@sjcrh/proteinpaint-shared 2.180.0 → 2.180.1

package/src/common.js

@@ -8,40 +8,40 @@ exported functions
 
 
 */
-import { rgb } from 'd3-color'
-import * as d3scale from 'd3-scale'
-import * as d3 from 'd3'
-import { getWrappedTvslst } from './filter.js'
+import { rgb } from "d3-color"
+import * as d3scale from "d3-scale"
+import * as d3 from "d3"
+import { getWrappedTvslst } from "./filter.js"
 
 // moved from `#shared/terms` to here, so that this can be passed as
 // part of 'common' argument to exported dataset js function, at server runtime
 export const TermTypeGroups = {
-	DICTIONARY_VARIABLES: 'Dictionary Variables',
-	DNA_METHYLATION: 'DNA Methylation',
-	GENE_DEPENDENCY: 'Gene Dependency',
-	GENE_EXPRESSION: 'Gene Expression',
-	GSEA: 'GSEA',
-	METABOLITE_INTENSITY: 'Metabolite Intensity',
-	WHOLE_PROTEOME_ABUNDANCE: 'Whole Proteome Abundance',
-	MUTATION_CNV_FUSION: 'Mutation/CNV/Fusion',
-	MUTATION_SIGNATURE: 'Mutation Signature',
-	PROTEIN_EXPRESSION: 'Protein Expression',
-	SINGLECELL_CELLTYPE: 'Single-cell Cell Type',
-	SINGLECELL_GENE_EXPRESSION: 'Single-cell Gene Expression',
-	SNP: 'SNP Genotype',
-	SNP_LIST: 'SNP List',
-	SNP_LOCUS: 'SNP Locus',
-	SPLICE_JUNCTION: 'Splice Junction',
-	SSGSEA: 'Geneset Expression',
-	TERM_COLLECTION: 'Term Collection',
-	VARIANT_GENOTYPE: 'Variant Genotype'
-}
-
-export const defaultcolor = rgb('#8AB1D4').darker()
-export const default_text_color = rgb('#aaa').darker().darker()
-
-export const exoncolor = '#4F8053'
-export const plotColor = '#ce768e'
+	DICTIONARY_VARIABLES: "Dictionary Variables",
+	DNA_METHYLATION: "DNA Methylation",
+	GENE_DEPENDENCY: "Gene Dependency",
+	GENE_EXPRESSION: "Gene Expression",
+	GSEA: "GSEA",
+	METABOLITE_INTENSITY: "Metabolite Intensity",
+	PROTEOME_ABUNDANCE: "Whole Proteome Abundance",
+	MUTATION_CNV_FUSION: "Mutation/CNV/Fusion",
+	MUTATION_SIGNATURE: "Mutation Signature",
+	PROTEIN_EXPRESSION: "Protein Expression",
+	SINGLECELL_CELLTYPE: "Single-cell Cell Type",
+	SINGLECELL_GENE_EXPRESSION: "Single-cell Gene Expression",
+	SNP: "SNP Genotype",
+	SNP_LIST: "SNP List",
+	SNP_LOCUS: "SNP Locus",
+	SPLICE_JUNCTION: "Splice Junction",
+	SSGSEA: "Geneset Expression",
+	TERM_COLLECTION: "Term Collection",
+	VARIANT_GENOTYPE: "Variant Genotype",
+}
+
+export const defaultcolor = rgb("#8AB1D4").darker()
+export const default_text_color = rgb("#aaa").darker().darker()
+
+export const exoncolor = "#4F8053"
+export const plotColor = "#ce768e"
 
 // something that has something to do with coding gene reading frame
 export const IN_frame = true
@@ -68,46 +68,48 @@ export const dtloh = 10
 export const dtmetaboliteintensity = 11
 export const dtssgsea = 12
 export const dtdnamethylation = 13
-export const dtwholeproteomeabundance = 14
+export const dtproteomeabundance = 14
 // add new dt value here. !!!DO NOT change value of existing dt!!!
 
 export const dt2label = {
-	[dtsnvindel]: 'SNV/indel',
-	[dtfusionrna]: 'Fusion RNA',
-	[dtcnv]: 'CNV',
-	[dtsv]: 'SV',
-	[dtitd]: 'ITD',
-	[dtdel]: 'Deletion',
-	[dtnloss]: 'N-loss',
-	[dtcloss]: 'C-loss',
-	[dtloh]: 'LOH',
-	[dtgeneexpression]: 'Gene Expression',
-	[dtmetaboliteintensity]: 'Metabolite Intensity',
-	[dtwholeproteomeabundance]: 'Whole Proteome Abundance'
+	[dtsnvindel]: "SNV/indel",
+	[dtfusionrna]: "Fusion RNA",
+	[dtcnv]: "CNV",
+	[dtsv]: "SV",
+	[dtitd]: "ITD",
+	[dtdel]: "Deletion",
+	[dtnloss]: "N-loss",
+	[dtcloss]: "C-loss",
+	[dtloh]: "LOH",
+	[dtgeneexpression]: "Gene Expression",
+	[dtmetaboliteintensity]: "Metabolite Intensity",
+	[dtproteomeabundance]: "Whole Proteome Abundance",
 }
 
 // Maps dt types to UI labels and lesion types for GRIN2
 // All dt types use lesionTypes array for consistency
 export const dt2lesion = {
 	[dtsnvindel]: {
-		uilabel: 'SNV/INDEL (Mutation)',
-		lesionTypes: [{ name: 'Mutation', lesionType: 'mutation', color: '#44AA44' }]
+		uilabel: "SNV/INDEL (Mutation)",
+		lesionTypes: [
+			{ name: "Mutation", lesionType: "mutation", color: "#44AA44" },
+		],
 	},
 	[dtcnv]: {
-		uilabel: 'CNV (Copy Number Variation)',
+		uilabel: "CNV (Copy Number Variation)",
 		lesionTypes: [
-			{ name: 'Loss', lesionType: 'loss', color: '#4444FF' },
-			{ name: 'Gain', lesionType: 'gain', color: '#FF4444' }
-		]
+			{ name: "Loss", lesionType: "loss", color: "#4444FF" },
+			{ name: "Gain", lesionType: "gain", color: "#FF4444" },
+		],
 	},
 	[dtsv]: {
-		uilabel: 'SV (Structural Variation)',
-		lesionTypes: [{ name: 'SV', lesionType: 'sv', color: '#9932CC' }]
+		uilabel: "SV (Structural Variation)",
+		lesionTypes: [{ name: "SV", lesionType: "sv", color: "#9932CC" }],
 	},
 	[dtfusionrna]: {
-		uilabel: 'Fusion (RNA Fusion)',
-		lesionTypes: [{ name: 'Fusion', lesionType: 'fusion', color: '#FFA500' }]
-	}
+		uilabel: "Fusion (RNA Fusion)",
+		lesionTypes: [{ name: "Fusion", lesionType: "fusion", color: "#FFA500" }],
+	},
 }
 
 // Maps GRIN2 option types to their corresponding dt values
@@ -115,166 +117,190 @@ export const optionToDt = {
 	snvindelOptions: dtsnvindel,
 	cnvOptions: dtcnv,
 	fusionOptions: dtfusionrna,
-	svOptions: dtsv
+	svOptions: dtsv,
 }
 
