@sjcrh/proteinpaint-server 2.44.0 → 2.46.0

package/shared/common.js

@@ -1,1080 +0,0 @@
-/*
-shared between client and server
-
-exported functions
-- bplen()
-- mclasstester()
-- basecompliment()
-
-
-*/
-import { rgb } from 'd3-color'
-import * as d3scale from 'd3-scale'
-import * as d3 from 'd3'
-
-export const defaultcolor = rgb('#8AB1D4').darker()
-export const default_text_color = rgb('#aaa').darker().darker()
-
-export const exoncolor = '#4F8053'
-
-// something that has something to do with coding gene reading frame
-export const IN_frame = true
-export const OUT_frame = false
-
-export const dtsnvindel = 1
-export const dtfusionrna = 2
-export const dtgeneexpression = 3
-export const dtcnv = 4
-export const dtsv = 5
-export const dtitd = 6
-export const dtdel = 7
-export const dtnloss = 8
-export const dtcloss = 9
-export const dtloh = 10 // to be used in svcnv track
-export const plotColor = '#ce768e'
-
-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'
-}
-
-export const mclass = {
-	M: {
-		label: 'MISSENSE',
-		color: '#3987CC',
-		dt: dtsnvindel,
-		desc: 'A substitution variant in the coding region resulting in altered protein coding.',
-		key: 'M'
-	},
-	E: { label: 'EXON', color: '#bcbd22', dt: dtsnvindel, desc: 'A variant in the exon of a non-coding RNA.', key: 'E' },
-	F: {
-		label: 'FRAMESHIFT',
-		color: '#db3d3d',
-		dt: dtsnvindel,
-		desc: 'An insertion or deletion variant that alters the protein coding frame.',
-		key: 'F'
-	},
-	N: {
-		label: 'NONSENSE',
-		color: '#ff7f0e',
-		dt: dtsnvindel,
-		desc: 'A variant altering protein coding to produce a premature stopgain or stoploss.',
-		key: 'N'
-	},
-	S: {
-		label: 'SILENT',
-		color: '#2ca02c',
-		dt: dtsnvindel,
-		desc: 'A substitution variant in the coding region that does not alter protein coding.',
-		key: 'S'
-	},
-	D: {
-		label: 'PROTEINDEL',
-		color: '#7f7f7f',
-		dt: dtsnvindel,
-		desc: 'A deletion resulting in a loss of one or more codons from the product, but not altering the protein coding frame.',
-		key: 'D'
-	},
-	I: {
-		label: 'PROTEININS',
-		color: '#8c564b',
-		dt: dtsnvindel,
-		desc: 'An insertion introducing one or more codons into the product, but not altering the protein coding frame.',
-		key: 'I'
-	},
-	P: {
-		label: 'SPLICE_REGION',
-		color: '#9467bd',
-		dt: dtsnvindel,
-		desc: 'A variant in an intron within 10 nt of an exon boundary.',
-		key: 'P'
-	},
-	L: {
-		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: 'An intronic variant.', key: 'Intron' },
-
-	// 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' },
-
-	WT: { label: 'Wildtype', color: '#D3D3D3', dt: dtsnvindel, desc: 'Wildtype', key: 'WT' }
-}
-export const mclassitd = 'ITD'
-mclass[mclassitd] = {
-	label: 'ITD',
-	color: '#ff70ff',
-	dt: dtitd,
-	desc: 'In-frame internal tandem duplication.',
-	key: mclassitd
-}
-
-export const mclassdel = 'DEL'
-mclass[mclassdel] = {
-	label: 'DELETION, intragenic',
-	color: '#858585',
-	dt: dtdel,
-	desc: 'Intragenic deletion.',
-	key: mclassdel
-}
-
-export const mclassnloss = 'NLOSS'
-mclass[mclassnloss] = {
-	label: 'N-terminus loss',
-	color: '#545454',
-	dt: dtnloss,
-	desc: 'N-terminus loss due to translocation',
-	key: mclassnloss
-}
-
-export const mclasscloss = 'CLOSS'
-mclass[mclasscloss] = {
-	label: 'C-terminus loss',
-	color: '#545454',
-	dt: dtcloss,
-	desc: 'C-terminus loss due to translocation',
-	key: mclasscloss
-}
-
-export const mclassutr3 = 'Utr3'
-mclass[mclassutr3] = {
-	label: 'UTR_3',
-	color: '#998199',
-	dt: dtsnvindel,
-	desc: "A variant in the 3' untranslated region.",
-	key: mclassutr3
-}
-
-export const mclassutr5 = 'Utr5'
-mclass[mclassutr5] = {
-	label: 'UTR_5',
-	color: '#819981',
-	dt: dtsnvindel,
-	desc: "A variant in the 5' untranslated region.",
-	key: mclassutr5
