@jbrowse/plugin-variants 2.6.1 → 2.6.3

package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap

@@ -1,325 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch variants from volvox.vcf 1`] = `
-[
-  "ctgA",
-]
-`;
-
-exports[`adapter can fetch variants from volvox.vcf 2`] = `
-[
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        3,
-      ],
-      "DP4": [
-        0,
-        0,
-        3,
-        0,
-      ],
-      "FQ": [
-        -36,
-      ],
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0186,
-      ],
-    },
-    "POS": 277,
-    "QUAL": 10.4,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 277,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          13,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          42,
-          9,
-          0,
-        ],
-      },
-    },
-    "start": 276,
-    "type": "SNV",
-    "uniqueId": "test-0",
-  },
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        23,
-      ],
-      "DP4": [
-        0,
-        1,
-        8,
-        14,
-      ],
-      "FQ": [
-        -73,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        1,
-        1,
-        0.42,
-        1,
-      ],
-      "VDB": [
-        0.0308,
-      ],
-    },
-    "POS": 1694,
-    "QUAL": 107,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 1694,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          89,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          140,
-          46,
-          0,
-        ],
-      },
-    },
-    "start": 1693,
-    "type": "SNV",
-    "uniqueId": "test-1",
-  },
-  {
-    "ALT": [
-      "G",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        1,
-      ],
-      "AF1": [
-        0.5,
-      ],
-      "DP": [
-        22,
-      ],
-      "DP4": [
-        6,
-        5,
-        3,
-        8,
-      ],
-      "FQ": [
-        45.3,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        0.39,
-        1,
-        1,
-        1,
-      ],
-      "VDB": [
-        0.0253,
-      ],
-    },
-    "POS": 2644,
-    "QUAL": 44,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> G",
-    "end": 2644,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          75,
-        ],
-        "GT": [
-          "0/1",
-        ],
-        "PL": [
-          74,
-          0,
-          77,
-        ],
-      },
-    },
-    "start": 2643,
-    "type": "SNV",
-    "uniqueId": "test-2",
-  },
-  {
-    "ALT": [
-      "A",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        19,
-      ],
-      "DP4": [
-        0,
-        0,
-        8,
-        11,
-      ],
-      "FQ": [
-        -84,
-      ],
-      "MQ": [
-        36,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3213,
-    "QUAL": 124,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> A",
-    "end": 3213,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          99,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          157,
-          57,
-          0,
-        ],
-      },
-    },
-    "start": 3212,
-    "type": "SNV",
-    "uniqueId": "test-3",
-  },
-  {
-    "ALT": [
-      "ct",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        15,
-      ],
-      "DP4": [
-        0,
-        0,
-        5,
-        6,
-      ],
-      "FQ": [
-        -67.5,
-      ],
-      "INDEL": true,
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3858,
-    "QUAL": 160,
-    "REF": "ctt",
-    "aliases": undefined,
-    "description": "deletion ctt -> ct",
-    "end": 3860,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          63,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          201,
-          33,
-          0,
-        ],
-      },
-    },
-    "start": 3857,
-    "type": "deletion",
-    "uniqueId": "test-4",
-  },
-]
-`;

package/src/VcfAdapter/configSchema.ts

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config VcfAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const VcfAdapter = ConfigurationSchema(
-  'VcfAdapter',
-  {
-    /**
-     * #slot
-     */
-    vcfLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default VcfAdapter

package/src/VcfAdapter/index.ts

@@ -1,15 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'VcfAdapter',
-        displayName: 'VCF adapter',
-        configSchema,
-        getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/VcfAdapter/test_data/volvox.filtered.vcf