 export const mclass = {
 	M: {
-		label: 'MISSENSE',
-		color: '#3987CC',
+		label: "MISSENSE",
+		color: "#3987CC",
 		dt: dtsnvindel,
-		desc: 'A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved',
-		key: 'M'
+		desc: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved",
+		key: "M",
+	},
+	E: {
+		label: "EXON",
+		color: "#bcbd22",
+		dt: dtsnvindel,
+		desc: "A variant in the exon of a non-coding RNA.",
+		key: "E",
 	},
-	E: { label: 'EXON', color: '#bcbd22', dt: dtsnvindel, desc: 'A variant in the exon of a non-coding RNA.', key: 'E' },
 	F: {
-		label: 'FRAMESHIFT',
-		color: 'rgb(200, 61, 61)',
+		label: "FRAMESHIFT",
+		color: "rgb(200, 61, 61)",
 		dt: dtsnvindel,
-		desc: 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three',
-		key: 'F'
+		desc: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three",
+		key: "F",
 	},
 	N: {
-		label: 'NONSENSE',
-		color: '#ff7f0e',
+		label: "NONSENSE",
+		color: "#ff7f0e",
 		dt: dtsnvindel,
-		desc: 'A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript',
-		key: 'N'
+		desc: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript",
+		key: "N",
 	},
 	S: {
-		label: 'SILENT',
-		color: '#2ca02c',
+		label: "SILENT",
+		color: "#2ca02c",
 		dt: dtsnvindel,
-		desc: 'A sequence variant where there is no resulting change to the encoded amino acid',
-		key: 'S'
+		desc: "A sequence variant where there is no resulting change to the encoded amino acid",
+		key: "S",
 	},
 	D: {
-		label: 'PROTEINDEL',
-		color: 'rgb(100, 100, 100)',
+		label: "PROTEINDEL",
+		color: "rgb(100, 100, 100)",
 		dt: dtsnvindel,
-		desc: 'An inframe non synonymous variant that deletes bases from the coding sequence',
-		key: 'D'
+		desc: "An inframe non synonymous variant that deletes bases from the coding sequence",
+		key: "D",
 	},
 	I: {
-		label: 'PROTEININS',
-		color: '#8c564b',
+		label: "PROTEININS",
+		color: "#8c564b",
 		dt: dtsnvindel,
-		desc: 'An inframe non synonymous variant that inserts bases into in the coding sequence',
-		key: 'I'
+		desc: "An inframe non synonymous variant that inserts bases into in the coding sequence",
+		key: "I",
 	},
 	ProteinAltering: {
-		label: 'PROTEINALTERING',
-		color: '#5a0034',
+		label: "PROTEINALTERING",
+		color: "#5a0034",
 		dt: dtsnvindel,
-		desc: 'An inframe complex change to the coding sequence',
-		key: 'ProteinAltering'
+		desc: "An inframe complex change to the coding sequence",
+		key: "ProteinAltering",
 	},
 	P: {
-		label: 'SPLICE_REGION',
-		color: '#9467bd',
+		label: "SPLICE_REGION",
+		color: "#9467bd",
 		dt: dtsnvindel,
-		desc: 'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron',
-		key: 'P'
+		desc: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron",
+		key: "P",
 	},
 	L: {
-		label: 'SPLICE',
-		color: '#6633FF',
+		label: "SPLICE",
+		color: "#6633FF",
+		dt: dtsnvindel,
+		desc: "A variant near an exon edge that may affect splicing functionality",
+		key: "L",
+	},
+	Intron: {
+		label: "INTRON",
+		color: "#656565",
 		dt: dtsnvindel,
-		desc: 'A variant near an exon edge that may affect splicing functionality',
-		key: 'L'
+		desc: "An intronic variant.",
+		key: "Intron",
 	},
-	Intron: { label: 'INTRON', color: '#656565', dt: dtsnvindel, desc: 'An intronic variant.', key: 'Intron' },
 
 	StopLost: {
-		label: 'Stop lost',
-		color: '#ff7f0e',
+		label: "Stop lost",
+		color: "#ff7f0e",
 		dt: dtsnvindel,
-		desc: 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript',
-		key: 'StopLost'
+		desc: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript",
+		key: "StopLost",
 	},
 	StartLost: {
-		label: 'Start lost',
-		color: '#ff7f0e',
+		label: "Start lost",
+		color: "#ff7f0e",
 		dt: dtsnvindel,
-		desc: 'A codon variant that changes at least one base of the canonical start codon',
-		key: 'StartLost'
+		desc: "A codon variant that changes at least one base of the canonical start codon",
+		key: "StartLost",
 	},
 
 	// quick fix!! for showing genes that are not tested in samples (e.g. gene panels) in the heatmap
-	Blank: { label: 'Not tested', color: '#fff', dt: dtsnvindel, desc: 'This gene is not tested.', key: 'Blank' },
+	Blank: {
+		label: "Not tested",
+		color: "#fff",
+		dt: dtsnvindel,
+		desc: "This gene is not tested.",
+		key: "Blank",
+	},
 
-	WT: { label: 'Wildtype', color: '#D3D3D3', dt: dtsnvindel, desc: 'Wildtype', key: 'WT' }
+	WT: {
+		label: "Wildtype",
+		color: "#D3D3D3",
+		dt: dtsnvindel,
+		desc: "Wildtype",
+		key: "WT",
+	},
 }
-export const mclassitd = 'ITD'
+export const mclassitd = "ITD"
 mclass[mclassitd] = {
-	label: 'ITD',
-	color: '#ff70ff',
+	label: "ITD",
+	color: "#ff70ff",
 	dt: dtitd,
-	desc: 'In-frame internal tandem duplication.',
-	key: mclassitd
+	desc: "In-frame internal tandem duplication.",
+	key: mclassitd,
 }
 
-export const mclassdel = 'DEL'
+export const mclassdel = "DEL"
 mclass[mclassdel] = {
-	label: 'DELETION, intragenic',
-	color: '#858585',
+	label: "DELETION, intragenic",
+	color: "#858585",
 	dt: dtdel,
-	desc: 'Intragenic deletion.',
-	key: mclassdel
+	desc: "Intragenic deletion.",
+	key: mclassdel,
 }
 
-export const mclassnloss = 'NLOSS'
+export const mclassnloss = "NLOSS"
 mclass[mclassnloss] = {
-	label: 'N-terminus loss',
-	color: '#545454',
+	label: "N-terminus loss",
+	color: "#545454",
 	dt: dtnloss,
-	desc: 'N-terminus loss due to translocation',
-	key: mclassnloss
+	desc: "N-terminus loss due to translocation",
+	key: mclassnloss,
 }
 
-export const mclasscloss = 'CLOSS'
+export const mclasscloss = "CLOSS"
 mclass[mclasscloss] = {
-	label: 'C-terminus loss',
-	color: '#545454',
+	label: "C-terminus loss",
+	color: "#545454",
 	dt: dtcloss,
-	desc: 'C-terminus loss due to translocation',
-	key: mclasscloss
+	desc: "C-terminus loss due to translocation",
+	key: mclasscloss,
 }
 
-export const mclassutr3 = 'Utr3'
+export const mclassutr3 = "Utr3"
 mclass[mclassutr3] = {
-	label: 'UTR_3',
-	color: '#998199',
+	label: "UTR_3",
+	color: "#998199",
 	dt: dtsnvindel,
 	desc: "A variant in the 3' untranslated region.",
-	key: mclassutr3
+	key: mclassutr3,
 }
 
-export const mclassutr5 = 'Utr5'
+export const mclassutr5 = "Utr5"
 mclass[mclassutr5] = {
-	label: 'UTR_5',
-	color: '#819981',
+	label: "UTR_5",
+	color: "#819981",
 	dt: dtsnvindel,
 	desc: "A variant in the 5' untranslated region.",
-	key: mclassutr5
+	key: mclassutr5,
 }
 
-export const mclassnonstandard = 'X'
+export const mclassnonstandard = "X"
 mclass[mclassnonstandard] = {
-	label: 'NONSTANDARD',
-	color: 'black',
+	label: "NONSTANDARD",
+	color: "black",
 	dt: dtsnvindel,
-	desc: 'A mutation class that either does not match our notation, or is unspecified.',
-	key: mclassnonstandard
+	desc: "A mutation class that either does not match our notation, or is unspecified.",
+	key: mclassnonstandard,
 }
 
-export const mclassnoncoding = 'noncoding'
+export const mclassnoncoding = "noncoding"
 mclass[mclassnoncoding] = {
-	label: 'NONCODING',
-	color: 'black',
+	label: "NONCODING",
+	color: "black",
 	dt: dtsnvindel,
-	desc: 'Noncoding mutation.',
-	key: mclassnoncoding
+	desc: "Noncoding mutation.",
+	key: mclassnoncoding,
 }
 
