jbrowse-plugin-mafviewer 1.0.6 → 1.0.8

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -0,0 +1,181 @@
+import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { featureSpanPx, renderToAbstractCanvas, } from '@jbrowse/core/util';
+import { getColorBaseMap, getContrastBaseMap } from './util';
+function makeImageData({ ctx, renderArgs, }) {
+    const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
+    const [region] = regions;
+    const h = rowHeight * rowProportion;
+    const theme = createJBrowseTheme(configTheme);
+    const colorForBase = getColorBaseMap(theme);
+    const contrastForBase = getContrastBaseMap(theme);
+    const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]));
+    const scale = 1 / bpPerPx;
+    const f = 0.4;
+    const h2 = rowHeight / 2;
+    const hp2 = h / 2;
+    const offset = (rowHeight - h) / 2;
+    // sample as alignments
+    ctx.font = 'bold 10px Courier New,monospace';
+    for (const feature of features.values()) {
+        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
+        const vals = feature.get('alignments');
+        const seq = feature.get('seq').toLowerCase();
+        for (const [sample, val] of Object.entries(vals)) {
+            const origAlignment = val.data;
+            const alignment = origAlignment.toLowerCase();
+            const row = sampleToRowMap.get(sample);
+            if (row === undefined) {
+                throw new Error(`unknown sample encountered: ${sample}`);
+            }
+            const t = rowHeight * row;
+            // gaps
+            ctx.beginPath();
+            ctx.fillStyle = 'black';
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                if (seq[i] !== '-') {
+                    if (alignment[i] === '-') {
+                        const l = leftPx + scale * o;
+                        ctx.moveTo(l, t + h2);
+                        ctx.lineTo(l + scale + f, t + h2);
+                    }
+                    o++;
+                }
+            }
+            ctx.stroke();
+            if (!showAllLetters) {
+                // matches
+                ctx.beginPath();
+                ctx.fillStyle = 'lightgrey';
+                for (let i = 0, o = 0; i < alignment.length; i++) {
+                    if (seq[i] !== '-') {
+                        const c = alignment[i];
+                        const l = leftPx + scale * o;
+                        if (seq[i] === c && c !== '-') {
+                            ctx.rect(l, offset + t, scale + f, h);
+                        }
+                        o++;
+                    }
+                }
+                ctx.fill();
+            }
+            // mismatches
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                const c = alignment[i];
+                if (seq[i] !== '-') {
+                    if (c !== '-') {
+                        const l = leftPx + scale * o;
+                        if (seq[i] !== c) {
+                            ctx.fillStyle = mismatchRendering
+                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    (colorForBase[c] ?? 'black')
+                                : 'orange';
+                            ctx.fillRect(l, offset + t, scale + f, h);
+                        }
+                        else if (showAllLetters) {
+                            ctx.fillStyle = mismatchRendering
+                                ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+                                    (colorForBase[c] ?? 'black')
+                                : 'lightblue';
+                            ctx.fillRect(l, offset + t, scale + f, h);
+                        }
+                    }
+                    o++;
+                }
+            }
+            // font
+            const charSizeW = 10;
+            if (scale >= charSizeW) {
+                for (let i = 0, o = 0; i < alignment.length; i++) {
+                    if (seq[i] !== '-') {
+                        const l = leftPx + scale * o;
+                        const offset = (scale - charSizeW) / 2 + 1;
+                        const c = alignment[i];
+                        if ((showAllLetters || seq[i] !== c) && c !== '-') {
+                            ctx.fillStyle = contrastForBase[c] ?? 'white';
+                            ctx.fillText(origAlignment[i], l + offset, hp2 + t + 3);
+                        }
+                        o++;
+                    }
+                }
+            }
+        }
+    }
+    // second pass for insertions, has slightly improved look since the
+    // insertions are always 'on top' of the other features
+    for (const feature of features.values()) {
+        const [leftPx] = featureSpanPx(feature, region, bpPerPx);
+        const vals = feature.get('alignments');
+        const seq = feature.get('seq').toLowerCase();
+        for (const [sample, val] of Object.entries(vals)) {
+            const origAlignment = val.data;
+            const alignment = origAlignment.toLowerCase();
+            const row = sampleToRowMap.get(sample);
+            if (row === undefined) {
+                throw new Error(`unknown sample encountered: ${sample}`);
+            }
+            const t = rowHeight * row;
+            ctx.beginPath();
+            ctx.fillStyle = 'purple';
+            for (let i = 0, o = 0; i < alignment.length; i++) {
+                let ins = '';
+                while (seq[i] === '-') {
+                    if (alignment[i] !== '-') {
+                        ins += alignment[i];
+                    }
+                    i++;
+                }
+                if (ins.length > 0) {
+                    const l = leftPx + scale * o - 1;
+                    ctx.rect(l, offset + t + 1, 1, h - 1);
+                    ctx.rect(l - 2, offset + t, 5, 1);
+                    ctx.rect(l - 2, offset + t + h - 1, 5, 1);
+                }
+                o++;
+            }
+            ctx.fill();
+        }
+    }
+}
+export default class LinearMafRenderer extends FeatureRendererType {
+    getExpandedRegion(region) {
+        const { start, end } = region;
+        const bpExpansion = 1;
+        return {
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...region,
+            start: Math.floor(Math.max(start - bpExpansion, 0)),
+            end: Math.ceil(end + bpExpansion),
+        };
+    }
+    async render(renderProps) {
+        const { regions, bpPerPx, samples, rowHeight } = renderProps;
+        const [region] = regions;
+        const height = samples.length * rowHeight + 100;
+        const width = (region.end - region.start) / bpPerPx;
+        const features = await this.getFeatures(renderProps);
+        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+            makeImageData({
+                ctx,
+                renderArgs: {
+                    ...renderProps,
+                    features,
+                },
+            });
+            return undefined;
+        });
+        const results = await super.render({
+            ...renderProps,
+            ...res,
+            width,
+            height,
+        });
+        return {
+            ...results,
+            ...res,
+            width,
+            height,
+        };
+    }
+}
+//# sourceMappingURL=LinearMafRenderer.js.map

