@jbrowse/plugin-variants 1.7.11 → 2.0.0

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -0,0 +1,129 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React, { useState } from 'react';
+import { Divider, Link, Paper, FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { DataGrid } from '@mui/x-data-grid';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import { getEnv } from 'mobx-state-tree';
+import { FeatureDetails, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import BreakendOptionDialog from './BreakendOptionDialog';
+import { parseBreakend } from '@gmod/vcf';
+function VariantSamples(props) {
+    const [filter, setFilter] = useState({});
+    const [showFilters, setShowFilters] = useState(false);
+    const { feature } = props;
+    const { samples = {} } = feature;
+    const preFilteredRows = Object.entries(samples);
+    if (!preFilteredRows.length) {
+        return null;
+    }
+    const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(field => ({
+        field,
+    }));
+    let error;
+    let rows = [];
+    const filters = Object.keys(filter);
+    // catch some error thrown from regex
+    // note: maps all values into a string, if this is not done rows are not
+    // sortable by the data-grid
+    try {
+        rows = preFilteredRows
+            .map((row) => ({
+            ...Object.fromEntries(Object.entries(row[1]).map(entry => [entry[0], String(entry[1])])),
+            sample: row[0],
+            id: row[0],
+        }))
+            .filter((row) => {
+            return filters.length
+                ? filters.every(key => {
+                    const val = row[key];
+                    const currFilter = filter[key];
+                    return currFilter ? val.match(new RegExp(currFilter, 'i')) : true;
+                })
+                : true;
+        });
+    }
+    catch (e) {
+        error = e;
+    }
+    // disableSelectionOnClick helps avoid
+    // https://github.com/mui-org/material-ui-x/issues/1197
+    return (React.createElement(BaseCard, { ...props, title: "Samples" },
+        error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
+        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
+        showFilters ? (React.createElement(React.Fragment, null,
+            React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
+            infoFields.map(({ field }) => {
+                return (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }));
+            }))) : null,
+        React.createElement("div", { style: { height: 600, width: '100%', overflow: 'auto' } },
+            React.createElement(DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, disableColumnMenu: true }))));
+}
+function BreakendPanel(props) {
+    const { model, locStrings, feature } = props;
+    const session = getSession(model);
+    const { pluginManager } = getEnv(session);
+    const [breakpointDialog, setBreakpointDialog] = useState(false);
+    let viewType;
+    try {
+        viewType = pluginManager.getViewType('BreakpointSplitView');
+    }
+    catch (e) {
+        // ignore
+    }
+    const simpleFeature = new SimpleFeature(feature);
+    return (React.createElement(BaseCard, { ...props, title: "Breakends" },
+        React.createElement(Typography, null, "Link to linear view of breakend endpoints"),
+        React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
+            React.createElement(Link, { href: "#", onClick: event => {
+                    var _a;
+                    event.preventDefault();
+                    const { view } = model;
+                    try {
+                        if (view) {
+                            (_a = view.navToLocString) === null || _a === void 0 ? void 0 : _a.call(view, locString);
+                        }
+                        else {
+                            throw new Error('No view associated with this feature detail panel anymore');
+                        }
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                } }, `LGV - ${locString}`))))),
+        viewType ? (React.createElement("div", null,
+            React.createElement(Typography, null, "Launch split views with breakend source and target"),
+            React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
+                React.createElement(Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        setBreakpointDialog(true);
+                    } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
+            breakpointDialog ? (React.createElement(BreakendOptionDialog, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
+                    setBreakpointDialog(false);
+                } })) : null)) : null));
+}
+function VariantFeatureDetails(props) {
+    const { model } = props;
+    const { featureData, descriptions } = model;
+    const feat = JSON.parse(JSON.stringify(featureData));
+    const { samples, ...rest } = feat;
+    const basicDescriptions = {
+        CHROM: 'chromosome: An identifier from the reference genome',
+        POS: 'position: The reference position, with the 1st base having position 1',
+        ID: 'identifier: Semi-colon separated list of unique identifiers where available',
+        REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
+        ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
+        QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
+        FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
+    };
+    return (React.createElement(Paper, { "data-testid": "variant-side-drawer" },
+        React.createElement(FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
+        React.createElement(Divider, null),
+        feat.type === 'breakend' ? (React.createElement(BreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = parseBreakend(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
+        feat.type === 'translocation' ? (React.createElement(BreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
+        React.createElement(VariantSamples, { feature: feat, ...props })));
+}
+export default observer(VariantFeatureDetails);
+//# sourceMappingURL=VariantFeatureWidget.js.map