 /*
@@ -289,46 +315,46 @@ from this array derives multiple types of lookup tables to perform mapping on bo
 */
 const SOterms = [
 	//transcript_ablation // not supported: 1) do not expect this in maf/vcf 2) should be represented as cnv deletion but not the legacy unused value "dtdel"; if needed can reenable
-	['splice_acceptor_variant', 'L'],
-	['splice_donor_variant', 'L'],
-	['stop_gained', 'N'],
-	['frameshift_variant', 'F'],
-	['stop_lost', 'StopLost'],
-	['start_lost', 'StartLost'],
+	["splice_acceptor_variant", "L"],
+	["splice_donor_variant", "L"],
+	["stop_gained", "N"],
+	["frameshift_variant", "F"],
+	["stop_lost", "StopLost"],
+	["start_lost", "StartLost"],
 	//transcript_amplification // not supported, should be represented by cnv instead
-	['feature_elongation', mclassnoncoding],
-	['feature_truncation', mclassnoncoding],
-	['inframe_insertion', 'I'],
-	['inframe_deletion', 'D'],
-	['missense_variant', 'M'],
-	['protein_altering_variant', 'ProteinAltering'],
-	['splice_donor_5th_base_variant', 'P'],
-	['splice_region_variant', 'P'],
-	['splice_donor_region_variant', 'P'],
-	['splice_polypyrimidine_tract_variant', 'P'],
-	['incomplete_terminal_codon_variant', 'N'],
-	['start_retained_variant', 'S'],
-	['stop_retained_variant', 'S'],
-	['synonymous_variant', 'S'],
-	['coding_sequence_variant', 'E'],
-	['mature_miRNA_variant', 'E'],
-	['5_prime_UTR_variant', mclassutr5],
-	['3_prime_UTR_variant', mclassutr3],
-	['non_coding_transcript_exon_variant', 'E'],
-	['intron_variant', 'Intron'],
-	['NMD_transcript_variant', 'F'],
-	['non_coding_transcript_variant', 'E'],
-	['coding_transcript_variant', 'E'],
-	['upstream_gene_variant', mclassnoncoding],
-	['downstream_gene_variant', mclassnoncoding],
-	['TFBS_ablation', mclassnoncoding],
-	['TFBS_amplification', mclassnoncoding],
-	['TF_binding_site_variant', mclassnoncoding],
-	['regulatory_region_ablation', mclassnoncoding],
-	['regulatory_region_amplification', mclassnoncoding],
-	['regulatory_region_variant', mclassnoncoding],
-	['intergenic_variant', mclassnoncoding],
-	['sequence_variant', mclassnonstandard]
+	["feature_elongation", mclassnoncoding],
+	["feature_truncation", mclassnoncoding],
+	["inframe_insertion", "I"],
+	["inframe_deletion", "D"],
+	["missense_variant", "M"],
+	["protein_altering_variant", "ProteinAltering"],
+	["splice_donor_5th_base_variant", "P"],
+	["splice_region_variant", "P"],
+	["splice_donor_region_variant", "P"],
+	["splice_polypyrimidine_tract_variant", "P"],
+	["incomplete_terminal_codon_variant", "N"],
+	["start_retained_variant", "S"],
+	["stop_retained_variant", "S"],
+	["synonymous_variant", "S"],
+	["coding_sequence_variant", "E"],
+	["mature_miRNA_variant", "E"],
+	["5_prime_UTR_variant", mclassutr5],
+	["3_prime_UTR_variant", mclassutr3],
+	["non_coding_transcript_exon_variant", "E"],
+	["intron_variant", "Intron"],
+	["NMD_transcript_variant", "F"],
+	["non_coding_transcript_variant", "E"],
+	["coding_transcript_variant", "E"],
+	["upstream_gene_variant", mclassnoncoding],
+	["downstream_gene_variant", mclassnoncoding],
+	["TFBS_ablation", mclassnoncoding],
+	["TFBS_amplification", mclassnoncoding],
+	["TF_binding_site_variant", mclassnoncoding],
+	["regulatory_region_ablation", mclassnoncoding],
+	["regulatory_region_amplification", mclassnoncoding],
+	["regulatory_region_variant", mclassnoncoding],
+	["intergenic_variant", mclassnoncoding],
+	["sequence_variant", mclassnonstandard],
 ]
 
 // maps a pp class to an array of consequences
@@ -350,30 +376,30 @@ for (const [csq, cls] of SOterms) {
 // DO NOT USE to map vep consequences
 export function mclasstester(s) {
 	switch (s.toLowerCase()) {
-		case 'missense_mutation':
-			return 'M'
-		case 'nonsense_mutation':
-			return 'N'
-		case 'splice_site':
-			return 'L'
-		case 'splice_region':
-			return 'P'
-		case 'rna':
+		case "missense_mutation":
+			return "M"
+		case "nonsense_mutation":
+			return "N"
+		case "splice_site":
+			return "L"
+		case "splice_region":
+			return "P"
+		case "rna":
 			return mclassnoncoding
-		case 'frame_shift_del':
-			return 'F'
-		case 'frame_shift_ins':
-			return 'F'
-		case 'in_frame_del':
-			return 'D'
-		case 'in_frame_ins':
-			return 'I'
-		case 'protein_altering_variant':
-			return 'ProteinAltering'
-		case 'translation_start_site':
+		case "frame_shift_del":
+			return "F"
+		case "frame_shift_ins":
+			return "F"
+		case "in_frame_del":
+			return "D"
+		case "in_frame_ins":
+			return "I"
+		case "protein_altering_variant":
+			return "ProteinAltering"
+		case "translation_start_site":
 			return mclassnonstandard
-		case 'nonstop_mutation':
-			return 'N'
+		case "nonstop_mutation":
+			return "N"
 		case "3'utr":
 			return mclassutr3
 		case "3'flank":
@@ -382,115 +408,121 @@ export function mclasstester(s) {
 			return mclassutr5
 		case "5'flank":
 			return mclassnoncoding
-		case 'silent':
-			return 'S'
-		case 'blank':
-			return 'Blank'
+		case "silent":
+			return "S"
+		case "blank":
+			return "Blank"
 		default:
 			return null
 	}
 }
 
-export const mclassfusionrna = 'Fuserna'
+export const mclassfusionrna = "Fuserna"
 mclass[mclassfusionrna] = {
-	label: 'Fusion transcript',
-	color: '#545454',
+	label: "Fusion transcript",
+	color: "#545454",
 	dt: dtfusionrna,
 	desc:
-		'Marks the break points leading to fusion transcripts.<br>' +
-		'<span style="font-size:150%">&#9680;</span> - 3\' end of the break point is fused to the 5\' end of another break point in a different gene.<br>' +
-		'<span style="font-size:150%">&#9681;</span> - 5\' end of the break point is fused to the 3\' end of another break point in a different gene.',
-	key: mclassfusionrna
+		"Marks the break points leading to fusion transcripts.<br>" +
+		"<span style=\"font-size:150%\">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br>" +
+		"<span style=\"font-size:150%\">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.",
+	key: mclassfusionrna,
 }
-export const mclasssv = 'SV'
+export const mclasssv = "SV"
 mclass[mclasssv] = {
-	label: 'Structural variation',
-	color: '#858585',
+	label: "Structural variation",
+	color: "#858585",
 	dt: dtsv,
 	desc:
-		'<span style="font-size:150%">&#9680;</span> - 3\' end of the break point is fused to the 5\' end of another break point in a different gene.<br>' +
-		'<span style="font-size:150%">&#9681;</span> - 5\' end of the break point is fused to the 3\' end of another break point in a different gene.',
-	key: mclasssv
+		"<span style=\"font-size:150%\">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br>" +
+		"<span style=\"font-size:150%\">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.",
+	key: mclasssv,
 }
 
 // "CNV_amp" represents "CNV Gain" and is used in both 2-category and 5-category CNV data representation
 // "CNV_amplification" represents CNV amplification and is used in 5-category CNV
 // "CNV_amp" have to stay as-is since it may be hardcoded in lots of data beyond portal code.
-export const mclasscnvgain = 'CNV_amp'
+export const mclasscnvgain = "CNV_amp"
 mclass[mclasscnvgain] = {
-	label: 'Copy number gain', // TODO change to 'Gain'
-	color: '#e9a3c9',
+	label: "Copy number gain", // TODO change to 'Gain'
+	color: "#e9a3c9",
 	dt: dtcnv,
-	desc: 'Copy number gain',
-	key: mclasscnvgain
+	desc: "Copy number gain",
+	key: mclasscnvgain,
 }
 
-export const mclasscnvloss = 'CNV_loss'
+export const mclasscnvloss = "CNV_loss"
 mclass[mclasscnvloss] = {
-	label: 'Copy number loss',
-	color: '#a1d76a',
+	label: "Copy number loss",
+	color: "#a1d76a",
 	dt: dtcnv,
-	desc: 'Copy number loss',
-	key: mclasscnvloss
+	desc: "Copy number loss",
+	key: mclasscnvloss,
 }
 