-}
-
-export const mclassnonstandard = 'X'
-mclass[mclassnonstandard] = {
-	label: 'NONSTANDARD',
-	color: 'black',
-	dt: dtsnvindel,
-	desc: 'A mutation class that either does not match our notation, or is unspecified.',
-	key: mclassnonstandard
-}
-
-export const mclassnoncoding = 'noncoding'
-mclass[mclassnoncoding] = {
-	label: 'NONCODING',
-	color: 'black',
-	dt: dtsnvindel,
-	desc: 'Noncoding mutation.',
-	key: mclassnoncoding
-}
-// done point mutations
-
-export function mclasstester(s) {
-	switch (s.toLowerCase()) {
-		case 'missense_mutation':
-			return 'M'
-		case 'nonsense_mutation':
-			return 'N'
-		case 'splice_site':
-			return 'L'
-		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 'translation_start_site':
-			return mclassnonstandard
-		case 'nonstop_mutation':
-			return 'N'
-		case "3'utr":
-			return mclassutr3
-		case "3'flank":
-			return mclassnoncoding
-		case "5'utr":
-			return mclassutr5
-		case "5'flank":
-			return mclassnoncoding
-		case 'blank':
-			return 'Blank'
-		default:
-			return null
-	}
-}
-
-export const mclassfusionrna = 'Fuserna'
-mclass[mclassfusionrna] = {
-	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
-}
-export const mclasssv = 'SV'
-mclass[mclasssv] = {
-	label: 'Structural variation',
-	color: '#858585',
-	dt: dtsv,
-	desc: 'Structural variation detected in genomic DNA.',
-	key: mclasssv
-}
-
-export const mclasscnvgain = 'CNV_amp'
-mclass[mclasscnvgain] = {
-	label: 'Copy number gain',
-	color: '#e9a3c9',
-	dt: dtcnv,
-	desc: 'Copy number gain',
-	key: mclasscnvgain
-}
-
-export const mclasscnvloss = 'CNV_loss'
-mclass[mclasscnvloss] = {
-	label: 'Copy number loss',
-	color: '#a1d76a',
-	dt: dtcnv,
-	desc: 'Copy number loss',
-	key: mclasscnvloss
-}
-
-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'
-mclass[mclasssnv] = {
-	label: 'SNV',
-	color: '#92a2d4',
-	dt: dtsnvindel,
-	desc: 'Single nucleotide variation',
-	key: mclasssnv
-}
-
-export const mclassmnv = 'mnv'
-mclass[mclassmnv] = {
-	label: 'MNV',
-	color: '#92a2d4',
-	dt: dtsnvindel,
-	desc: 'Multiple nucleotide variation',
-	key: mclassmnv
-}
-
-export const mclassinsertion = 'insertion'
-mclass[mclassinsertion] = {
-	label: 'Sequence insertion',
-	color: '#bd8e91',
-	dt: dtsnvindel,
-	desc: 'Sequence insertion',
-	key: mclassinsertion
-}
-
-export const mclassdeletion = 'deletion'
-mclass[mclassdeletion] = {
-	label: 'Sequence deletion',
-	color: '#b5a174',
-	dt: dtsnvindel,
-	desc: 'Sequence deletion',
-	key: mclassdeletion
-}
-// TODO complex indel
-
-export const dt2color = {
-	[dtsnvindel]: mclass.M.color // general color for snvindel irrespective of class (when class is not available)
-	// add new dt as needed
-}
-
-// option to override mutation class attribute values
-export function applyOverrides(overrides = {}) {
-	if (overrides.mclass) {
-		for (const key in overrides.mclass) {
-			// allow to fill-in mutation class that are missing from mclass;
-			// may be useful for things like 'Not tested', etc, that may not be in mclass by default
-			// but are used by a customer with its own PP server instance
-			if (!mclass[key]) mclass[key] = {}
-			for (const subkey in overrides.mclass[key]) {
-				mclass[key][subkey] = overrides.mclass[key][subkey]
-			}
-		}
-	}
-}
-
-export const vepinfo = function (s) {
-	const l = s.toLowerCase().split(',')
-	let rank = 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]
-	rank++
-	if (l.indexOf('splice_donor_variant') != -1) return [dtsnvindel, 'L', rank]
-	rank++
-	if (l.indexOf('stop_gained') != -1) return [dtsnvindel, 'N', rank]
-	rank++
-	if (l.indexOf('frameshift_variant') != -1) return [dtsnvindel, 'F', rank]
-	rank++
-	if (l.indexOf('stop_lost') != -1) return [dtsnvindel, 'N', rank]
-	rank++
-	if (l.indexOf('start_lost') != -1) return [dtsnvindel, 'N', rank]