@@ -1,73 +0,0 @@
-##fileformat=VCFv4.1
-##samtoolsVersion=0.1.18 (r982:295)
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
-##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
-##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
-##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
-##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
-##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
-##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
-##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
-##contig=<ID=ctgA,length=248956422,assembly=GRCh38.d1.vd1>
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_data/raw/volvox/volvox-sorted.bam
-ctgA	277	.	T	C	10.4	.	DP=3;VDB=0.0186;AF1=1;AC1=2;DP4=0,0,3,0;MQ=37;FQ=-36	GT:PL:GQ	1/1:42,9,0:13
-ctgA	1694	.	T	C	107	.	DP=23;VDB=0.0308;AF1=1;AC1=2;DP4=0,1,8,14;MQ=37;FQ=-73;PV4=1,1,0.42,1	GT:PL:GQ	1/1:140,46,0:89
-ctgA	2644	.	T	G	44	.	DP=22;VDB=0.0253;AF1=0.5;AC1=1;DP4=6,5,3,8;MQ=37;FQ=45.3;PV4=0.39,1,1,1	GT:PL:GQ	0/1:74,0,77:75
-ctgA	3213	.	T	A	124	.	DP=19;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,8,11;MQ=36;FQ=-84	GT:PL:GQ	1/1:157,57,0:99
-ctgA	3858	.	ctt	ct	160	.	INDEL;DP=15;VDB=0.0384;AF1=1;AC1=2;DP4=0,0,5,6;MQ=37;FQ=-67.5	GT:PL:GQ	1/1:201,33,0:63
-ctgA	5496	.	C	G	6.98	.	DP=18;VDB=0.0011;AF1=0.4999;AC1=1;DP4=5,7,4,2;MQ=37;FQ=9.53;PV4=0.62,1,1,1	GT:PL:GQ	0/1:36,0,92:37
-ctgA	8471	.	G	T	124	.	DP=21;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,10;MQ=37;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
-ctgA	9603	.	A	T	126	.	DP=21;VDB=0.0356;AF1=1;AC1=2;DP4=0,0,10,11;MQ=36;FQ=-90	GT:PL:GQ	1/1:159,63,0:99
-ctgA	10423	.	T	A	25	.	DP=19;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,7,3,6;MQ=37;FQ=28;PV4=1,1,1,0.27	GT:PL:GQ	0/1:55,0,73:58
-ctgA	13202	.	G	T	40	.	DP=22;VDB=0.0399;AF1=0.5;AC1=1;DP4=4,8,5,5;MQ=37;FQ=42.8;PV4=0.67,1,1,1	GT:PL:GQ	0/1:70,0,84:73
-ctgA	14247	.	ac	aCc	61.5	.	INDEL;DP=22;VDB=0.0404;AF1=0.5;AC1=1;DP4=3,4,6,0;MQ=37;FQ=62.4;PV4=0.07,1,1,1	GT:PL:GQ	0/1:99,0,101:99
-ctgA	14481	.	G	A	42	.	DP=21;VDB=0.0394;AF1=0.5;AC1=1;DP4=4,6,5,6;MQ=37;FQ=42;PV4=1,1,1,0.12	GT:PL:GQ	0/1:72,0,72:72
-ctgA	15078	.	T	A	96	.	DP=12;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,4,8;MQ=37;FQ=-63	GT:PL:GQ	1/1:129,36,0:69
-ctgA	15163	.	gcc	gCcc	213	.	INDEL;DP=20;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,10,7;MQ=37;FQ=-85.5	GT:PL:GQ	1/1:254,51,0:99
-ctgA	15418	.	A	G	64	.	DP=19;VDB=0.0253;AF1=0.5003;AC1=1;DP4=5,1,5,8;MQ=35;FQ=4.13;PV4=0.14,0.26,0.11,1	GT:PL:GQ	0/1:94,0,29:32
-ctgA	17042	.	C	T	119	.	DP=22;VDB=0.0394;AF1=1;AC1=2;DP4=0,0,13,9;MQ=37;FQ=-93	GT:PL:GQ	1/1:152,66,0:99
-ctgA	18948	.	A	G	57	.	DP=23;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,4,4,9;MQ=37;FQ=39;PV4=0.22,1,0.2,1	GT:PL:GQ	0/1:87,0,66:69
-ctgA	19882	.	acg	a	98.5	.	INDEL;DP=22;VDB=0.0374;AF1=0.5;AC1=1;DP4=4,6,3,5;MQ=37;FQ=101;PV4=1,0.049,1,1	GT:PL:GQ	0/1:136,0,202:99
-ctgA	20675	.	T	C	40	.	DP=18;VDB=0.0401;AF1=0.5;AC1=1;DP4=5,3,4,6;MQ=36;FQ=31.7;PV4=0.64,1,0.19,0.15	GT:PL:GQ	0/1:70,0,59:62