 // mclasscnvAmp is next level above mclasscnvgain and is used in 5-category CNV data
-export const mclasscnvAmp = 'CNV_amplification'
+export const mclasscnvAmp = "CNV_amplification"
 mclass[mclasscnvAmp] = {
-	label: 'Copy number amplification',
-	color: '#ff0000',
+	label: "Copy number amplification",
+	color: "#ff0000",
 	dt: dtcnv,
-	desc: 'Copy number amplification',
-	key: mclasscnvAmp
+	desc: "Copy number amplification",
+	key: mclasscnvAmp,
 }
 
-export const mclasscnvHomozygousDel = 'CNV_homozygous_deletion'
+export const mclasscnvHomozygousDel = "CNV_homozygous_deletion"
 mclass[mclasscnvHomozygousDel] = {
-	label: 'Copy number homozygous deletion',
-	color: '#0000ff',
+	label: "Copy number homozygous deletion",
+	color: "#0000ff",
 	dt: dtcnv,
-	desc: 'Copy number homozygous deletion',
-	key: mclasscnvHomozygousDel
+	desc: "Copy number homozygous deletion",
+	key: mclasscnvHomozygousDel,
 }
 
-export const mclasscnvloh = 'CNV_loh'
-mclass[mclasscnvloh] = { label: 'LOH', color: '#12EDFC', dt: dtcnv, desc: 'Loss of heterozygosity', key: mclasscnvloh }
+export const mclasscnvloh = "CNV_loh"
+mclass[mclasscnvloh] = {
+	label: "LOH",
+	color: "#12EDFC",
+	dt: dtcnv,
+	desc: "Loss of heterozygosity",
+	key: mclasscnvloh,
+}
 
 // for VCF
-export const mclasssnv = 'snv'
+export const mclasssnv = "snv"
 mclass[mclasssnv] = {
-	label: 'SNV',
-	color: '#92a2d4',
+	label: "SNV",
+	color: "#92a2d4",
 	dt: dtsnvindel,
-	desc: 'Single nucleotide variation',
-	key: mclasssnv
+	desc: "Single nucleotide variation",
+	key: mclasssnv,
 }
 
-export const mclassmnv = 'mnv'
+export const mclassmnv = "mnv"
 mclass[mclassmnv] = {
-	label: 'MNV',
-	color: '#92a2d4',
+	label: "MNV",
+	color: "#92a2d4",
 	dt: dtsnvindel,
-	desc: 'Multiple nucleotide variation',
-	key: mclassmnv
+	desc: "Multiple nucleotide variation",
+	key: mclassmnv,
 }
 
-export const mclassinsertion = 'insertion'
+export const mclassinsertion = "insertion"
 mclass[mclassinsertion] = {
-	label: 'Sequence insertion',
-	color: '#bd8e91',
+	label: "Sequence insertion",
+	color: "#bd8e91",
 	dt: dtsnvindel,
-	desc: 'Sequence insertion',
-	key: mclassinsertion
+	desc: "Sequence insertion",
+	key: mclassinsertion,
 }
 
-export const mclassdeletion = 'deletion'
+export const mclassdeletion = "deletion"
 mclass[mclassdeletion] = {
-	label: 'Sequence deletion',
-	color: '#b5a174',
+	label: "Sequence deletion",
+	color: "#b5a174",
 	dt: dtsnvindel,
-	desc: 'Sequence deletion',
-	key: mclassdeletion
+	desc: "Sequence deletion",
+	key: mclassdeletion,
 }
 // TODO complex indel
 
@@ -502,16 +534,16 @@ the tricky case doesn't apply to other plots
 export function mds3tkMclass(k) {
 	if (k == dtcnv) {
 		return {
-			color: '#858585',
-			label: 'CNV',
-			desc: 'Copy number variation'
+			color: "#858585",
+			label: "CNV",
+			desc: "Copy number variation",
 		}
 	}
 	return mclass[k]
 }
 
 export const dt2color = {
-	[dtsnvindel]: mclass.M.color // general color for snvindel irrespective of class (when class is not available)
+	[dtsnvindel]: mclass.M.color, // general color for snvindel irrespective of class (when class is not available)
 	// add new dt as needed
 }
 
@@ -535,93 +567,111 @@ performs case insensitive match and returns severity rank
 TODO share data with SOterms
 */
 export const vepinfo = function (s) {
-	const l = s.toLowerCase().split(',')
+	const l = s.toLowerCase().split(",")
 	let rank = 1
-	if (l.indexOf('transcript_ablation') != -1) {
+	if (l.indexOf("transcript_ablation") != -1) {
 		// FIXME no class for whole gene deletion
 		return [dtdel, mclassdel, rank]
 	}
 	rank++
-	if (l.indexOf('splice_acceptor_variant') != -1) return [dtsnvindel, 'L', rank]
+	if (l.indexOf("splice_acceptor_variant") != -1) return [dtsnvindel, "L", rank]
 	rank++
-	if (l.indexOf('splice_donor_variant') != -1) return [dtsnvindel, 'L', rank]
+	if (l.indexOf("splice_donor_variant") != -1) return [dtsnvindel, "L", rank]
 	rank++
-	if (l.indexOf('stop_gained') != -1) return [dtsnvindel, 'N', rank]
+	if (l.indexOf("stop_gained") != -1) return [dtsnvindel, "N", rank]
 	rank++
-	if (l.indexOf('frameshift_variant') != -1) return [dtsnvindel, 'F', rank]
+	if (l.indexOf("frameshift_variant") != -1) return [dtsnvindel, "F", rank]
 	rank++
-	if (l.indexOf('stop_lost') != -1) return [dtsnvindel, 'N', rank]
+	if (l.indexOf("stop_lost") != -1) return [dtsnvindel, "N", rank]
 	rank++
-	if (l.indexOf('start_lost') != -1) return [dtsnvindel, 'N', rank]
+	if (l.indexOf("start_lost") != -1) return [dtsnvindel, "N", rank]
 	rank++
-	if (l.indexOf('transcript_amplification') != -1) {
+	if (l.indexOf("transcript_amplification") != -1) {
 		// FIXME no class for whole gene amp
 		return [dtsnvindel, mclassnonstandard, rank]
 	}
 	rank++
 	if (
-		l.indexOf('inframe_insertion') != -1 ||
-		l.indexOf('conservative_inframe_insertion') != -1 ||
-		l.indexOf('disruptive_inframe_insertion') != -1
+		l.indexOf("inframe_insertion") != -1 ||
+		l.indexOf("conservative_inframe_insertion") != -1 ||
+		l.indexOf("disruptive_inframe_insertion") != -1
 	)
-		return [dtsnvindel, 'I', rank]
+		return [dtsnvindel, "I", rank]
 	rank++
 	if (
-		l.indexOf('inframe_deletion') != -1 ||
-		l.indexOf('conservative_inframe_deletion') != -1 ||
-		l.indexOf('disruptive_inframe_deletion') != -1
+		l.indexOf("inframe_deletion") != -1 ||
+		l.indexOf("conservative_inframe_deletion") != -1 ||
+		l.indexOf("disruptive_inframe_deletion") != -1
 	)
-		return [dtsnvindel, 'D', rank]
+		return [dtsnvindel, "D", rank]
 	rank++
-	if (l.indexOf('missense_variant') != -1) return [dtsnvindel, 'M', rank]
+	if (l.indexOf("missense_variant") != -1) return [dtsnvindel, "M", rank]
 	rank++
-	if (l.indexOf('protein_altering_variant') != -1) return [dtsnvindel, 'ProteinAltering', rank]
+	if (l.indexOf("protein_altering_variant") != -1)
+		return [dtsnvindel, "ProteinAltering", rank]
 	rank++
-	if (l.indexOf('splice_region_variant') != -1) return [dtsnvindel, 'P', rank]
+	if (l.indexOf("splice_region_variant") != -1) return [dtsnvindel, "P", rank]
 	rank++
-	if (l.indexOf('incomplete_terminal_codon_variant') != -1) return [dtsnvindel, 'N', rank]
+	if (l.indexOf("incomplete_terminal_codon_variant") != -1)
+		return [dtsnvindel, "N", rank]
 	rank++
-	if (l.indexOf('stop_retained_variant') != -1) return [dtsnvindel, 'S', rank]
+	if (l.indexOf("stop_retained_variant") != -1) return [dtsnvindel, "S", rank]
 	rank++
-	if (l.indexOf('synonymous_variant') != -1) return [dtsnvindel, 'S', rank]
+	if (l.indexOf("synonymous_variant") != -1) return [dtsnvindel, "S", rank]
 	rank++
-	if (l.indexOf('coding_sequence_variant') != -1) return [dtsnvindel, mclassnonstandard, rank]
+	if (l.indexOf("coding_sequence_variant") != -1)
+		return [dtsnvindel, mclassnonstandard, rank]
 	rank++
-	if (l.indexOf('mature_mirna_variant') != -1) return [dtsnvindel, 'E', rank]
+	if (l.indexOf("mature_mirna_variant") != -1) return [dtsnvindel, "E", rank]
 	rank++
-	if (l.indexOf('5_prime_utr_variant') != -1) return [dtsnvindel, mclassutr5, rank]
+	if (l.indexOf("5_prime_utr_variant") != -1)
+		return [dtsnvindel, mclassutr5, rank]
 	rank++
-	if (l.indexOf('3_prime_utr_variant') != -1) return [dtsnvindel, mclassutr3, rank]
+	if (l.indexOf("3_prime_utr_variant") != -1)
+		return [dtsnvindel, mclassutr3, rank]
 	rank++
-	if (l.indexOf('non_coding_transcript_exon_variant') != -1) return [dtsnvindel, 'E', rank]
+	if (l.indexOf("non_coding_transcript_exon_variant") != -1)
+		return [dtsnvindel, "E", rank]
 	rank++
-	if (l.indexOf('intron_variant') != -1) return [dtsnvindel, 'Intron', rank]
+	if (l.indexOf("intron_variant") != -1) return [dtsnvindel, "Intron", rank]
 	rank++
-	if (l.indexOf('nmd_transcript_variant') != -1) return [dtsnvindel, 'S', rank]
+	if (l.indexOf("nmd_transcript_variant") != -1) return [dtsnvindel, "S", rank]
 	rank++
-	if (l.indexOf('non_coding_transcript_variant') != -1) return [dtsnvindel, 'E', rank]
+	if (l.indexOf("non_coding_transcript_variant") != -1)
+		return [dtsnvindel, "E", rank]
 	rank++
-	if (l.indexOf('upstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("upstream_gene_variant") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('downstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("downstream_gene_variant") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('tfbs_ablation') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("tfbs_ablation") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('tfbs_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("tfbs_amplification") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('tf_binding_site_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("tf_binding_site_variant") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('regulatory_region_ablation') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("regulatory_region_ablation") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('regulatory_region_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("regulatory_region_amplification") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('feature_elongation') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("feature_elongation") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('regulatory_region_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("regulatory_region_variant") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('feature_truncation') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("feature_truncation") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
-	if (l.indexOf('intergenic_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
+	if (l.indexOf("intergenic_variant") != -1)
+		return [dtsnvindel, mclassnoncoding, rank]
 	rank++
 	return [dtsnvindel, mclassnonstandard, rank]
 }
@@ -632,65 +682,65 @@ export const germlinelegend =
 