package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"VariantFeatureWidget.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/VariantFeatureWidget.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EACL,OAAO,EACP,IAAI,EACJ,KAAK,EACL,gBAAgB,EAChB,QAAQ,EACR,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,aAEN,MAAM,kCAAkC,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAA;AAC3C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAA;AACxC,OAAO,EACL,cAAc,EACd,QAAQ,GACT,MAAM,mDAAmD,CAAA;AAC1D,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAEzC,SAAS,cAAc,CAAC,KAAU;IAChC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAM,EAAE,CAAC,CAAA;IAC7C,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACrD,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAEzB,MAAM,EAAE,OAAO,GAAG,EAAE,EAAE,GAAG,OAAO,CAAA;IAChC,MAAM,eAAe,GAAQ,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IACpD,IAAI,CAAC,eAAe,CAAC,MAAM,EAAE;QAC3B,OAAO,IAAI,CAAA;KACZ;IACD,MAAM,UAAU,GAAG,CAAC,QAAQ,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CACtE,KAAK,CAAC,EAAE,CAAC,CAAC;QACR,KAAK;KACN,CAAC,CACH,CAAA;IACD,IAAI,KAAK,CAAA;IACT,IAAI,IAAI,GAAG,EAAE,CAAA;IACb,MAAM,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;IAEnC,qCAAqC;IACrC,wEAAwE;IACxE,4BAA4B;IAC5B,IAAI;QACF,IAAI,GAAG,eAAe;aACnB,GAAG,CAAC,CAAC,GAAQ,EAAE,EAAE,CAAC,CAAC;YAClB,GAAG,MAAM,CAAC,WAAW,CACnB,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAClE;YACD,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC;YACd,EAAE,EAAE,GAAG,CAAC,CAAC,CAAC;SACX,CAAC,CAAC;aACF,MAAM,CAAC,CAAC,GAAQ,EAAE,EAAE;YACnB,OAAO,OAAO,CAAC,MAAM;gBACnB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE;oBAClB,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;oBACpB,MAAM,UAAU,GAAG,MAAM,CAAC,GAAG,CAAC,CAAA;oBAC9B,OAAO,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,MAAM,CAAC,UAAU,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;gBACnE,CAAC,CAAC;gBACJ,CAAC,CAAC,IAAI,CAAA;QACV,CAAC,CAAC,CAAA;KACL;IAAC,OAAO,CAAC,EAAE;QACV,KAAK,GAAG,CAAC,CAAA;KACV;IACD,sCAAsC;IACtC,uDAAuD;IACvD,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,SAAS;QACjC,KAAK,CAAC,CAAC,CAAC,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CAAC,CAAC,CAAC,IAAI;QAEnE,oBAAC,gBAAgB,IACf,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,WAAW,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,GACvC,EAEJ,KAAK,EAAC,qBAAqB,GAC3B;QACD,WAAW,CAAC,CAAC,CAAC,CACb;YACE,oBAAC,UAAU,yQAKE;YACZ,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE;gBAC5B,OAAO,CACL,oBAAC,SAAS,IACR,GAAG,EAAE,UAAU,KAAK,EAAE,EACtB,WAAW,EAAE,UAAU,KAAK,EAAE,EAC9B,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,IAAI,EAAE,EAC1B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAChB,SAAS,CAAC,EAAE,GAAG,MAAM,EAAE,CAAC,KAAK,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,GAEvD,CACH,CAAA;YACH,CAAC,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI;QACR,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