@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/esm/shared/{FilterByTagDialog.js → components/FilterByTagDialog.js}

@@ -1,7 +1,7 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, Link, Paper, TextField, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Link, Paper, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     paper: {
@@ -78,7 +78,11 @@ const FilterByTagDialog = observer(function (props) {
                 React.createElement(Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),
                 React.createElement(TextField, { className: classes.field, value: tag, onChange: event => {
                         setTag(event.target.value);
-                    }, placeholder: "Enter tag name", inputProps: { maxLength: 2 }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', slotProps: {
+                        htmlInput: {
+                            maxLength: 2,
+                        },
+                    } }),
                 React.createElement(TextField, { className: classes.field, value: tagValue, onChange: event => {
                         setTagValue(event.target.value);
                     }, placeholder: "Enter tag value" })),

package/esm/shared/fetchChains.d.ts

@@ -1,5 +1,5 @@
-import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
-import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
+import type { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+import type { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
 export interface ReducedFeature {
     name: string;
     strand: number;

package/esm/shared/fetchChains.js

@@ -1,18 +1,16 @@
 import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
-import { getSnapshot } from 'mobx-state-tree';
 export async function fetchChains(self) {
-    // @ts-expect-error
     const { rpcSessionId: sessionId } = getContainingTrack(self);
     const { rpcManager } = getSession(self);
     const view = getContainingView(self);
-    if (!view.initialized || self.error || self.regionTooLarge) {
+    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
         return;
     }
     self.setLoading(true);
     const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
         sessionId,
         regions: view.staticBlocks.contentBlocks,
-        filterBy: getSnapshot(self.filterBy),
+        filterBy: self.filterBy,
         adapterConfig: self.adapterConfig,
     }));
     self.setChainData(ret);

package/esm/shared/getMaximumModificationAtEachPosition.d.ts

@@ -0,0 +1,8 @@
+import type { Feature } from '@jbrowse/core/util';
+interface MaximumProbabilityMod {
+    type: string;
+    prob: number;
+    allProbs: number[];
+}
+export declare function getMaxProbModAtEachPosition(feature: Feature, cigarOps?: string[]): MaximumProbabilityMod[] | undefined;
+export {};

package/esm/shared/getMaximumModificationAtEachPosition.js

@@ -0,0 +1,38 @@
+import { getNextRefPos, parseCigar } from '../MismatchParser';
+import { getModPositions, getModProbabilities } from '../ModificationParser';
+import { getTagAlt } from '../util';
+export function getMaxProbModAtEachPosition(feature, cigarOps) {
+    const fstrand = feature.get('strand');
+    const seq = feature.get('seq');
+    const mm = getTagAlt(feature, 'MM', 'Mm') || '';
+    const ops = cigarOps || parseCigar(feature.get('CIGAR'));
+    if (seq) {
+        const modifications = getModPositions(mm, seq, fstrand);
+        const probabilities = getModProbabilities(feature);
+        const maxProbModForPosition = [];
+        let probIndex = 0;
+        for (const { type, positions } of modifications) {
+            for (const { ref, idx } of getNextRefPos(ops, positions)) {
+                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx)]) || 0;
+                if (!maxProbModForPosition[ref]) {
+                    maxProbModForPosition[ref] = {
+                        type,
+                        prob,
+                        allProbs: [prob],
+                    };
+                }
+                else {
+                    const old = maxProbModForPosition[ref];
+                    maxProbModForPosition[ref] = {
+                        allProbs: [...old.allProbs, prob],
+                        prob: Math.max(old.prob, prob),
+                        type: old.prob > prob ? old.type : type,
+                    };
+                }
+            }
+            probIndex += positions.length;
+        }
+        return maxProbModForPosition;
+    }
+    return undefined;
+}

package/esm/shared/getUniqueModifications.d.ts

@@ -0,0 +1,14 @@
+import type { ModificationType } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BlockSet } from '@jbrowse/core/util/blockTypes';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function getUniqueModifications({ self, adapterConfig, blocks, opts, }: {
+    self: IAnyStateTreeNode;
+    adapterConfig: AnyConfigurationModel;
+    blocks: BlockSet;
+    opts?: {
+        headers?: Record<string, string>;
+        stopToken?: string;
+        filters: string[];
+    };
+}): Promise<ModificationType[]>;

package/esm/shared/getUniqueModifications.js

@@ -0,0 +1,13 @@
+import { getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+export async function getUniqueModifications({ self, adapterConfig, blocks, opts, }) {
+    const { rpcManager } = getSession(self);
+    const sessionId = getRpcSessionId(self);
+    const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
+        adapterConfig,
+        sessionId,
+        regions: blocks.contentBlocks,
+        ...opts,
+    });
+    return values;
+}