 export const morigin = {}
 
-export const moriginsomatic = 'S'
+export const moriginsomatic = "S"
 morigin[moriginsomatic] = {
-	label: 'Somatic',
-	desc: 'A variant found only in a tumor sample. The proportion is indicated by lack of any arc.',
-	legend: '<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'
+	label: "Somatic",
+	desc: "A variant found only in a tumor sample. The proportion is indicated by lack of any arc.",
+	legend: '<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>',
 }
-export const morigingermline = 'G'
+export const morigingermline = "G"
 morigin[morigingermline] = {
-	label: 'Germline',
-	desc: 'A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.',
-	legend: germlinelegend
+	label: "Germline",
+	desc: "A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.",
+	legend: germlinelegend,
 }
 
 morigin.germline = morigin[morigingermline]
 morigin.somatic = morigin[moriginsomatic]
 
-export const moriginrelapse = 'R'
+export const moriginrelapse = "R"
 morigin[moriginrelapse] = {
-	label: 'Relapse',
-	desc: 'A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.',
+	label: "Relapse",
+	desc: "A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.",
 	legend:
-		'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="none" stroke="#858585"></path>'
+		'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="none" stroke="#858585"></path>',
 }
-export const morigingermlinepathogenic = 'GP'
+export const morigingermlinepathogenic = "GP"
 morigin[morigingermlinepathogenic] = {
-	label: 'Germline pathogenic',
-	desc: 'A constitutional variant with pathogenic allele.',
-	legend: germlinelegend
+	label: "Germline pathogenic",
+	desc: "A constitutional variant with pathogenic allele.",
+	legend: germlinelegend,
 }
-export const morigingermlinenonpathogenic = 'GNP'
+export const morigingermlinenonpathogenic = "GNP"
 morigin[morigingermlinenonpathogenic] = {
-	label: 'Germline non-pathogenic',
-	desc: 'A constitutional variant with non-pathogenic allele.',
+	label: "Germline non-pathogenic",
+	desc: "A constitutional variant with non-pathogenic allele.",
 	legend: germlinelegend,
-	hidden: true
+	hidden: true,
 }
 
 export const tkt = {
-	usegm: 'usegm',
-	ds: 'dataset',
-	bigwig: 'bigwig',
-	bigwigstranded: 'bigwigstranded',
-	junction: 'junction',
-	mdsjunction: 'mdsjunction',
-	mdssvcnv: 'mdssvcnv', // replaced by mds3
-	mdsexpressionrank: 'mdsexpressionrank',
-	mdsvcf: 'mdsvcf', // for snv/indels, currently vcf, may include MAF
+	usegm: "usegm",
+	ds: "dataset",
+	bigwig: "bigwig",
+	bigwigstranded: "bigwigstranded",
+	junction: "junction",
+	mdsjunction: "mdsjunction",
+	mdssvcnv: "mdssvcnv", // replaced by mds3
+	mdsexpressionrank: "mdsexpressionrank",
+	mdsvcf: "mdsvcf", // for snv/indels, currently vcf, may include MAF
 	//mdsgeneral:'mdsgeneral', // replaces mdssvcnv   ****** not ready yet
-	bedj: 'bedj',
-	pgv: 'profilegenevalue',
-	bampile: 'bampile',
-	hicstraw: 'hicstraw',
-	expressionrank: 'expressionrank',
-	aicheck: 'aicheck',
-	ase: 'ase',
-	mds3: 'mds3', //
-	bedgraphdot: 'bedgraphdot',
-	bam: 'bam',
-	ld: 'ld'
+	bedj: "bedj",
+	pgv: "profilegenevalue",
+	bampile: "bampile",
+	hicstraw: "hicstraw",
+	expressionrank: "expressionrank",
+	aicheck: "aicheck",
+	ase: "ase",
+	mds3: "mds3", //
+	bedgraphdot: "bedgraphdot",
+	bam: "bam",
+	ld: "ld",
 }
 
 export function validtkt(what) {
@@ -708,7 +758,7 @@ to get rid of hardcoded strings
 in future may include MAF format files
 */
 export const mdsvcftype = {
-	vcf: 'vcf'
+	vcf: "vcf",
 }
 
 /*
@@ -717,77 +767,77 @@ or general track
 to avoid using hard-coded string
 */
 export const custommdstktype = {
-	vcf: 'vcf',
-	svcnvitd: 'svcnvitd',
-	geneexpression: 'geneexpression'
+	vcf: "vcf",
+	svcnvitd: "svcnvitd",
+	geneexpression: "geneexpression",
 }
 