;YAC1D,oBAAC,QAAQ,IACP,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,UAAU,EACnB,uBAAuB,QACvB,SAAS,EAAE,EAAE,EACb,iBAAiB,SACjB,CACE,CACG,CACZ,CAAA;AACH,CAAC;AAED,SAAS,aAAa,CAAC,KAItB;IACC,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;IACzC,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/D,IAAI,QAAQ,CAAA;IAEZ,IAAI;QACF,QAAQ,GAAG,aAAa,CAAC,WAAW,CAAC,qBAAqB,CAAC,CAAA;KAC5D;IAAC,OAAO,CAAC,EAAE;QACV,SAAS;KACV;IAED,MAAM,aAAa,GAAG,IAAI,aAAa,CAAC,OAAO,CAAC,CAAA;IAChD,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,WAAW;QACpC,oBAAC,UAAU,oDAAuD;QAClE,gCACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,4BAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;YACrC,oBAAC,IAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;;oBACf,KAAK,CAAC,cAAc,EAAE,CAAA;oBACtB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,IAAI;wBACF,IAAI,IAAI,EAAE;4BACR,MAAA,IAAI,CAAC,cAAc,qDAAG,SAAS,CAAC,CAAA;yBACjC;6BAAM;4BACL,MAAM,IAAI,KAAK,CACb,2DAA2D,CAC5D,CAAA;yBACF;qBACF;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;gBACH,CAAC,IAEA,SAAS,SAAS,EAAE,CAChB,CACJ,CACN,CAAC,CACC;QACJ,QAAQ,CAAC,CAAC,CAAC,CACV;YACE,oBAAC,UAAU,6DAEE;YACb,gCACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,4BAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;gBACrC,oBAAC,IAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;wBACf,KAAK,CAAC,cAAc,EAAE,CAAA;wBACtB,mBAAmB,CAAC,IAAI,CAAC,CAAA;oBAC3B,CAAC,IAEA,GAAG,OAAO,CAAC,OAAO,IAAI,OAAO,CAAC,KAAK,OAAO,SAAS,eAAe,CAC9D,CACJ,CACN,CAAC,CACC;YACJ,gBAAgB,CAAC,CAAC,CAAC,CAClB,oBAAC,oBAAoB,IACnB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,GAAG,EAAE;oBAChB,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACC,CACZ,CAAA;AACH,CAAC;AAED,SAAS,qBAAqB,CAAC,KAAU;IACvC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC3C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC,CAAA;IACpD,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;IACjC,MAAM,iBAAiB,GAAG;QACxB,KAAK,EAAE,qDAAqD;QAC5D,GAAG,EAAE,uEAAuE;QAC5E,EAAE,EAAE,6EAA6E;QACjF,GAAG,EAAE,2EAA2E;QAChF,GAAG,EAAE,4EAA4E;QACjF,IAAI,EAAE,mEAAmE;QACzE,MAAM,EACJ,kIAAkI;KACrI,CAAA;IAED,OAAO,CACL,oBAAC,KAAK,mBAAa,qBAAqB;QACtC,oBAAC,cAAc,IACb,OAAO,EAAE,IAAI,EACb,YAAY,EAAE,EAAE,GAAG,iBAAiB,EAAE,GAAG,YAAY,EAAE,KACnD,KAAK,GACT;QACF,oBAAC,OAAO,OAAG;QACV,IAAI,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,CAC1B,oBAAC,aAAa,IACZ,OAAO,EAAE,IAAI,EACb,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,CACtB,CAAC,GAAW,EAAE,EAAE,WAAC,OAAA,CAAA,MAAA,aAAa,CAAC,GAAG,CAAC,0CAAE,YAAY,KAAI,EAAE,CAAA,EAAA,CACxD,EACD,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,CAAC,IAAI,KAAK,eAAe,CAAC,CAAC,CAAC,CAC/B,oBAAC,aAAa,IACZ,OAAO,EAAE,IAAI,EACb,KAAK,EAAE,KAAK,EACZ,UAAU,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,GACrD,CACH,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,cAAc,IAAC,OAAO,EAAE,IAAI,KAAM,KAAK,GAAI,CACtC,CACT,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,qBAAqB,CAAC,CAAA"}