-	rank++
-	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
-	)
-		return [dtsnvindel, 'I', rank]
-	rank++
-	if (
-		l.indexOf('inframe_deletion') != -1 ||
-		l.indexOf('conservative_inframe_deletion') != -1 ||
-		l.indexOf('disruptive_inframe_deletion') != -1
-	)
-		return [dtsnvindel, 'D', rank]
-	rank++
-	if (l.indexOf('missense_variant') != -1) return [dtsnvindel, 'M', rank]
-	rank++
-	if (l.indexOf('protein_altering_variant') != -1) return [dtsnvindel, 'N', rank]
-	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]
-	rank++
-	if (l.indexOf('stop_retained_variant') != -1) return [dtsnvindel, 'S', rank]
-	rank++
-	if (l.indexOf('synonymous_variant') != -1) return [dtsnvindel, 'S', rank]
-	rank++
-	if (l.indexOf('coding_sequence_variant') != -1) return [dtsnvindel, mclassnonstandard, rank]
-	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]
-	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]
-	rank++
-	if (l.indexOf('intron_variant') != -1) return [dtsnvindel, 'Intron', rank]
-	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]
-	rank++
-	if (l.indexOf('upstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('downstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('tfbs_ablation') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('tfbs_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	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]
-	rank++
-	if (l.indexOf('regulatory_region_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('feature_elongation') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('regulatory_region_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('feature_truncation') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	if (l.indexOf('intergenic_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]
-	rank++
-	return [dtsnvindel, mclassnonstandard, rank]
-}
-
-// m orgin
-export const germlinelegend =
-	'<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="#858585" stroke="none"></path>'
-
-export const morigin = {}
-
-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>'
-}
-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
-}
-
-morigin.germline = morigin[morigingermline]
-morigin.somatic = morigin[moriginsomatic]
-
-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.',
-	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>'
-}
-export const morigingermlinepathogenic = 'GP'
-morigin[morigingermlinepathogenic] = {
-	label: 'Germline pathogenic',
-	desc: 'A constitutional variant with pathogenic allele.',
-	legend: germlinelegend
-}
-export const morigingermlinenonpathogenic = 'GNP'
-morigin[morigingermlinenonpathogenic] = {
-	label: 'Germline non-pathogenic',
-	desc: 'A constitutional variant with non-pathogenic allele.',
-	legend: germlinelegend,
-	hidden: true
-}
-
-export const tkt = {
-	usegm: 'usegm',
-	ds: 'dataset',
-	bigwig: 'bigwig',
-	bigwigstranded: 'bigwigstranded',
-	junction: 'junction',
-	mdsjunction: 'mdsjunction',
-	mdscnv: 'mdscnv',
-	mdssvcnv: 'mdssvcnv', // no longer use as driver
-	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',
-	mds2: 'mds2', // mds 2nd gen
-	mds3: 'mds3', // 3rd gen
-	bedgraphdot: 'bedgraphdot',
-	bam: 'bam',
-	ld: 'ld'
-}
-
-export function validtkt(what) {
-	for (const k in tkt) {
-		if (what == tkt[k]) {
-			return true
-		}
-	}
-	return false
-}
-
-/*
-member track types from mdsvcf
-to get rid of hardcoded strings
-in future may include MAF format files
-*/
-export const mdsvcftype = {
-	vcf: 'vcf'
-}
-
-/*
-for custom mdssvcnv track
-or general track
-to avoid using hard-coded string
-*/
-export const custommdstktype = {
-	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 = '*'
-
-export function nt2aa(gm) {
-	// must convert genome seq to upper case!!!