 // codons that are not here are stop codon!!
 export const codon = {
-	GCT: 'A',
-	GCC: 'A',
-	GCA: 'A',
-	GCG: 'A',
-	CGT: 'R',
-	CGC: 'R',
-	CGA: 'R',
-	CGG: 'R',
-	AGA: 'R',
-	AGG: 'R',
-	AAT: 'N',
-	AAC: 'N',
-	GAT: 'D',
-	GAC: 'D',
-	TGT: 'C',
-	TGC: 'C',
-	CAA: 'Q',
-	CAG: 'Q',
-	GAA: 'E',
-	GAG: 'E',
-	GGT: 'G',
-	GGC: 'G',
-	GGA: 'G',
-	GGG: 'G',
-	CAT: 'H',
-	CAC: 'H',
-	ATT: 'I',
-	ATC: 'I',
-	ATA: 'I',
-	TTA: 'L',
-	TTG: 'L',
-	CTT: 'L',
-	CTC: 'L',
-	CTA: 'L',
-	CTG: 'L',
-	AAA: 'K',
-	AAG: 'K',
-	ATG: 'M',
-	TTT: 'F',
-	TTC: 'F',
-	CCT: 'P',
-	CCC: 'P',
-	CCA: 'P',
-	CCG: 'P',
-	TCT: 'S',
-	TCC: 'S',
-	TCA: 'S',
-	TCG: 'S',
-	AGT: 'S',
-	AGC: 'S',
-	ACT: 'T',
-	ACC: 'T',
-	ACA: 'T',
-	ACG: 'T',
-	TGG: 'W',
-	TAT: 'Y',
-	TAC: 'Y',
-	GTT: 'V',
-	GTC: 'V',
-	GTA: 'V',
-	GTG: 'V'
-}
-
-export const codon_stop = '*'
+	GCT: "A",
+	GCC: "A",
+	GCA: "A",
+	GCG: "A",
+	CGT: "R",
+	CGC: "R",
+	CGA: "R",
+	CGG: "R",
+	AGA: "R",
+	AGG: "R",
+	AAT: "N",
+	AAC: "N",
+	GAT: "D",
+	GAC: "D",
+	TGT: "C",
+	TGC: "C",
+	CAA: "Q",
+	CAG: "Q",
+	GAA: "E",
+	GAG: "E",
+	GGT: "G",
+	GGC: "G",
+	GGA: "G",
+	GGG: "G",
+	CAT: "H",
+	CAC: "H",
+	ATT: "I",
+	ATC: "I",
+	ATA: "I",
+	TTA: "L",
+	TTG: "L",
+	CTT: "L",
+	CTC: "L",
+	CTA: "L",
+	CTG: "L",
+	AAA: "K",
+	AAG: "K",
+	ATG: "M",
+	TTT: "F",
+	TTC: "F",
+	CCT: "P",
+	CCC: "P",
+	CCA: "P",
+	CCG: "P",
+	TCT: "S",
+	TCC: "S",
+	TCA: "S",
+	TCG: "S",
+	AGT: "S",
+	AGC: "S",
+	ACT: "T",
+	ACC: "T",
+	ACA: "T",
+	ACG: "T",
+	TGG: "W",
+	TAT: "Y",
+	TAC: "Y",
+	GTT: "V",
+	GTC: "V",
+	GTA: "V",
+	GTG: "V",
+}
+
+export const codon_stop = "*"
 
 export function nt2aa(gm) {
 	// must convert genome seq to upper case!!!
@@ -796,14 +846,14 @@ export function nt2aa(gm) {
 	if (gm.coding) {
 		for (const [i, e] of gm.coding.entries()) {
 			const s = gm.genomicseq.substr(e[0] - gm.start, e[1] - e[0])
-			if (gm.strand == '-') {
+			if (gm.strand == "-") {
 				enlst.push(reversecompliment(s))
 			} else {
 				enlst.push(s)
 			}
 		}
 	}
-	const nt = enlst.join('')
+	const nt = enlst.join("")
 	const pep = []
 
 	/*
@@ -817,44 +867,44 @@ export function nt2aa(gm) {
 		pep.push(a || codon_stop)
 	}
 	gm.cdseq = nt
-	return pep.join('')
+	return pep.join("")
 }
 
 export function bplen(len, isfile) {
 	// if "isfile" is true, to measure file size instead of basepair len
-	if (len >= 1000000000) return (len / 1000000000).toFixed(1) + ' Gb'
-	if (len >= 10000000) return Math.ceil(len / 1000000) + ' Mb'
-	if (len >= 1000000) return (len / 1000000).toFixed(1) + ' Mb'
-	if (len >= 10000) return Math.ceil(len / 1000) + ' Kb'
-	if (len >= 1000) return (len / 1000).toFixed(1) + ' Kb'
-	return len + (isfile ? 'bytes' : ' bp')
+	if (len >= 1000000000) return (len / 1000000000).toFixed(1) + " Gb"
+	if (len >= 10000000) return Math.ceil(len / 1000000) + " Mb"
+	if (len >= 1000000) return (len / 1000000).toFixed(1) + " Mb"
+	if (len >= 10000) return Math.ceil(len / 1000) + " Kb"
+	if (len >= 1000) return (len / 1000).toFixed(1) + " Kb"
+	return len + (isfile ? "bytes" : " bp")
 }
 
 export const basecolor = {
-	A: '#ca0020',
-	T: '#f4a582',
-	C: '#92c5de',
-	G: '#0571b0'
+	A: "#ca0020",
+	T: "#f4a582",
+	C: "#92c5de",
+	G: "#0571b0",
 }
 
 export function basecompliment(nt) {
 	switch (nt) {
-		case 'A':
-			return 'T'
-		case 'T':
-			return 'A'
-		case 'C':
-			return 'G'
-		case 'G':
-			return 'C'
-		case 'a':
-			return 't'
-		case 't':
-			return 'a'
-		case 'c':
-			return 'g'
-		case 'g':
-			return 'c'
+		case "A":
+			return "T"
+		case "T":
+			return "A"
+		case "C":
+			return "G"
+		case "G":
+			return "C"
+		case "a":
+			return "t"
+		case "t":
+			return "a"
+		case "c":
+			return "g"
+		case "g":
+			return "c"
 		default:
 			return nt
 	}
@@ -865,7 +915,7 @@ export function reversecompliment(s) {
 	for (let i = s.length - 1; i >= 0; i--) {
 		tmp.push(basecompliment(s[i]))
 	}
-	return tmp.join('')
+	return tmp.join("")
 }
 
 export function spliceeventchangegmexon(gm, evt) {
@@ -879,7 +929,7 @@ export function spliceeventchangegmexon(gm, evt) {
 		start: gm.start,
 		stop: gm.stop,
 		strand: gm.strand,
-		coding: []
+		coding: [],
 	}
 	if (evt.isskipexon || evt.isaltexon) {
 		for (let i = 0; i < gm.exon.length; i++) {
@@ -899,8 +949,8 @@ export function spliceeventchangegmexon(gm, evt) {
 	} else if (evt.a5ss || evt.a3ss) {
 		// still equal number of exons
 		// adjust the affected exon first, then figure out coding[]
-		const exons = gm.exon.map(e => [e[0], e[1]])
-		const forward = gm.strand == '+'
+		const exons = gm.exon.map((e) => [e[0], e[1]])
+		const forward = gm.strand == "+"
 		if (evt.a5ss) {
 			if (forward) {
 				exons[evt.exon5idx][1] = evt.junctionB.start
@@ -940,10 +990,10 @@ export function fasta2gmframecheck(gm, str) {
 	str
 		samtools faidx output
 	*/
-	const lines = str.split('\n')
+	const lines = str.split("\n")
 	// remove fasta header
 	lines.shift()
-	gm.genomicseq = lines.join('').toUpperCase()
+	gm.genomicseq = lines.join("").toUpperCase()
 
 	const aaseq = nt2aa(gm)
 
@@ -961,12 +1011,12 @@ export function validate_vcfinfofilter(obj) {
 	validate vcfinfofilter as from embedding api or dataset
 	*/
 
-	if (!obj.lst) return '.lst missing'
+	if (!obj.lst) return ".lst missing"
 
-	if (!Array.isArray(obj.lst)) return 'input is not an array'
+	if (!Array.isArray(obj.lst)) return "input is not an array"
 
 	for (const set of obj.lst) {
-		if (!set.name) return 'name missing from a set of .vcfinfofilter.lst'
+		if (!set.name) return "name missing from a set of .vcfinfofilter.lst"
 
 		if (set.autocategory || set.categories) {
 			// categorical info, auto or defined
@@ -975,7 +1025,12 @@ export function validate_vcfinfofilter(obj) {
 				for (const k in set.categories) {
 					const v = set.categories[k]
 					if (!set.autocolor && !v.color)
-						return '.color missing for class ' + k + ' from .categories of set ' + set.name
+						return (
+							".color missing for class " +
+							k +
+							" from .categories of set " +
+							set.name
+						)
 					if (!v.label) {
 						v.label = k
 					}
@@ -984,7 +1039,13 @@ export function validate_vcfinfofilter(obj) {
 