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/components/ReactComponent.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+declare const LinearMafRendering: (props: {
+    width: number;
+    height: number;
+}) => React.JSX.Element;
+export default LinearMafRendering;

package/dist/LinearMafRenderer/components/ReactComponent.js

@@ -0,0 +1,8 @@
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import React from 'react';
+const LinearMafRendering = observer(function (props) {
+    return React.createElement(PrerenderedCanvas, { ...props });
+});
+export default LinearMafRendering;
+//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearMafRenderer/components/ReactComponent.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/dist/LinearMafRenderer/configSchema.js

@@ -0,0 +1,13 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config LinearMafRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('LinearMafRenderer', {}, {
+    /**
+     * #baseConfiguration
+     */
+    explicitlyTyped: true,
+});
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearMafRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB,EAAE,EACF;IACE;;OAEG;IACH,eAAe,EAAE,IAAI;CACtB,CACF,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/LinearMafRenderer/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function LinearMafRendererF(pluginManager: PluginManager): void;

package/dist/LinearMafRenderer/index.js

@@ -0,0 +1,12 @@
+import configSchema from './configSchema';
+import LinearMafRenderer from './LinearMafRenderer';
+import ReactComponent from './components/ReactComponent';
+export default function LinearMafRendererF(pluginManager) {
+    pluginManager.addRendererType(() => new LinearMafRenderer({
+        name: 'LinearMafRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/LinearMafRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,cAAc,MAAM,6BAA6B,CAAA;AAExD,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,mBAAmB;QACzB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/LinearMafRenderer/util.d.ts

@@ -0,0 +1,10 @@
+import { Theme } from '@mui/material';
+export declare function getContrastBaseMap(theme: Theme): {
+    [k: string]: string;
+};
+export declare function getColorBaseMap(theme: Theme): {
+    a: string;
+    c: string;
+    g: string;
+    t: string;
+};

package/dist/LinearMafRenderer/util.js

@@ -0,0 +1,16 @@
+export function getContrastBaseMap(theme) {
+    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
+        key,
+        theme.palette.getContrastText(value),
+    ]));
+}
+export function getColorBaseMap(theme) {
+    const { bases } = theme.palette;
+    return {
+        a: bases.A.main,
+        c: bases.C.main,
+        g: bases.G.main,
+        t: bases.T.main,
+    };
+}
+//# sourceMappingURL=util.js.map

package/dist/LinearMafRenderer/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,kBAAkB,CAAC,KAAY;IAC7C,OAAO,MAAM,CAAC,WAAW,CACvB,MAAM,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QAC3D,GAAG;QACH,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC;KACrC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAY;IAC1C,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;IAC/B,OAAO;QACL,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;KAChB,CAAA;AACH,CAAC"}

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.d.ts

@@ -0,0 +1,5 @@
+import React from 'react';
+import { AddTrackModel } from '@jbrowse/plugin-data-management';
+export default function MultiMAFWidget({ model }: {
+    model: AddTrackModel;
+}): React.JSX.Element;