package/esm/VariantFeatureWidget/index.d.ts

@@ -0,0 +1,37 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
+    descriptions: import("mobx-state-tree").IType<any, any, any>;
+}, {
+    setFeatureData(featureData: Record<string, unknown>): void;
+    clearFeatureData(): void;
+    setFormattedData(feat: Record<string, unknown>): void;
+} & {
+    afterCreate(): void;
+}, {
+    type: "BaseFeatureWidget";
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
+    id: string;
+    type: "BaseFeatureWidget";
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    formattedFields: any;
+    finalizedFeatureData: any;
+} & import("mobx-state-tree")._NotCustomized>;

package/esm/VariantFeatureWidget/index.js

@@ -0,0 +1,12 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
+export const configSchema = ConfigurationSchema('VariantFeatureWidget', {});
+export function stateModelFactory(pluginManager) {
+    const baseModel = baseModelFactory(pluginManager);
+    return types.compose(baseModel, types.model('VariantFeatureWidget', {
+        type: types.literal('VariantFeatureWidget'),
+        descriptions: types.frozen(),
+    }));
+}
+//# sourceMappingURL=index.js.map

package/esm/VariantFeatureWidget/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,iBAAiB,IAAI,gBAAgB,EAAE,MAAM,iCAAiC,CAAA;AAEvF,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAAC,sBAAsB,EAAE,EAAE,CAAC,CAAA;AAE3E,MAAM,UAAU,iBAAiB,CAAC,aAA4B;IAC5D,MAAM,SAAS,GAAG,gBAAgB,CAAC,aAAa,CAAC,CAAA;IACjD,OAAO,KAAK,CAAC,OAAO,CAClB,SAAS,EACT,KAAK,CAAC,KAAK,CAAC,sBAAsB,EAAE;QAClC,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,YAAY,EAAE,KAAK,CAAC,MAAM,EAAE;KAC7B,CAAC,CACH,CAAA;AACH,CAAC"}

package/esm/VcfAdapter/VcfAdapter.d.ts

@@ -0,0 +1,24 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import IntervalTree from '@flatten-js/interval-tree';
+export default class VcfAdapter extends BaseFeatureDataAdapter {
+    static capabilities: string[];
+    protected vcfFeatures?: Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree>;
+    }>;
+    getHeader(): Promise<string>;
+    getMetadata(): Promise<any>;
+    setupP(): Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree<any>>;
+    }>;
+    setup(): Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree<any>>;
+    }>;
+    getRefNames(_?: BaseOptions): Promise<string[]>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/VcfAdapter/VcfAdapter.js

@@ -0,0 +1,99 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { readConfObject } from '@jbrowse/core/configuration';
+import IntervalTree from '@flatten-js/interval-tree';
+import { unzip } from '@gmod/bgzf-filehandle';
+import VCF from '@gmod/vcf';
+import VcfFeature from '../VcfTabixAdapter/VcfFeature';
+const readVcf = (f) => {
+    const lines = f.split('\n');
+    const header = [];
+    const rest = [];
+    lines.forEach(line => {
+        if (line.startsWith('#')) {
+            header.push(line);
+        }
+        else if (line) {
+            rest.push(line);
+        }
+    });
+    return { header: header.join('\n'), lines: rest };
+};
+function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+export default class VcfAdapter extends BaseFeatureDataAdapter {
+    async getHeader() {
+        const { header } = await this.setup();
+        return header;
+    }
+    async getMetadata() {
+        const { header } = await this.setup();
+        const parser = new VCF({ header: header });
+        return parser.getMetadata();
+    }
+    // converts lines into an interval tree
+    async setupP() {
+        const buffer = await openLocation(readConfObject(this.config, 'vcfLocation'), this.pluginManager).readFile();
+        const buf = isGzip(buffer) ? await unzip(buffer) : buffer;
+        // 512MB  max chrome string length is 512MB
+        if (buf.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const str = new TextDecoder().decode(buf);
+        const { header, lines } = readVcf(str);
+        const intervalTree = lines
+            .map((line, id) => {
+            var _a;
+            const [refName, startP, , ref, , , , info] = line.split('\t');
+            const start = +startP - 1;
+            const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
+            return { line, refName, start, end, id };
+        })
+            .reduce((acc, obj) => {
+            const key = obj.refName;
+            if (!acc[key]) {
+                acc[key] = new IntervalTree();
+            }
+            acc[key].insert([obj.start, obj.end], obj);
+            return acc;
+        }, {});
+        return { header, intervalTree };
+    }
+    async setup() {
+        if (!this.vcfFeatures) {
+            this.vcfFeatures = this.setupP().catch(e => {
+                this.vcfFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.vcfFeatures;
+    }
+    async getRefNames(_ = {}) {
+        const { intervalTree } = await this.setup();
+        return Object.keys(intervalTree);
+    }
+    getFeatures(region, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            var _a;
+            try {
+                const { start, end, refName } = region;
+                const { header, intervalTree } = await this.setup();
+                const parser = new VCF({ header: header });
+                (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature({
+                    variant: parser.parseLine(f.line),
+                    parser,
+                    id: `${this.id}-${f.id}`,
+                })));
+                observer.complete();
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        }, opts.signal);
+    }
+    freeResources() { }
+}
+VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+//# sourceMappingURL=VcfAdapter.js.map