 			if (set.categoryhidden) {
 				for (const k in set.categoryhidden) {
-					if (!set.categories[k]) return 'unknown hidden-by-default category ' + k + ' from set ' + set.name
+					if (!set.categories[k])
+						return (
+							"unknown hidden-by-default category " +
+							k +
+							" from set " +
+							set.name
+						)
 				}
 			} else {
 				set.categoryhidden = {}
@@ -993,15 +1054,15 @@ export function validate_vcfinfofilter(obj) {
 			// otherwise, numerical value, the style of population frequency filter
 			const lst = []
 			for (const v of set.numericfilter) {
-				if (typeof v == 'number') {
+				if (typeof v == "number") {
 					/*
 					just a number, defaults to 'lower-than'
 					*/
-					lst.push({ side: '<', value: v })
+					lst.push({ side: "<", value: v })
 				} else {
 					lst.push({
-						side: v.side || '<',
-						value: v.value
+						side: v.side || "<",
+						value: v.value,
 					})
 				}
 			}
@@ -1012,14 +1073,16 @@ export function validate_vcfinfofilter(obj) {
 
 		if (set.altalleleinfo) {
 			if (!set.altalleleinfo.key) {
-				return '.key missing from .altalleleinfo from set ' + set.name
+				return ".key missing from .altalleleinfo from set " + set.name
 			}
 		} else if (set.locusinfo) {
 			if (!set.locusinfo.key) {
-				return '.key missing from .locusinfo from set ' + set.name
+				return ".key missing from .locusinfo from set " + set.name
 			}
 		} else {
-			return 'neither .altalleleinfo or .locusinfo is available from set ' + set.name
+			return (
+				"neither .altalleleinfo or .locusinfo is available from set " + set.name
+			)
 		}
 	}
 }
@@ -1029,13 +1092,13 @@ export function contigNameNoChr(genome, chrlst) {
 	FIXME hard-coded for human genome styled chromosome names
 	*/
 	for (const n in genome.majorchr) {
-		if (chrlst.indexOf(n.replace('chr', '')) != -1) {
+		if (chrlst.indexOf(n.replace("chr", "")) != -1) {
 			return true
 		}
 	}
 	if (genome.minorchr) {
 		for (const n in genome.minorchr) {
-			if (chrlst.indexOf(n.replace('chr', '')) != -1) {
+			if (chrlst.indexOf(n.replace("chr", "")) != -1) {
 				return true
 			}
 		}
@@ -1051,7 +1114,7 @@ export function contigNameNoChr2(genome, chrlst) {
 	for (const n in genome.majorchr) {
 		if (chrlst.includes(n)) {
 			haschrcount++
-		} else if (chrlst.includes(n.replace('chr', ''))) {
+		} else if (chrlst.includes(n.replace("chr", ""))) {
 			nochrcount++
 		}
 	}
@@ -1059,7 +1122,7 @@ export function contigNameNoChr2(genome, chrlst) {
 		for (const n in genome.minorchr) {
 			if (chrlst.includes(n)) {
 				haschrcount++
-			} else if (chrlst.includes(n.replace('chr', ''))) {
+			} else if (chrlst.includes(n.replace("chr", ""))) {
 				nochrcount++
 			}
 		}
@@ -1084,18 +1147,18 @@ export function getMax_byiqr(lst, novaluemax) {
 
 export function alleleInGenotypeStr(genotype, allele) {
 	if (!genotype) return false
-	if (genotype.indexOf('/') != -1) {
-		return genotype.split('/').indexOf(allele) != -1
+	if (genotype.indexOf("/") != -1) {
+		return genotype.split("/").indexOf(allele) != -1
 	}
-	return genotype.split('|').indexOf(allele) != -1
+	return genotype.split("|").indexOf(allele) != -1
 }
 
 export const gmmode = {
-	genomic: 'genomic',
-	splicingrna: 'splicing RNA', // if just 1 exon, use "RNA" as label
-	exononly: 'exon only',
-	protein: 'protein',
-	gmsum: 'aggregated exons'
+	genomic: "genomic",
+	splicingrna: "splicing RNA", // if just 1 exon, use "RNA" as label
+	exononly: "exon only",
+	protein: "protein",
+	gmsum: "aggregated exons",
 }
 
 /*
@@ -1134,13 +1197,13 @@ export function vcfcopymclass(m, block) {
 
 		if (block.usegm) {
 			// block is in gm mode, find a csq matching with the genemodel isoform
-			useone = m.csq.find(i => i._isoform == block.usegm.isoform)
+			useone = m.csq.find((i) => i._isoform == block.usegm.isoform)
 		}
 
 		if (!useone) {
 			// no match to usegm isoform; can be due to in genomic mode and zoomed out, where this variant is from a neighboring gene near block.usegm
 			// find one using canonical isoform
-			useone = m.csq.find(i => i.CANONICAL)
+			useone = m.csq.find((i) => i.CANONICAL)
 
 			if (!useone) {
 				// none of the elements in m.csq[] is using a canonical isoform, as that's a vep optional output
@@ -1211,7 +1274,7 @@ export function vcfcopymclass(m, block) {
 		if (mclass[m.type]) {
 			m.class = m.type
 			m.dt = mclass[m.type].dt
-			m.mname = m.id && m.id != '.' ? m.id : m.ref + '>' + m.alt
+			m.mname = m.id && m.id != "." ? m.id : m.ref + ">" + m.alt
 			if (m.mname.length > 15) {
 				// avoid long indel
 				m.mname = m.type
@@ -1230,14 +1293,17 @@ export function vcfcopymclass(m, block) {
 used in:
 	mdssvcnv track, mutation attributes, items that are not annotated by an attribute for showing in legend, and server-side filtering
 */
-export const not_annotated = 'Unannotated'
+export const not_annotated = "Unannotated"
 
 // kernal density estimator as from https://www.d3-graph-gallery.com/graph/density_basic.html
 
 export function kernelDensityEstimator(kernel, X) {
 	return function (V) {
-		return X.map(x => {
-			return [x, V.map(v => kernel(x - v)).reduce((i, j) => i + j, 0) / V.length]
+		return X.map((x) => {
+			return [
+				x,
+				V.map((v) => kernel(x - v)).reduce((i, j) => i + j, 0) / V.length,
+			]
 		})
 	}
 }
@@ -1251,33 +1317,34 @@ export function kernelEpanechnikov(k) {
 /////////////////////// color sets /////////////////////////
 
 export const schemeCategory20 = [
-	'#1f77b4',
-	'#aec7e8',
-	'#ff7f0e',
-	'#ffbb78',
-	'#2ca02c',
-	'#98df8a',
-	'#d62728',
-	'#ff9896',
-	'#9467bd',
-	'#c5b0d5',
-	'#8c564b',
-	'#c49c94',
-	'#e377c2',
-	'#f7b6d2',
-	'#7f7f7f',
-	'#c7c7c7',
-	'#bcbd22',
-	'#dbdb8d',
-	'#17becf',
-	'#9edae5'
+	"#1f77b4",
+	"#aec7e8",
+	"#ff7f0e",
+	"#ffbb78",
+	"#2ca02c",
+	"#98df8a",
+	"#d62728",
+	"#ff9896",
+	"#9467bd",
+	"#c5b0d5",
+	"#8c564b",
+	"#c49c94",
+	"#e377c2",
+	"#f7b6d2",
+	"#7f7f7f",
+	"#c7c7c7",
+	"#bcbd22",
+	"#dbdb8d",
+	"#17becf",
+	"#9edae5",
 ]
-export const schemeCategory2 = ['#e75480', 'blue']
+export const schemeCategory2 = ["#e75480", "blue"]
 
 export function getColorScheme(number) {
 	if (number > 20) {
 		const scheme = []
-		for (let i = 0; i < number; i++) scheme.push(d3.interpolateRainbow(i / number))
+		for (let i = 0; i < number; i++)
+			scheme.push(d3.interpolateRainbow(i / number))
 		return scheme
 	}
 	if (number > 12) return schemeCategory20
@@ -1292,16 +1359,16 @@ export function getColors(number) {
 
 // for now not using getColorScheme() for protein domains, because this color list have been in use since 2015...
 const proteinDomainColors = [
-	'#8dd3c7',
-	'#bebada',
-	'#fb8072',
-	'#80b1d3',
-	'#E8E89E',
-	'#a6d854',
-	'#fdb462',
-	'#ffd92f',
-	'#e5c494',
-	'#b3b3b3'
+	"#8dd3c7",
+	"#bebada",
+	"#fb8072",
+	"#80b1d3",
+	"#E8E89E",
+	"#a6d854",
+	"#fdb462",
+	"#ffd92f",
+	"#e5c494",
+	"#b3b3b3",
 ]
 export function proteinDomainColorScale() {
 	return d3scale.scaleOrdinal().range(proteinDomainColors)
@@ -1309,70 +1376,86 @@ export function proteinDomainColorScale() {
 