package/esm/shared/getUniqueTags.d.ts

@@ -0,0 +1,15 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BlockSet } from '@jbrowse/core/util/blockTypes';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function getUniqueTags({ self, tag, blocks, opts, }: {
+    self: IAnyStateTreeNode & {
+        adapterConfig: AnyConfigurationModel;
+    };
+    tag: string;
+    blocks: BlockSet;
+    opts?: {
+        headers?: Record<string, string>;
+        stopToken?: string;
+        filters: string[];
+    };
+}): Promise<string[]>;

package/esm/shared/getUniqueTags.js

@@ -0,0 +1,15 @@
+import { getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+export async function getUniqueTags({ self, tag, blocks, opts, }) {
+    const { rpcManager } = getSession(self);
+    const { adapterConfig } = self;
+    const sessionId = getRpcSessionId(self);
+    const values = await rpcManager.call(getRpcSessionId(self), 'PileupGetGlobalValueForTag', {
+        adapterConfig,
+        tag,
+        sessionId,
+        regions: blocks.contentBlocks,
+        ...opts,
+    });
+    return values;
+}

package/esm/shared/{renderSvg.js → renderSvgUtil.js}

@@ -1,6 +1,5 @@
 import React from 'react';
 import { getContainingView } from '@jbrowse/core/util';
-// stabilize clipid under test for snapshot
 function getId(id) {
     const isJest = typeof jest === 'undefined';
     return `arc-clip-${isJest ? id : 'jest'}`;
@@ -22,7 +21,6 @@ export async function renderSvg(self, opts, cb) {
         return (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
     }
     else {
-        // @ts-ignore
         const C2S = await import('canvas2svg');
         const ctx = new C2S.default(width, height);
         cb(self, ctx, width, height);

package/esm/shared/types.d.ts

@@ -0,0 +1,94 @@
+export type SkipMap = Record<string, {
+    score: number;
+    feature: unknown;
+    start: number;
+    end: number;
+    strand: number;
+    effectiveStrand: number;
+}>;
+export interface BinEntry {
+    entryDepth: number;
+    '-1': number;
+    '0': number;
+    '1': number;
+    avgProbability?: number;
+}
+type BinType = Record<string, BinEntry>;
+export interface BaseCoverageBin {
+    refbase?: string;
+    depth: number;
+    readsCounted: number;
+    ref: BinEntry;
+    snps: BinType;
+    mods: BinType;
+    nonmods: BinType;
+    delskips: BinType;
+    noncov: BinType;
+}
+export interface PreBinEntry {
+    entryDepth: number;
+    '-1': number;
+    '0': number;
+    '1': number;
+    probabilities: number[];
+}
+type PreBinType = Record<string, PreBinEntry>;
+export interface PreBaseCoverageBin extends PreBaseCoverageBinSubtypes {
+    refbase?: string;
+    depth: number;
+    readsCounted: number;
+    ref: PreBinEntry;
+}
+export interface PreBaseCoverageBinSubtypes {
+    snps: PreBinType;
+    mods: PreBinType;
+    nonmods: PreBinType;
+    delskips: PreBinType;
+    noncov: PreBinType;
+}
+export interface ModificationType {
+    type: string;
+    base: string;
+    strand: string;
+}
+export interface ModificationTypeWithColor {
+    color: string;
+    type: string;
+    base: string;
+    strand: string;
+}
+export interface ColorBy {
+    type: string;
+    tag?: string;
+    modifications?: {
+        twoColor?: boolean;
+        isolatedModification?: string;
+    };
+}
+export interface FilterBy {
+    flagExclude: number;
+    flagInclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value?: string;
+    };
+}
+export interface SortedBy {
+    type: string;
+    pos: number;
+    refName: string;
+    assemblyName: string;
+    tag?: string;
+}
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export {};

package/esm/shared/types.js

@@ -0,0 +1 @@
+export {};

package/esm/shared/util.d.ts

@@ -1,2 +1,20 @@
-import { ChainData } from './fetchChains';
+import type { ChainData } from './fetchChains';
 export declare function hasPairedReads(features: ChainData): boolean;
+export declare function alphaColor(baseColor: string, p: number): string;
+export declare const defaultFilterFlags: {
+    flagInclude: number;
+    flagExclude: number;
+};
+export declare const negFlags: {
+    flagInclude: number;
+    flagExclude: number;
+};
+export declare const posFlags: {
+    flagInclude: number;
+    flagExclude: number;
+};
+export declare function cacheGetter<T>(ctor: {
+    prototype: T;
+}, prop: keyof T): void;
+export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
+export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;