package/esm/VcfAdapter/VcfAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,UAAU,MAAM,+BAA+B,CAAA;AAEtD,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACF,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,MAAM,GAAG,MAAM,YAAY,CAC/B,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,aAAa,CAAC,EAC1C,IAAI,CAAC,aAAa,CACnB,CAAC,QAAQ,EAAE,CAAA;QAEZ,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QAEzD,2CAA2C;QAC3C,IAAI,GAAG,CAAC,MAAM,GAAG,SAAW,EAAE;YAC5B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QACzC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;gBAC1C,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AA3FjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}

package/esm/VcfAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/VcfAdapter/configSchema.js

@@ -0,0 +1,8 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('VcfAdapter', {
+    vcfLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/VcfAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/VcfAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/esm/VcfAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/VcfAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/VcfAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/VcfTabixAdapter/VcfFeature.d.ts

@@ -0,0 +1,59 @@
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+/**
+ * VCF Feature creation with lazy genotype evaluation.
+ */
+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 {
+    private variant;
+    private parser;
+    private data;
+    private _id;
+    constructor(args: {
+        variant: any;
+        parser: any;
+        id: string;
+    });
+    get(field: string): any;
+    set(): void;
+    parent(): undefined;
+    children(): undefined;
+    tags(): string[];
+    id(): string;
+    dataFromVariant(variant: {
+        REF: string;
+        POS: number;
+        ALT: string[];
+        CHROM: string;
+        INFO: any;
+        ID: string[];
+    }): FeatureData;
+    /**
+     * Get a sequence ontology (SO) term that describes the variant type
+     */
+    _getSOTermAndDescription(ref: string, alt: string[]): [string, string] | [undefined, undefined];
+    static _altTypeToSO: {
+        [key: string]: string | undefined;
+    };
+    _getSOAndDescFromAltDefs(ref: string, alt: string): [string, string] | [undefined, undefined];
+    _getSOAndDescByExamination(ref: string, alt: string): [string, string];
+    _makeDescriptionString(soTerm: string, ref: string, alt: string): string;
+    toJSON(): any;
+}
+export {};