-	if (!gm.genomicseq) return undefined
-	const enlst = []
-	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 == '-') {
-				enlst.push(reversecompliment(s))
-			} else {
-				enlst.push(s)
-			}
-		}
-	}
-	const nt = enlst.join('')
-	const pep = []
-
-	/*
-	if startCodonFrame is set, will not begin translation from first nt, but will skip 1 or 2 nt at the beginning
-	in case of IGKC, frame=1 means it will borrow 1 nt from the previous IGKJ exons
-	so the first two nucleotides from the current exon will have to be skipped when translating IGKC alone
-	*/
-	const startntidx = gm.startCodonFrame ? 3 - gm.startCodonFrame : 0
-	for (let i = startntidx; i < nt.length; i += 3) {
-		const a = codon[nt.substr(i, 3)]
-		pep.push(a || codon_stop)
-	}
-	gm.cdseq = nt
-	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')
-}
-
-export const basecolor = {
-	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'
-		default:
-			return nt
-	}
-}
-
-export function reversecompliment(s) {
-	const tmp = []
-	for (let i = s.length - 1; i >= 0; i--) {
-		tmp.push(basecompliment(s[i]))
-	}
-	return tmp.join('')
-}
-
-export function spliceeventchangegmexon(gm, evt) {
-	/*
-	alter gm.coding[], by exon-skip/alt events
-	for frame checking
-	gm must have coding
-	*/
-	const gm2 = {
-		chr: gm.chr,
-		start: gm.start,
-		stop: gm.stop,
-		strand: gm.strand,
-		coding: []
-	}
-	if (evt.isskipexon || evt.isaltexon) {
-		for (let i = 0; i < gm.exon.length; i++) {
-			const codingstart = Math.max(gm.codingstart, gm.exon[i][0])
-			const codingstop = Math.min(gm.codingstop, gm.exon[i][1])
-			if (codingstart > codingstop) {
-				// not coding exon
-				continue
-			}
-			if (evt.skippedexon.indexOf(i) == -1) {
-				// not skipped
-				gm2.coding.push([codingstart, codingstop])
-			} else {
-				// skipped
-			}
-		}
-	} 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 == '+'
-		if (evt.a5ss) {
-			if (forward) {
-				exons[evt.exon5idx][1] = evt.junctionB.start
-			} else {
-				exons[evt.exon5idx + 1][0] = evt.junctionB.stop
-			}
-		} else {
-			if (forward) {
-				exons[evt.exon5idx + 1][0] = evt.junctionB.stop
-			} else {
-				exons[evt.exon5idx][1] = evt.junctionB.start
-			}
-		}
-		// from new exons, figure out coding exons
-		for (const e of exons) {
-			const codingstart = Math.max(gm.codingstart, e[0])
-			const codingstop = Math.min(gm.codingstop, e[1])
-			if (codingstart > codingstop) {
-				// not coding exon
-				continue
-			}
-			gm2.coding.push([codingstart, codingstop])
-		}
-	}
-	return gm2
-}
-
-export function fasta2gmframecheck(gm, str) {
-	/*
-	gm{}
-		.chr
-		.start
-		.stop
-			start/stop is transcript position
-		.strand
-		.coding[]
-	str
-		samtools faidx output
-	*/
-	const lines = str.split('\n')
-	// remove fasta header
-	lines.shift()
-	gm.genomicseq = lines.join('').toUpperCase()
-
-	const aaseq = nt2aa(gm)
-
-	let thisframe = OUT_frame
-	const stopcodonidx = aaseq.indexOf(codon_stop)
-	if (stopcodonidx == aaseq.length - 1) {
-		// the first appearance of stop codon is at the last of translation
-		thisframe = IN_frame
-	}
-	return thisframe
-}
-