-ctgA	21485	.	C	T,A	118	.	DP=20;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,8,12;MQ=36;FQ=-84	GT:PL:GQ	1/1:151,57,0,150,42,147:99
-ctgA	22326	.	C	T	107	.	DP=14;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,6,8;MQ=36;FQ=-69	GT:PL:GQ	1/1:140,42,0:81
-ctgA	23636	.	A	C	58	.	DP=19;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,5,5,7;MQ=37;FQ=18.1;PV4=0.66,0.23,1,0.037	GT:PL:GQ	0/1:88,0,45:48
-ctgA	23959	.	A	G	118	.	DP=19;VDB=0.0374;AF1=1;AC1=2;DP4=0,0,7,11;MQ=36;FQ=-81	GT:PL:GQ	1/1:151,54,0:99
-ctgA	24978	.	C	G	127	.	DP=22;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,11,11;MQ=35;FQ=-93	GT:PL:GQ	1/1:160,66,0:99
-ctgA	25558	.	A	C	104	.	DP=27;VDB=0.0371;AF1=1;AC1=2;DP4=0,0,18,7;MQ=36;FQ=-102	GT:PL:GQ	1/1:137,75,0:99
-ctgA	26079	.	C	A	29	.	DP=18;VDB=0.0339;AF1=0.5;AC1=1;DP4=6,4,4,4;MQ=36;FQ=31.9;PV4=1,0.14,0.44,0.13	GT:PL:GQ	0/1:59,0,76:62
-ctgA	28463	.	T	A	27	.	DP=20;VDB=0.0399;AF1=0.5;AC1=1;DP4=5,6,4,5;MQ=36;FQ=30;PV4=1,1,1,1	GT:PL:GQ	0/1:57,0,82:60
-ctgA	28719	.	T	G	39	.	DP=18;VDB=0.0333;AF1=0.5;AC1=1;DP4=6,3,5,4;MQ=37;FQ=36.6;PV4=1,1,1,1	GT:PL:GQ	0/1:69,0,65:67
-ctgA	29032	.	G	T	103	.	DP=19;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,13,6;MQ=37;FQ=-84	GT:PL:GQ	1/1:136,57,0:99
-ctgA	29848	.	C	T	91	.	DP=11;VDB=0.0333;AF1=1;AC1=2;DP4=0,0,5,6;MQ=36;FQ=-60	GT:PL:GQ	1/1:124,33,0:63
-ctgA	34015	.	T	A	85	.	DP=10;VDB=0.0339;AF1=1;AC1=2;DP4=0,0,4,6;MQ=37;FQ=-57	GT:PL:GQ	1/1:118,30,0:57
-ctgA	35771	.	T	A	99	.	DP=16;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,3,13;MQ=36;FQ=-75	GT:PL:GQ	1/1:132,48,0:93
-ctgA	38156	.	C	G	16.1	.	DP=12;VDB=0.0168;AF1=0.5;AC1=1;DP4=3,2,3,2;MQ=37;FQ=16.1;PV4=1,1,1,0.43	GT:PL:GQ	0/1:46,0,46:46
-ctgA	39952	.	C	T	124	.	DP=21;VDB=0.0404;AF1=1;AC1=2;DP4=0,0,11,10;MQ=33;FQ=-90	GT:PL:GQ	1/1:157,63,0:99
-ctgA	39966	.	T	C	11.3	.	DP=27;VDB=0.0299;AF1=0.5;AC1=1;DP4=11,5,2,7;MQ=34;FQ=14.2;PV4=0.041,1,0.01,1	GT:PL:GQ	0/1:41,0,88:43
-ctgA	39983	.	A	T	127	.	DP=24;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,13,11;MQ=34;FQ=-99	GT:PL:GQ	1/1:160,72,0:99
-ctgA	41826	.	T	C	110	.	DP=18;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,11,7;MQ=36;FQ=-81	GT:PL:GQ	1/1:143,54,0:99
-ctgA	42608	.	G	T	31	.	DP=24;VDB=0.0404;AF1=0.5;AC1=1;DP4=10,4,3,7;MQ=36;FQ=34;PV4=0.095,0.12,0.044,1	GT:PL:GQ	0/1:61,0,82:64
-ctgA	43007	.	T	A	36	.	DP=19;VDB=0.0355;AF1=0.5;AC1=1;DP4=3,5,9,2;MQ=36;FQ=30.4;PV4=0.074,1,0.11,1	GT:PL:GQ	0/1:66,0,58:60
-ctgA	43354	.	A	C	35	.	DP=20;VDB=0.0147;AF1=0.5;AC1=1;DP4=5,6,5,4;MQ=37;FQ=37.9;PV4=1,1,1,0.39	GT:PL:GQ	0/1:65,0,82:68
-ctgA	45666	.	G	T,A	91	.	DP=16;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,10,6;MQ=36;FQ=-72	GT:PL:GQ	1/1:124,45,0,122,31,119:87
-ctgA	46994	.	T	A	40	.	DP=24;VDB=0.0308;AF1=0.5;AC1=1;DP4=6,7,7,4;MQ=37;FQ=43;PV4=0.44,1,1,0.49	GT:PL:GQ	0/1:70,0,89:73
-ctgA	47847	.	C	A,T	126	.	DP=23;VDB=0.0388;AF1=1;AC1=2;DP4=0,0,9,14;MQ=36;FQ=-93	GT:PL:GQ	1/1:159,66,0,158,51,155:99
-ctgA	48199	.	A	T	22	.	DP=17;VDB=0.0320;AF1=0.5;AC1=1;DP4=2,8,4,3;MQ=36;FQ=25;PV4=0.16,1,0.12,0.0062	GT:PL:GQ	0/1:52,0,71:55
-ctgA	49288	.	G	A	106	.	DP=23;VDB=0.0399;AF1=1;AC1=2;DP4=0,0,16,7;MQ=35;FQ=-96	GT:PL:GQ	1/1:139,69,0:99