package/esm/VcfTabixAdapter/VcfFeature.js

@@ -0,0 +1,184 @@
+import { parseBreakend } from '@gmod/vcf';
+export default class VCFFeature {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    constructor(args) {
+        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) {
+        return field === 'samples'
+            ? this.variant.SAMPLES
+            : this.data[field] || this.variant[field];
+    }
+    set() { }
+    parent() {
+        return undefined;
+    }
+    children() {
+        return undefined;
+    }
+    tags() {
+        const t = [
+            ...Object.keys(this.data),
+            ...Object.keys(this.variant),
+            'samples',
+        ];
+        return t;
+    }
+    id() {
+        return this._id;
+    }
+    dataFromVariant(variant) {
+        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
+        const start = POS - 1;
+        const [SO_term, description] = this._getSOTermAndDescription(REF, ALT);
+        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
+        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
+        return {
+            refName: CHROM,
+            start,
+            end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
+            description,
+            type: SO_term,
+            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+            aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
+        };
+    }
+    /**
+     * Get a sequence ontology (SO) term that describes the variant type
+     */
+    _getSOTermAndDescription(ref, alt) {
+        // it's just a remark if there are no alternate alleles
+        if (!alt || alt === []) {
+            return ['remark', 'no alternative alleles'];
+        }
+        const soTerms = new Set();
+        let descriptions = new Set();
+        alt.forEach(a => {
+            let [soTerm, description] = this._getSOAndDescFromAltDefs(ref, a);
+            if (!soTerm) {
+                ;
+                [soTerm, description] = this._getSOAndDescByExamination(ref, a);
+            }
+            if (soTerm && description) {
+                soTerms.add(soTerm);
+                descriptions.add(description);
+            }
+        });
+        // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
+        if (descriptions.size > 1) {
+            const prefixes = new Set([...descriptions].map(desc => {
+                const prefix = desc.split('->');
+                return prefix[1] ? prefix[0] : desc;
+            }));
+            const new_descs = [...prefixes].map(prefix => {
+                const suffixes = [...descriptions]
+                    .map(desc => {
+                    const pref = desc.split('-> ');
+                    return pref[1] && pref[0] === prefix ? pref[1] : '';
+                })
+                    .filter(f => !!f);
+                return suffixes.length
+                    ? prefix + '-> ' + suffixes.join(',')
+                    : [...descriptions].join(',');
+            });
+            descriptions = new Set(new_descs);
+        }
+        if (soTerms.size) {
+            return [[...soTerms].join(','), [...descriptions].join(',')];
+        }
+        return [undefined, undefined];
+    }
+    _getSOAndDescFromAltDefs(ref, alt) {
+        if (typeof alt === 'string' && !alt.startsWith('<')) {
+            return [undefined, undefined];
+        }
+        // look for a definition with an SO type for this
+        let soTerm = VCFFeature._altTypeToSO[alt];
+        // if no SO term but ALT is in metadata, assume sequence_variant
+        if (!soTerm && this.parser.getMetadata('ALT', alt)) {
+            soTerm = 'sequence_variant';
+        }
+        if (soTerm) {
+            return [soTerm, alt];
+        }
+        // try to look for a definition for a parent term if we can
+        const modAlt = alt.split(':');
+        if (modAlt.length > 1) {
+            return this._getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`);
+        }
+        // no parent
+        return [undefined, undefined];
+    }
+    // note: term SNV is used instead of SNP because SO definition of SNP says
+    // abundance must be at least 1% in population, and can't be sure we meet
+    // that
+    _getSOAndDescByExamination(ref, alt) {
+        const bnd = parseBreakend(alt);
+        if (bnd) {
+            return ['breakend', alt];
+        }
+        else if (ref.length === 1 && alt.length === 1) {
+            return ['SNV', this._makeDescriptionString('SNV', ref, alt)];
+        }
+        else if (alt === '<INS>') {
+            return ['insertion', alt];
+        }
+        else if (alt === '<DEL>') {
+            return ['deletion', alt];
+        }
+        else if (alt === '<INV>') {
+            return ['deletion', alt];
+        }
+        else if (alt === '<TRA>') {
+            return ['translocation', alt];
+        }
+        else if (alt.includes('<')) {
+            return ['sv', alt];
+        }
+        else if (ref.length === alt.length) {
+            if (ref.split('').reverse().join('') === alt) {
+                return ['inversion', this._makeDescriptionString('inversion', ref, alt)];
+            }
+            return [
+                'substitution',
+                this._makeDescriptionString('substitution', ref, alt),
+            ];
+        }
+        else if (ref.length <= alt.length) {
+            return ['insertion', this._makeDescriptionString('insertion', ref, alt)];
+        }
+        else if (ref.length > alt.length) {
+            return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
+        }
+        return ['indel', this._makeDescriptionString('indel', ref, alt)];
+    }
+    _makeDescriptionString(soTerm, ref, alt) {
+        return `${soTerm} ${ref} -> ${alt}`;
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    toJSON() {
+        return {
+            uniqueId: this._id,
+            ...this.variant,
+            ...this.data,
+            samples: this.variant.SAMPLES,
+        };
+    }
+}
+VCFFeature._altTypeToSO = {
+    DEL: 'deletion',
+    INS: 'insertion',
+    DUP: 'duplication',
+    INV: 'inversion',
+    INVDUP: 'inverted duplication',
+    CNV: 'copy_number_variation',
+    TRA: 'translocation',
+    'DUP:TANDEM': 'tandem_duplication',
+    NON_REF: 'sequence_variant',
+    '*': 'sequence_variant',
+};
+//# sourceMappingURL=VcfFeature.js.map

