]
}
],
"plugins": [
{
"name": "UMDUrlPlugin",
"umdLoc": {
"uri": "umd_plugin.js"
}
}
],
"aggregateTextSearchAdapters": [
{
"type": "TrixTextSearchAdapter",
"ixFilePath": {
"uri": "trix/volvox.ix",
"locationType": "UriLocation"
},
"ixxFilePath": {
"uri": "trix/volvox.ixx",
"locationType": "UriLocation"
},
"assemblyNames": ["volvox"]
},
{
"type": "TrixTextSearchAdapter",
"ixFilePath": {
"uri": "trix/volvox-rev-del.ix",
"locationType": "UriLocation"
},
"ixxFilePath": {
"uri": "trix/volvox-rev-del.ixx",
"locationType": "UriLocation"
},
"assemblyNames": ["volvox-rev-del"]
}
]
}