package/src/VcfFeature/index.test.ts

@@ -1,132 +0,0 @@
-import VcfParser from '@gmod/vcf'
-import VcfFeature from './index'
-
-test('test usage of the VcfFeature', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `lcl|Scaffald_1\t80465\trs118266897\tR\tA\t29\tPASS\tNS=3;0,14;AF=0.5;DB;112;PG2.1`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.id()).toEqual('myuniqueid')
-  expect(f.get('name')).toEqual('rs118266897')
-})
-
-test('try INS feature with END less than start', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tR\tA\t29\tPASS\tEND=1;SVTYPE=INS`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.id()).toEqual('myuniqueid')
-  expect(f.get('start')).toEqual(99)
-  expect(f.get('end')).toEqual(100)
-})
-
-test('try DEL feature with END info field valid', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tR\t<DEL>\t29\tPASS\tEND=1000;SVTYPE=DEL`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.id()).toEqual('myuniqueid')
-  expect(f.get('start')).toEqual(99)
-  expect(f.get('end')).toEqual(1000)
-})
-
-test('multiple SVs', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tR\t<INVDUP>,<INV>\t29\tPASS\tEND=1000;SVTYPE=DEL`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.get('description')).toEqual('<INVDUP>,<INV>')
-})
-test('BND', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tR\tG[ctgA:34200[\t29\tPASS\tEND=1000;SVTYPE=BND`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.get('description')).toEqual('G[ctgA:34200[')
-})
-test('multiple BND', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tR\tG[ctgA:34200[,G[ctgA:44200[\t29\tPASS\tEND=1000;SVTYPE=BND`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.get('description')).toEqual('G[ctgA:34200[,G[ctgA:44200[')
-})
-test('multiple SNV', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tG\tA,C\t29\tPASS\tHELLO=world`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.get('description')).toEqual('SNV G -> A,C')
-})
-
-test('multiple SNV2', () => {
-  const parser = new VcfParser({
-    header: `#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam`,
-  })
-  const line = `chr1\t100\trs123\tG\tAT,<*>\t29\tPASS\tHELLO=world`
-
-  const variant = parser.parseLine(line)
-
-  const f = new VcfFeature({
-    parser,
-    variant,
-    id: 'myuniqueid',
-  })
-  expect(f.get('description')).toEqual('insertion G -> AT,<*>')
-})

package/src/VcfFeature/index.ts

@@ -1,104 +0,0 @@
-import { Feature } from '@jbrowse/core/util'
-import VCF from '@gmod/vcf'
-
-// locals
-import { getSOTermAndDescription } from './util'
-
-/* eslint-disable no-underscore-dangle */
-
-interface Samples {
-  [key: string]: {
-    [key: string]: { values: string[] | number[] | null }
-  }
-}
-
-interface FeatureData {
-  [key: string]: unknown
-  refName: string
-  start: number
-  end: number
-  description?: string
-  type?: string
-  name?: string
-  aliases?: string[]
-  samples?: Samples
-}
-
-export default class VCFFeature implements Feature {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private variant: any
-
-  private parser: VCF
-
-  private data: FeatureData
-
-  private _id: string
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  constructor(args: { variant: any; parser: VCF; id: string }) {
-    this.variant = args.variant
-    this.parser = args.parser
-    this.data = this.dataFromVariant(this.variant)
-    this._id = args.id
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  get(field: string): any {
-    return field === 'samples'
-      ? this.variant.SAMPLES
-      : this.data[field] || this.variant[field]
-  }
-
-  set() {}
-
-  parent() {
-    return undefined
-  }
-
-  children() {
-    return undefined
-  }
-
-  tags() {
-    return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples']
-  }
-
-  id() {
-    return this._id
-  }
-
-  dataFromVariant(variant: {
-    REF: string
-    POS: number
-    ALT: string[]
-    CHROM: string
-    INFO: any // eslint-disable-line @typescript-eslint/no-explicit-any
-    ID: string[]
-  }): FeatureData {
-    const { REF, ALT, POS, CHROM, INFO, ID } = variant
-    const start = POS - 1
-    const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
-    const isTRA = ALT?.some(f => f === '<TRA>')
-    const isSymbolic = ALT?.some(f => f.includes('<'))
-
-    return {
-      refName: CHROM,
-      start,
-      end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-      description,
-      type,
-      name: ID?.join(','),
-      aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
-    }
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  toJSON(): any {
-    return {
-      uniqueId: this._id,
-      ...this.variant,
-      ...this.data,
-      samples: this.variant.SAMPLES,
-    }
-  }
-}