 /////////////////////// end of color sets /////////////////////////
 
-export const truncatingMutations = ['F', 'N', 'L', 'P']
-export const proteinChangingMutations = ['F', 'N', 'L', 'P', 'D', 'I', 'ProteinAltering', 'M']
-export const synonymousMutations = ['S', 'Intron', 'Utr3', 'Utr5', 'noncoding', 'E']
+export const truncatingMutations = ["F", "N", "L", "P"]
+export const proteinChangingMutations = [
+	"F",
+	"N",
+	"L",
+	"P",
+	"D",
+	"I",
+	"ProteinAltering",
+	"M",
+]
+export const synonymousMutations = [
+	"S",
+	"Intron",
+	"Utr3",
+	"Utr5",
+	"noncoding",
+	"E",
+]
 export const mutationClasses = Object.values(mclass)
-	.filter(m => m.dt == dtsnvindel)
-	.map(m => m.key)
+	.filter((m) => m.dt == dtsnvindel)
+	.map((m) => m.key)
 export const CNVClasses = Object.values(mclass)
-	.filter(m => m.dt == dtcnv)
-	.map(m => m.key)
+	.filter((m) => m.dt == dtcnv)
+	.map((m) => m.key)
 
 // dt terms used for filtering variants for geneVariant term
 const dtTerms_temp = [
 	{
-		id: 'snvindel',
-		query: 'snvindel',
+		id: "snvindel",
+		query: "snvindel",
 		name: dt2label[dtsnvindel],
 		parent_id: null,
 		isleaf: true,
-		type: 'dtsnvindel',
+		type: "dtsnvindel",
 		dt: dtsnvindel,
-		values: {}
+		values: {},
 	},
 	{
-		id: 'cnv',
-		query: 'cnv',
+		id: "cnv",
+		query: "cnv",
 		name: dt2label[dtcnv],
 		parent_id: null,
 		isleaf: true,
-		type: 'dtcnv',
+		type: "dtcnv",
 		dt: dtcnv,
-		values: {}
+		values: {},
 	},
 	{
-		id: 'fusion',
-		query: 'svfusion',
+		id: "fusion",
+		query: "svfusion",
 		name: dt2label[dtfusionrna],
 		parent_id: null,
 		isleaf: true,
-		type: 'dtfusion',
+		type: "dtfusion",
 		dt: dtfusionrna,
-		values: {}
+		values: {},
 	},
 	{
-		id: 'sv',
-		query: 'svfusion',
+		id: "sv",
+		query: "svfusion",
 		name: dt2label[dtsv],
 		parent_id: null,
 		isleaf: true,
-		type: 'dtsv',
+		type: "dtsv",
 		dt: dtsv,
-		values: {}
-	}
+		values: {},
+	},
 ]
 // add origin annotations to dt terms
 const dtTerms_temp2 = []
 for (const dtTerm of dtTerms_temp) {
 	dtTerm.name_noOrigin = dtTerm.name // for labeling groups in groupsetting
 	dtTerms_temp2.push(dtTerm) // no origin
-	for (const origin of ['somatic', 'germline']) {
+	for (const origin of ["somatic", "germline"]) {
 		// add origins
 		const addOrigin = {
 			id: `${dtTerm.id}_${origin}`,
 			name: `${dtTerm.name} (${origin})`,
-			origin
+			origin,
 		}
 		dtTerms_temp2.push(Object.assign({}, dtTerm, addOrigin))
 	}
@@ -1380,39 +1463,63 @@ for (const dtTerm of dtTerms_temp) {
 export const dtTerms = dtTerms_temp2
 
 export const colorScaleMap = {
-	blueWhiteRed: { domain: [0, 0.5, 1], range: ['blue', 'white', 'red'] },
-	greenWhiteRed: { domain: [0, 0.5, 1], range: ['green', 'white', 'red'] },
+	blueWhiteRed: { domain: [0, 0.5, 1], range: ["blue", "white", "red"] },
+	greenWhiteRed: { domain: [0, 0.5, 1], range: ["green", "white", "red"] },
 	blueYellowRed: {
 		domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-		range: ['#313695', '#649AC7', '#BCE1ED', '#FFFFBF', '#FDBE70', '#EA5839', '#A50026']
+		range: [
+			"#313695",
+			"#649AC7",
+			"#BCE1ED",
+			"#FFFFBF",
+			"#FDBE70",
+			"#EA5839",
+			"#A50026",
+		],
 	},
 	greenBlackRed: {
 		domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-		range: ['#00FF00', '#14E10C', '#1AAF10', '#000000', '#B01205', '#E20E03', '#FF0000']
+		range: [
+			"#00FF00",
+			"#14E10C",
+			"#1AAF10",
+			"#000000",
+			"#B01205",
+			"#E20E03",
+			"#FF0000",
+		],
 	},
 	blueBlackYellow: {
 		domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-		range: ['#0000FF', '#0000CC', '#000099', '#202020', '#999900', '#CCCC00', '#FFFF00']
+		range: [
+			"#0000FF",
+			"#0000CC",
+			"#000099",
+			"#202020",
+			"#999900",
+			"#CCCC00",
+			"#FFFF00",
+		],
 	},
 	// when hierCluster z-score transformation is not performed, should use two-color scale
-	whiteRed: { domain: [0, 1], range: ['white', 'red'] }
+	whiteRed: { domain: [0, 1], range: ["white", "red"] },
 }
 
 export function invalidcoord(thisgenome, chrom, start, stop) {
-	if (!thisgenome) return 'no genome'
-	if (!chrom) return 'no chr name'
+	if (!thisgenome) return "no genome"
+	if (!chrom) return "no chr name"
 	const chr = thisgenome.chrlookup[chrom.toUpperCase()]
-	if (!chr) return 'Invalid chromosome name: ' + chr
-	if (!Number.isInteger(start)) return 'Non-numerical position: ' + start
-	if (start < 0 || start >= chr.len) return 'Position out of range: ' + start
-	if (!Number.isInteger(stop)) return 'Non-numerical position: ' + stop
-	if (stop < 0 || stop > chr.len) return 'Position out of range: ' + stop
-	if (start > stop) return 'Start position is greater than stop'
+	if (!chr) return "Invalid chromosome name: " + chr
+	if (!Number.isInteger(start)) return "Non-numerical position: " + start
+	if (start < 0 || start >= chr.len) return "Position out of range: " + start
+	if (!Number.isInteger(stop)) return "Non-numerical position: " + stop
+	if (stop < 0 || stop > chr.len) return "Position out of range: " + stop
+	if (start > stop) return "Start position is greater than stop"
 	return false
 }
 
 export function string2pos(s, genome, donotextend) {
-	s = s.replace(/,/g, '')
+	s = s.replace(/,/g, "")
 	const chr = genome.chrlookup[s.toUpperCase()]
 	if (chr) {
 		// chr name only, to middle
@@ -1420,12 +1527,12 @@ export function string2pos(s, genome, donotextend) {
 			chr: chr.name,
 			chrlen: chr.len,
 			start: Math.max(0, Math.ceil(chr.len / 2) - 10000),
-			stop: Math.min(chr.len, Math.ceil(chr.len / 2) + 10000)
+			stop: Math.min(chr.len, Math.ceil(chr.len / 2) + 10000),
 		}
 	}
 	{
 		// special handling for snv4
-		const tmp = s.split('.')
+		const tmp = s.split(".")
 		if (tmp.length >= 2) {
 			const chr = genome.chrlookup[tmp[0].toUpperCase()]
 			const pos = Number.parseInt(tmp[1])
@@ -1438,7 +1545,7 @@ export function string2pos(s, genome, donotextend) {
 					chrlen: chr.len,
 					start: Math.max(0, pos - Math.ceil(bpspan / 2)),
 					stop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),
-					actualposition: { position: pos, len: 1 }
+					actualposition: { position: pos, len: 1 },
 				}
 			}
 		}
@@ -1458,7 +1565,7 @@ export function string2pos(s, genome, donotextend) {
 			chrlen: chr.len,
 			start: Math.max(0, pos - Math.ceil(bpspan / 2)),
 			stop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),
-			actualposition: { position: pos, len: 1 }
+			actualposition: { position: pos, len: 1 },
 		}
 	}
 	if (tmp.length == 3) {
@@ -1489,7 +1596,7 @@ export function string2pos(s, genome, donotextend) {
 			chrlen: chr.len,
 			start,
 			stop,
-			actualposition
+			actualposition,
 		}
 	}
 	return null