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -0,0 +1,111 @@
+import React, { useState } from 'react';
+import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { getRoot } from 'mobx-state-tree';
+const useStyles = makeStyles()(theme => ({
+    textbox: {
+        width: '100%',
+    },
+    paper: {
+        margin: theme.spacing(),
+        padding: theme.spacing(),
+    },
+    submit: {
+        marginTop: 25,
+        marginBottom: 100,
+        display: 'block',
+    },
+}));
+export default function MultiMAFWidget({ model }) {
+    const { classes } = useStyles();
+    const [samples, setSamples] = useState('');
+    const [loc, setLoc] = useState();
+    const [indexLoc, setIndexLoc] = useState();
+    const [error, setError] = useState();
+    const [trackName, setTrackName] = useState('MAF track');
+    const [fileTypeChoice, setFileTypeChoice] = useState('BigMafAdapter');
+    const [indexTypeChoice, setIndexTypeChoice] = useState('TBI');
+    const rootModel = getRoot(model);
+    return (React.createElement(Paper, { className: classes.paper },
+        React.createElement(Paper, null,
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
+            React.createElement(FormControl, null,
+                React.createElement(FormLabel, null, "File type"),
+                React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                        setFileTypeChoice(event.target.value);
+                    } },
+                    React.createElement(FormControlLabel, { value: "BigMafAdapter", control: React.createElement(Radio, null), checked: fileTypeChoice === 'BigMafAdapter', label: "bigMaf" }),
+                    React.createElement(FormControlLabel, { value: "MafTabixAdapter", control: React.createElement(Radio, null), checked: fileTypeChoice === 'MafTabixAdapter', label: "mafTabix" }))),
+            fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
+                    setLoc(arg);
+                } })) : (React.createElement(React.Fragment, null,
+                React.createElement(FormControl, null,
+                    React.createElement(FormLabel, null, "Index type"),
+                    React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
+                            setIndexTypeChoice(event.target.value);
+                        } },
+                        React.createElement(FormControlLabel, { value: "TBI", control: React.createElement(Radio, null), checked: indexTypeChoice === 'TBI', label: "TBI" }),
+                        React.createElement(FormControlLabel, { value: "CSI", control: React.createElement(Radio, null), checked: indexTypeChoice === 'CSI', label: "CSI" }))),
+                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", setLocation: arg => {
+                        setLoc(arg);
+                    }, rootModel: rootModel }),
+                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", setLocation: arg => {
+                        setIndexLoc(arg);
+                    }, rootModel: rootModel })))),
+        React.createElement(TextField, { multiline: true, rows: 10, value: samples, onChange: event => {
+                setSamples(event.target.value);
+            }, placeholder: 'Enter sample names from the MAF file, one per line, or JSON formatted array of samples', variant: "outlined", fullWidth: true }),
+        React.createElement(TextField, { value: trackName, helperText: "Track name", onChange: event => {
+                setTrackName(event.target.value);
+            } }),
+        React.createElement(Button, { variant: "contained", className: classes.submit, onClick: () => {
+                try {
+                    const session = getSession(model);
+                    let sampleNames = [];
+                    try {
+                        sampleNames = JSON.parse(samples);
+                    }
+                    catch (e) {
+                        sampleNames = samples.split(/\n|\r\n|\r/);
+                    }
+                    const trackId = [
+                        `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join('');
+                    if (isSessionWithAddTracks(session)) {
+                        session.addTrackConf({
+                            trackId,
+                            type: 'MafTrack',
+                            name: trackName,
+                            assemblyNames: [model.assembly],
+                            adapter: fileTypeChoice === 'BigMafAdapter'
+                                ? {
+                                    type: fileTypeChoice,
+                                    bigBedLocation: loc,
+                                    samples: sampleNames,
+                                }
+                                : {
+                                    type: fileTypeChoice,
+                                    bedGzLocation: loc,
+                                    index: {
+                                        indexType: indexTypeChoice,
+                                        location: indexLoc,
+                                    },
+                                    samples: sampleNames,
+                                },
+                        });
+                        model.view?.showTrack(trackId);
+                    }
+                    model.clearData();
+                    if (isSessionModelWithWidgets(session)) {
+                        session.hideWidget(model);
+                    }
+                }
+                catch (e) {
+                    setError(e);
+                }
+            } }, "Submit")));
+}
+//# sourceMappingURL=AddTrackWorkflow.js.map