package/esm/shared/util.js

@@ -1,3 +1,4 @@
+import { colord } from '@jbrowse/core/util/colord';
 export function hasPairedReads(features) {
     for (const f of features.chains.values()) {
         if (f[0].flags & 1) {
@@ -6,3 +7,49 @@ export function hasPairedReads(features) {
     }
     return false;
 }
+export function alphaColor(baseColor, p) {
+    return p !== 1
+        ? colord(baseColor)
+            .alpha(p * p)
+            .toHslString()
+        : baseColor;
+}
+export const defaultFilterFlags = {
+    flagInclude: 0,
+    flagExclude: 1540,
+};
+export const negFlags = {
+    flagInclude: 16,
+    flagExclude: 1540,
+};
+export const posFlags = {
+    flagInclude: 0,
+    flagExclude: 1556,
+};
+export function cacheGetter(ctor, prop) {
+    const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
+    const getter = desc.get;
+    Object.defineProperty(ctor.prototype, prop, {
+        get() {
+            const ret = getter.call(this);
+            Object.defineProperty(this, prop, { value: ret });
+            return ret;
+        },
+    });
+}
+export function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    else if (flags & flagExclude) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+export function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}

package/esm/util.d.ts

@@ -1,8 +1,7 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, AugmentedRegion } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { IAutorunOptions } from 'mobx';
-export declare function getTag(feature: Feature, tag: string): any;
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
+import type { IAutorunOptions } from 'mobx';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {
     fr: Record<string, string>;
@@ -17,11 +16,15 @@ export declare const pairMap: {
 };
 export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
-export declare const modificationColors: Record<string, string>;
+interface ModificationData {
+    color: string;
+    name: string;
+}
+export declare const modificationData: Record<string, ModificationData>;
 type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
 export declare function randomColor(str: string): string;
+export declare function getColorForModification(str: string): string;
 export {};

package/esm/util.js

@@ -1,21 +1,12 @@
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
-export function getTag(feature, tag) {
-    const tags = feature.get('tags');
-    return tags !== undefined ? tags[tag] : feature.get(tag);
-}
-// use fallback alt tag, used in situations where upper case/lower case tags
-// exist e.g. Mm/MM for base modifications
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export function getTagAlt(feature, tag, alt) {
     var _a;
-    return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
+    const tags = feature.get('tags');
+    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
 }
-// orientation definitions from igv.js, see also
-// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 export const orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -73,8 +64,6 @@ export function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 export async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -82,28 +71,25 @@ export async function fetchSequence(region, adapter) {
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
+        end,
+        start,
     })
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// has to check underlying C-G (aka CpG) on the reference sequence
-export function shouldFetchReferenceSequence(type) {
-    return type === 'methylation';
-}
-// adapted from IGV
-// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
-export const modificationColors = {
-    m: 'rgb(255,0,0)',
-    h: 'rgb(11, 132, 165)',
-    o: 'rgb(111, 78, 129)',
-    f: 'rgb(246, 200, 95)',
-    c: 'rgb(157, 216, 102)',
-    g: 'rgb(255, 160, 86)',
-    e: 'rgb(141, 221, 208)',
-    b: 'rgb(202, 71, 47)',
-    a: 'hsl(136, 50%, 50%)',
+export const modificationData = {
+    m: { color: 'rgb(255,0,0)', name: '5mC' },
+    h: { color: 'rgb(255,0,255)', name: '5hmC' },
+    o: { color: 'rgb(111, 78, 129)', name: '8oxoG' },
+    f: { color: 'rgb(246, 200, 95)', name: '5fC' },
+    c: { color: 'rgb(157, 216, 102)', name: '5cac' },
+    g: { color: 'rgb(255, 160, 86)', name: '5hmu' },
+    e: { color: 'rgb(141, 221, 208)', name: '5fU' },
+    b: { color: 'rgb(0,100,47)', name: '5caU' },
+    a: { color: 'rgb(51,0,111)', name: '6mA' },
+    17082: { color: 'rgb(51,153,255)', name: 'pseU' },
+    17596: { color: 'rgb(102,153,0)', name: 'inosine' },
+    21839: { color: 'rgb(153,0,153)', name: '4mC' },
 };
 export function createAutorun(self, cb, opts) {
     addDisposer(self, autorun(async () => {
@@ -124,3 +110,7 @@ export function randomColor(str) {
     }
     return `hsl(${sum * 10}, 20%, 50%)`;
 }
+export function getColorForModification(str) {
+    var _a;
+    return ((_a = modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,12 +36,11 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bam": "^2.0.0",
+    "@gmod/bam": "^4.0.1",
     "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.16.1",
+    "@jbrowse/sv-core": "^2.18.0",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
-    "clone": "^2.1.2",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
     "generic-filehandle": "^3.0.0"
@@ -64,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }

package/dist/LinearPileupDisplay/components/ColorByModificationsDialog.d.ts

@@ -1,15 +0,0 @@
-import React from 'react';
-import { ObservableMap } from 'mobx';
-declare const ColorByModificationsDialog: ({ model, handleClose, }: {
-    model: {
-        setColorScheme: (arg: {
-            type: string;
-        }) => void;
-        modificationTagMap: ObservableMap<string, string>;
-        colorBy?: {
-            type: string;
-        };
-    };
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default ColorByModificationsDialog;

package/dist/LinearPileupDisplay/components/ColorByModificationsDialog.js

@@ -1,41 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-const ui_1 = require("@jbrowse/core/ui");
-const ModificationsTable_1 = __importDefault(require("./ModificationsTable"));
-const ColorByModificationsDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
-    const { colorBy, modificationTagMap } = model;
-    const modifications = [...modificationTagMap.entries()];
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),
-            react_1.default.createElement(material_1.Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
-            react_1.default.createElement("div", { style: { margin: 20 } },
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (react_1.default.createElement("div", null, modifications.length ? (react_1.default.createElement(react_1.default.Fragment, null,
-                    "Current modification-type-to-color mapping",
-                    react_1.default.createElement(ModificationsTable_1.default, { modifications: [...modificationTagMap.entries()] }))) : (react_1.default.createElement(react_1.default.Fragment, null,
-                    react_1.default.createElement(material_1.Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
-                    react_1.default.createElement(material_1.CircularProgress, { size: 15 }))))) : null,
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (react_1.default.createElement(ModificationsTable_1.default, { modifications: [
-                        ['methylated', 'red'],
-                        ['unmethylated', 'blue'],
-                    ] })) : null),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'modifications' });
-                        handleClose();
-                    } }, "Modifications"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'methylation' });
-                        handleClose();
-                    } }, "Methylation"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
-});
-exports.default = ColorByModificationsDialog;

package/dist/LinearPileupDisplay/components/ModificationsTable.d.ts

@@ -1,4 +0,0 @@
-import React from 'react';
-export default function ModificationTable({ modifications, }: {
-    modifications: [string, string | undefined][];
-}): React.JSX.Element;

package/dist/LinearPileupDisplay/components/ModificationsTable.js

@@ -1,28 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ModificationTable;
-const react_1 = __importDefault(require("react"));
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    table: {
-        border: '1px solid #888',
-        margin: theme.spacing(4),
-        '& td': {
-            padding: theme.spacing(1),
-        },
-    },
-}));
-function ModificationTable({ modifications, }) {
-    const { classes } = useStyles();
-    return (react_1.default.createElement("table", { className: classes.table },
-        react_1.default.createElement("tbody", null, modifications.map(([key, value]) => (react_1.default.createElement("tr", { key: key },
-            react_1.default.createElement("td", null, key),
-            react_1.default.createElement("td", null, value),
-            react_1.default.createElement("td", { style: {
-                    width: '1em',
-                    background: value,
-                } })))))));
-}

package/dist/shared/index.d.ts

@@ -1,49 +0,0 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export declare function getUniqueTagValues({ self, tag, blocks, opts, }: {
-    self: IAnyStateTreeNode & {
-        adapterConfig: AnyConfigurationModel;
-    };
-    tag: string;
-    blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        signal?: AbortSignal;
-        filters: string[];
-    };
-}): Promise<string[]>;
-type Track = IAnyStateTreeNode & {
-    configuration: AnyConfigurationModel;
-};
-export declare function getUniqueModificationValues({ self, adapterConfig, blocks, opts, }: {
-    self: IAnyStateTreeNode & {
-        parentTrack: Track;
-    };
-    adapterConfig: AnyConfigurationModel;
-    blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        signal?: AbortSignal;
-        filters: string[];
-    };
-}): Promise<string[]>;
-export declare const FilterModel: import("mobx-state-tree").IModelType<{
-    flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        tag: import("mobx-state-tree").ISimpleType<string>;
-        value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export interface IFilter {
-    flagExclude: number;
-    flagInclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value?: string;
-    };
-}
-export {};