@jbrowse/plugin-alignments 2.16.0 → 2.17.0

package/esm/util.d.ts

@@ -2,7 +2,6 @@ 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;
 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(): string;
+export declare function randomColor(str: string): string;
+export declare function getColorForModification(str: string): string;
 export {};

package/esm/util.js

@@ -2,17 +2,12 @@ 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
 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
@@ -73,8 +68,6 @@ 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;
@@ -82,27 +75,27 @@ 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)',
+// https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/resources/org/broad/igv/prefs/preferences.tab#L230-L242
+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 () => {
@@ -116,6 +109,14 @@ export function createAutorun(self, cb, opts) {
         }
     }, opts));
 }
-export function randomColor() {
-    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+export function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
+    }
+    return `hsl(${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": "2.16.0",
+  "version": "2.17.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bam": "^2.0.0",
+    "@gmod/bam": "^4.0.1",
     "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.16.0",
+    "@jbrowse/sv-core": "^2.17.0",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
 }

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/SNPCoverageAdapter/util.d.ts

@@ -1,25 +0,0 @@
-export type SkipMap = Record<string, {
-    score: number;
-    feature: unknown;
-    start: number;
-    end: number;
-    strand: number;
-    xs: string;
-}>;
-export interface BinType {
-    total?: number;
-    strands?: Record<string, number>;
-}
-export interface Bin {
-    refbase?: string;
-    total: number;
-    all: number;
-    ref: number;
-    '-1': number;
-    '0': number;
-    '1': number;
-    lowqual: BinType;
-    cov: BinType;
-    delskips: BinType;
-    noncov: BinType;
-}

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 {};

package/dist/shared/index.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.FilterModel = void 0;
-exports.getUniqueTagValues = getUniqueTagValues;
-exports.getUniqueModificationValues = getUniqueModificationValues;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-async function getUniqueTagValues({ self, tag, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const { adapterConfig } = self;
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const values = await rpcManager.call((0, tracks_1.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', {
-        adapterConfig,
-        tag,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-async function getUniqueModificationValues({ self, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
-        adapterConfig,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}
-exports.FilterModel = mobx_state_tree_1.types.model({
-    flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-    flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-    readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
-        tag: mobx_state_tree_1.types.string,
-        value: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-    })),
-});

package/esm/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/esm/LinearPileupDisplay/components/ColorByModificationsDialog.js

@@ -1,36 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { Button, CircularProgress, DialogActions, DialogContent, Typography, } from '@mui/material';
-import { Dialog } from '@jbrowse/core/ui';
-import ModificationTable from './ModificationsTable';
-const ColorByModificationsDialog = observer(function ({ model, handleClose, }) {
-    const { colorBy, modificationTagMap } = model;
-    const modifications = [...modificationTagMap.entries()];
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Color by modifications" },
-        React.createElement(DialogContent, null,
-            React.createElement(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.createElement(Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),
-            React.createElement("div", { style: { margin: 20 } },
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (React.createElement("div", null, modifications.length ? (React.createElement(React.Fragment, null,
-                    "Current modification-type-to-color mapping",
-                    React.createElement(ModificationTable, { modifications: [...modificationTagMap.entries()] }))) : (React.createElement(React.Fragment, null,
-                    React.createElement(Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
-                    React.createElement(CircularProgress, { size: 15 }))))) : null,
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (React.createElement(ModificationTable, { modifications: [
-                        ['methylated', 'red'],
-                        ['unmethylated', 'blue'],
-                    ] })) : null),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'modifications' });
-                        handleClose();
-                    } }, "Modifications"),
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        model.setColorScheme({ type: 'methylation' });
-                        handleClose();
-                    } }, "Methylation"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
-});
-export default ColorByModificationsDialog;

package/esm/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/esm/LinearPileupDisplay/components/ModificationsTable.js

@@ -1,22 +0,0 @@
-import React from 'react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    table: {
-        border: '1px solid #888',
-        margin: theme.spacing(4),
-        '& td': {
-            padding: theme.spacing(1),
-        },
-    },
-}));
-export default function ModificationTable({ modifications, }) {
-    const { classes } = useStyles();
-    return (React.createElement("table", { className: classes.table },
-        React.createElement("tbody", null, modifications.map(([key, value]) => (React.createElement("tr", { key: key },
-            React.createElement("td", null, key),
-            React.createElement("td", null, value),
-            React.createElement("td", { style: {
-                    width: '1em',
-                    background: value,
-                } })))))));
-}

package/esm/SNPCoverageAdapter/util.d.ts

@@ -1,25 +0,0 @@
-export type SkipMap = Record<string, {
-    score: number;
-    feature: unknown;
-    start: number;
-    end: number;
-    strand: number;
-    xs: string;
-}>;
-export interface BinType {
-    total?: number;
-    strands?: Record<string, number>;
-}
-export interface Bin {
-    refbase?: string;
-    total: number;
-    all: number;
-    ref: number;
-    '-1': number;
-    '0': number;
-    '1': number;
-    lowqual: BinType;
-    cov: BinType;
-    delskips: BinType;
-    noncov: BinType;
-}

package/esm/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 {};

package/esm/shared/index.js

@@ -1,36 +0,0 @@
-import { types } from 'mobx-state-tree';
-import { getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-export async function getUniqueTagValues({ 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;
-}
-export async function getUniqueModificationValues({ 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;
-}
-export const FilterModel = types.model({
-    flagInclude: types.optional(types.number, 0),
-    flagExclude: types.optional(types.number, 1540),
-    readName: types.maybe(types.string),
-    tagFilter: types.maybe(types.model({
-        tag: types.string,
-        value: types.maybe(types.string),
-    })),
-});