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -0,0 +1 @@
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package/dist/MafAddTrackWorkflow/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function MafAddTrackWorkflowF(pluginManager: PluginManager): void;

package/dist/MafAddTrackWorkflow/index.js

@@ -0,0 +1,12 @@
+import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
+import { types } from 'mobx-state-tree';
+// locals
+import MultiMAFWidget from './AddTrackWorkflow';
+export default function MafAddTrackWorkflowF(pluginManager) {
+    pluginManager.addAddTrackWorkflowType(() => new AddTrackWorkflowType({
+        name: 'MAF track',
+        ReactComponent: MultiMAFWidget,
+        stateModel: types.model({}),
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/MafAddTrackWorkflow/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafTabixAdapter/MafTabixAdapter.d.ts

@@ -0,0 +1,17 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+export default class MafTabixAdapter extends BaseFeatureDataAdapter {
+    setupP?: Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    setup(): Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    setupPre(): Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    getRefNames(): Promise<string[]>;
+    getHeader(): Promise<unknown>;
+    getFeatures(query: Region): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -0,0 +1,96 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { getSnapshot } from 'mobx-state-tree';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { firstValueFrom, toArray } from 'rxjs';
+export default class MafTabixAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    async setup() {
+        const config = this.config;
+        if (!this.getSubAdapter) {
+            throw new Error('no getSubAdapter available');
+        }
+        const adapter = await this.getSubAdapter({
+            ...getSnapshot(config),
+            type: 'BedTabixAdapter',
+        });
+        return {
+            adapter: adapter.dataAdapter,
+        };
+    }
+    async setupPre() {
+        if (!this.setupP) {
+            this.setupP = this.setup().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async getRefNames() {
+        const { adapter } = await this.setup();
+        return adapter.getRefNames();
+    }
+    async getHeader() {
+        const { adapter } = await this.setup();
+        return adapter.getHeader();
+    }
+    getFeatures(query) {
+        return ObservableCreate(async (observer) => {
+            const { adapter } = await this.setup();
+            const features = await firstValueFrom(adapter.getFeatures(query).pipe(toArray()));
+            const samples = this.getConf('samples');
+            const sampleStrings = typeof samples[0] === 'string'
+                ? samples
+                : samples.map(s => s.id);
+            const sampleSet = new Set(sampleStrings);
+            let i = 0;
+            for (const feature of features) {
+                const data = feature.get('field5').split(',');
+                const alignments = {};
+                const alns = data.map(elt => elt.split(':')[5]);
+                for (const [j, elt] of data.entries()) {
+                    const ad = elt.split(':');
+                    const idx = ad[0].lastIndexOf('.');
+                    const org = ad[0].slice(0, idx);
+                    const last = ad[0].slice(idx + 1);
+                    const s = sampleSet.has(org)
+                        ? org
+                        : sampleStrings.find(f => ad[0].startsWith(f));
+                    if (s) {
+                        alignments[s] = {
+                            chr: last,
+                            start: +ad[1],
+                            srcSize: +ad[2],
+                            strand: ad[3] === '-' ? -1 : 1,
+                            unknown: +ad[4],
+                            data: alns[j],
+                        };
+                    }
+                    else if (i < 100) {
+                        console.error(`line not processed ${ad[0]}`);
+                        i++;
+                    }
+                    else if (i > 100) {
+                        console.error('too many errors, not printing any more');
+                    }
+                }
+                observer.next(new SimpleFeature({
+                    id: feature.id(),
+                    data: {
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                        refName: feature.get('refName'),
+                        name: feature.get('name'),
+                        score: feature.get('score'),
+                        alignments,
+                        seq: alns[0],
+                    },
+                }));
+            }
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=MafTabixAdapter.js.map

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

@@ -0,0 +1 @@
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package/dist/MafTabixAdapter/configSchema.d.ts

@@ -0,0 +1,33 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    samples: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+    /**
+     * #slot
+     */
+    bedGzLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+            };
+        };
+        indexType: {
+            type: string;
+            defaultValue: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/dist/MafTabixAdapter/configSchema.js

@@ -0,0 +1,40 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config MafTabixAdapter
+ * used to configure MafTabix adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('MafTabixAdapter', {
+    /**
+     * #slot
+     */
+    samples: {
+        type: 'frozen',
+        description: 'string[] or {id:string,label:string,color?:string}[]',
+        defaultValue: [],
+    },
+    /**
+     * #slot
+     */
+    bedGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bed.gz.tbi',
+            locationType: 'UriLocation',
+        },
+    },
+    index: ConfigurationSchema('Index', {
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.bed.gz.tbi',
+            },
+        },
+        indexType: {
+            type: 'string',
+            defaultValue: 'TBI',
+        },
+    }),
+}, { explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map