package/esm/VcfTabixAdapter/VcfFeature.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAyBzC,MAAM,CAAC,OAAO,OAAO,UAAU;IAW7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,MAAM,CAAC,GAAG;YACR,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;YACzB,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;SACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,OAAO,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtE,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,wBAAwB,CACtB,GAAW,EACX,GAAa;QAEb,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,KAAK,EAAE,EAAE;YACtB,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAEjE,IAAI,CAAC,MAAM,EAAE;gBACX,CAAC;gBAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,0BAA0B,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;aACjE;YACD,IAAI,MAAM,IAAI,WAAW,EAAE;gBACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;gBACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;aAC9B;QACH,CAAC,CAAC,CAAA;QAEF,6EAA6E;QAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,CAAC,GAAG,YAAY,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;gBAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YACrC,CAAC,CAAC,CACH,CAAA;YAED,MAAM,SAAS,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC3C,MAAM,QAAQ,GAAG,CAAC,GAAG,YAAY,CAAC;qBAC/B,GAAG,CAAC,IAAI,CAAC,EAAE;oBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;gBACrD,CAAC,CAAC;qBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAEnB,OAAO,QAAQ,CAAC,MAAM;oBACpB,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrC,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACjC,CAAC,CAAC,CAAA;YAEF,YAAY,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;SAClC;QACD,IAAI,OAAO,CAAC,IAAI,EAAE;YAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAeD,wBAAwB,CACtB,GAAW,EACX,GAAW;QAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;SAC9B;QAED,iDAAiD;QACjD,IAAI,MAAM,GAAG,UAAU,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACzC,gEAAgE;QAChE,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;YAClD,MAAM,GAAG,kBAAkB,CAAA;SAC5B;QACD,IAAI,MAAM,EAAE;YACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;SACrB;QAED,2DAA2D;QAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,wBAAwB,CAClC,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CACpD,CAAA;SACF;QAED,YAAY;QACZ,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAED,0EAA0E;IAC1E,yEAAyE;IACzE,OAAO;IACP,0BAA0B,CAAC,GAAW,EAAE,GAAW;QACjD,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,GAAG,EAAE;YACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/C,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,sBAAsB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SAC7D;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;SAC1B;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;SAC9B;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;YAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;SACnB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;YACpC,IAAI,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE;gBAC5C,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;aACzE;YACD,OAAO;gBACL,cAAc;gBACd,IAAI,CAAC,sBAAsB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC;aACtD,CAAA;SACF;aAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;YACnC,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACzE;aAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;YAClC,OAAO,CAAC,UAAU,EAAE,IAAI,CAAC,sBAAsB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACvE;QAED,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,sBAAsB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAClE,CAAC;IAED,sBAAsB,CAAC,MAAc,EAAE,GAAW,EAAE,GAAW;QAC7D,OAAO,GAAG,MAAM,IAAI,GAAG,OAAO,GAAG,EAAE,CAAA;IACrC,CAAC;IAED,8DAA8D;IAC9D,MAAM;QACJ,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,GAAG;YAClB,GAAG,IAAI,CAAC,OAAO;YACf,GAAG,IAAI,CAAC,IAAI;YACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO;SAC9B,CAAA;IACH,CAAC;;AA5FM,uBAAY,GAA0C;IAC3D,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA"}