-export function validate_vcfinfofilter(obj) {
-	/*
-	validate vcfinfofilter as from embedding api or dataset
-	*/
-
-	if (!obj.lst) return '.lst missing'
-
-	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.autocategory || set.categories) {
-			// categorical info, auto or defined
-
-			if (!set.autocategory) {
-				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
-					if (!v.label) {
-						v.label = k
-					}
-				}
-			}
-
-			if (set.categoryhidden) {
-				for (const k in set.categoryhidden) {
-					if (!set.categories[k]) return 'unknown hidden-by-default category ' + k + ' from set ' + set.name
-				}
-			} else {
-				set.categoryhidden = {}
-			}
-		} else if (set.numericfilter) {
-			// otherwise, numerical value, the style of population frequency filter
-			const lst = []
-			for (const v of set.numericfilter) {
-				if (typeof v == 'number') {
-					/*
-					just a number, defaults to 'lower-than'
-					*/
-					lst.push({ side: '<', value: v })
-				} else {
-					lst.push({
-						side: v.side || '<',
-						value: v.value
-					})
-				}
-			}
-			set.numericfilter = lst
-
-			//return 'no .categories or .numericfilter from set '+set.name
-		}
-
-		if (set.altalleleinfo) {
-			if (!set.altalleleinfo.key) {
-				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
-			}
-		} else {
-			return 'neither .altalleleinfo or .locusinfo is available from set ' + set.name
-		}
-	}
-}
-
-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) {
-			return true
-		}
-	}
-	if (genome.minorchr) {
-		for (const n in genome.minorchr) {
-			if (chrlst.indexOf(n.replace('chr', '')) != -1) {
-				return true
-			}
-		}
-	}
-	return false
-}
-export function contigNameNoChr2(genome, chrlst) {
-	// returns number of matching chr names that either includes "chr" or not
-	// for detecting if chrlst entirely mismatch with what's in the genome build
-	// TODO replace contigNameNoChr
-	let nochrcount = 0,
-		haschrcount = 0
-	for (const n in genome.majorchr) {
-		if (chrlst.includes(n)) {
-			haschrcount++
-		} else if (chrlst.includes(n.replace('chr', ''))) {
-			nochrcount++
-		}
-	}
-	if (genome.minorchr) {
-		for (const n in genome.minorchr) {
-			if (chrlst.includes(n)) {
-				haschrcount++
-			} else if (chrlst.includes(n.replace('chr', ''))) {
-				nochrcount++
-			}
-		}
-	}
-	return [nochrcount, haschrcount]
-}
-
-export function getMax_byiqr(lst, novaluemax) {
-	/*
-	lst: array of numbers
-	novaluemax: when lst is empty, return this value
-	cutoff value based on IQR to exclude outlier values
-	*/
-	if (lst.length == 0) return novaluemax
-	lst.sort((i, j) => i - j)
-	const max = lst[lst.length - 1]
-	if (lst.length <= 5) return max
-	const q1 = lst[Math.floor(lst.length / 4)]
-	const q2 = lst[Math.floor((lst.length * 3) / 4)]
-	return Math.min(q2 + (q2 - q1) * 1.5, max)
-}
-
-export function alleleInGenotypeStr(genotype, allele) {
-	if (!genotype) return false
-	if (genotype.indexOf('/') != -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'
-}
-
-/*
-input:
-
-m={}
-	m.csq=[]
-		element: {
-			Allele: str,
-			Consequence: str,
-			CANONICAL: str, // true if _isoform is canonical
-			...
-			_isoform: str,
-			_class: str,
-			_csqrank: int
-		}
-	m.ann=[]
-		annovar output. may be derelict
-block={}
-	block.usegm={ isoform }
-	can be a mock object when running this function in node!
-
-does:
-	find an annotation from m.csq[] that's fitting the circumstance
-	- current gm isoform displayed in block gene mode
-	- any canonical isoform from m.csq[] (can be missing if vep is not instructed to do it)
-	- one with highest _csqrank
-	then, copy its class/mname to m{}
-	has many fall-back and always try to assign class/mname
-
-no return
-*/
-export function vcfcopymclass(m, block) {
-	if (m.csq) {
-		let useone // point to the element of m.csq[], from this class/mname is copied to m{}
-
-		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)
-		}
-
-		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)
-
-			if (!useone) {
-				// none of the elements in m.csq[] is using a canonical isoform, as that's a vep optional output
-				// last method: choose *colorful* annotation based on if is canonical, _csqrank
-				useone = m.csq[0]
-				for (const q of m.csq) {
-					if (q._csqrank < useone._csqrank) {
-						useone = q
-					}
-				}
-			}
-		}
-
-		if (useone) {
-			m.gene = useone._gene
-			m.isoform = useone._isoform
-			m.class = useone._class
-			m.dt = useone._dt
-			m.mname = useone._mname
-
-			if (m.class == mclassnoncoding) {
-				// noncoding converted from csq is not a meaningful, drab color, has no mname label, delete so later will be converted to non-protein class
-				delete m.class
-			}
-		}
-	} else if (m.ann) {
-		// there could be many applicable annotations, the first one not always desirable
-		// choose *colorful* annotation based on _csqrank
-		let useone = null
-		if (block.usegm) {
-			for (const q of m.ann) {
-				if (q._isoform != block.usegm.isoform) continue
-				if (useone) {
-					if (q._csqrank < useone._csqrank) {
-						useone = q
-					}
-				} else {
-					useone = q
-				}
-			}
-			if (!useone && block.gmmode == gmmode.genomic) {
-				// no match to this gene, but in genomic mode, maybe from other genes?
-				useone = m.ann[0]
-			}
-		} else {
-			useone = m.ann[0]
-			for (const q of m.ann) {
-				if (q._csqrank < useone._csqrank) {
-					useone = q
-				}
-			}
-		}
-		if (useone) {
-			m.gene = useone._gene
-			m.isoform = useone._isoform
-			m.class = useone._class
-			m.dt = useone._dt
-			m.mname = useone._mname
-
-			if (m.class == mclassnoncoding) {
-				delete m.class
-			}
-		}
-	}
-
-	if (m.class == undefined) {
-		// infer class from m.type, which was assigned by vcf.js
-		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
-			if (m.mname.length > 15) {
-				// avoid long indel
-				m.mname = m.type
-			}
-		} else {
-			m.class = mclassnonstandard
-			m.dt = dtsnvindel
-			m.mname = m.type
-		}
-	}
-
-	delete m.type
-}
-
-/*
-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'
-
-// 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]
-		})
-	}
-}
-
-export function kernelEpanechnikov(k) {
-	return function (v) {
-		return Math.abs((v /= k)) <= 1 ? (0.75 * (1 - v * v)) / k : 0
-	}
-}
-
-export const schemeCategory20 = [
-	'#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 function getColorScheme(number) {
-	if (number > 20) {
-		const scheme = []
-		for (let i = 0; i < number; i++) scheme.push(d3.interpolateRainbow(i / number))
-		return scheme
-	}
-	if (number > 12) return schemeCategory20
-	else if (number > 8) return d3.schemePaired
-	else if (number > 2) return d3.schemeDark2
-	else return schemeCategory2
-}
-export function getColors(number) {
-	const scheme = getColorScheme(number)
-	return d3scale.scaleOrdinal(scheme)
-}
-
-export const truncatingMutations = ['F', 'N', 'D', 'I', 'L']
-export const proteinChangingMutations = ['F', 'N', 'D', 'I', 'L', 'M', 'P']