@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/{esm/shared → dist/shared/components}/FilterByTagDialog.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
-import { IFilter } from '.';
+import type { FilterBy } from '../types';
 declare const FilterByTagDialog: (props: {
     model: {
-        filterBy: IFilter;
-        setFilterBy: (arg: IFilter) => void;
+        filterBy: FilterBy;
+        setFilterBy: (arg: FilterBy) => void;
     };
     handleClose: () => void;
 }) => React.JSX.Element;

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

@@ -24,9 +24,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     paper: {
@@ -103,7 +103,11 @@ const FilterByTagDialog = (0, mobx_react_1.observer)(function (props) {
                 react_1.default.createElement(material_1.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_1.default.createElement(material_1.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_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => {
                         setTagValue(event.target.value);
                     }, placeholder: "Enter tag value" })),

package/dist/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/dist/shared/fetchChains.js

@@ -2,20 +2,18 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
-const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
-    // @ts-expect-error
     const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
     const { rpcManager } = (0, util_1.getSession)(self);
     const view = (0, util_1.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: (0, mobx_state_tree_1.getSnapshot)(self.filterBy),
+        filterBy: self.filterBy,
         adapterConfig: self.adapterConfig,
     }));
     self.setChainData(ret);

package/dist/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/dist/shared/getMaximumModificationAtEachPosition.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMaxProbModAtEachPosition = getMaxProbModAtEachPosition;
+const MismatchParser_1 = require("../MismatchParser");
+const ModificationParser_1 = require("../ModificationParser");
+const util_1 = require("../util");
+function getMaxProbModAtEachPosition(feature, cigarOps) {
+    const fstrand = feature.get('strand');
+    const seq = feature.get('seq');
+    const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+    const ops = cigarOps || (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+    if (seq) {
+        const modifications = (0, ModificationParser_1.getModPositions)(mm, seq, fstrand);
+        const probabilities = (0, ModificationParser_1.getModProbabilities)(feature);
+        const maxProbModForPosition = [];
+        let probIndex = 0;
+        for (const { type, positions } of modifications) {
+            for (const { ref, idx } of (0, MismatchParser_1.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/dist/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/dist/shared/getUniqueModifications.js

@@ -0,0 +1,16 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getUniqueModifications = getUniqueModifications;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+async function getUniqueModifications({ 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;
+}

package/dist/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/dist/shared/getUniqueTags.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getUniqueTags = getUniqueTags;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+async function getUniqueTags({ 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;
+}

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

@@ -29,7 +29,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
-// stabilize clipid under test for snapshot
 function getId(id) {
     const isJest = typeof jest === 'undefined';
     return `arc-clip-${isJest ? id : 'jest'}`;
@@ -51,7 +50,6 @@ async function renderSvg(self, opts, cb) {
         return (react_1.default.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
     }
     else {
-        // @ts-ignore
         const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
         const ctx = new C2S.default(width, height);
         cb(self, ctx, width, height);

package/dist/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/dist/shared/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });

package/dist/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/dist/shared/util.js

@@ -1,6 +1,12 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.posFlags = exports.negFlags = exports.defaultFilterFlags = void 0;
 exports.hasPairedReads = hasPairedReads;
+exports.alphaColor = alphaColor;
+exports.cacheGetter = cacheGetter;
+exports.filterReadFlag = filterReadFlag;
+exports.filterTagValue = filterTagValue;
+const colord_1 = require("@jbrowse/core/util/colord");
 function hasPairedReads(features) {
     for (const f of features.chains.values()) {
         if (f[0].flags & 1) {
@@ -9,3 +15,49 @@ function hasPairedReads(features) {
     }
     return false;
 }
+function alphaColor(baseColor, p) {
+    return p !== 1
+        ? (0, colord_1.colord)(baseColor)
+            .alpha(p * p)
+            .toHslString()
+        : baseColor;
+}
+exports.defaultFilterFlags = {
+    flagInclude: 0,
+    flagExclude: 1540,
+};
+exports.negFlags = {
+    flagInclude: 16,
+    flagExclude: 1540,
+};
+exports.posFlags = {
+    flagInclude: 0,
+    flagExclude: 1556,
+};
+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;
+        },
+    });
+}
+function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    else if (flags & flagExclude) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}

package/dist/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/dist/util.js

@@ -1,31 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationColors = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTag = getTag;
+exports.modificationData = exports.pairMap = exports.orientationTypes = void 0;
 exports.getTagAlt = getTagAlt;
 exports.getColorWGBS = getColorWGBS;
 exports.fetchSequence = fetchSequence;
-exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
 exports.createAutorun = createAutorun;
 exports.randomColor = randomColor;
-const operators_1 = require("rxjs/operators");
-const rxjs_1 = require("rxjs");
-const mobx_state_tree_1 = require("mobx-state-tree");
+exports.getColorForModification = getColorForModification;
 const mobx_1 = require("mobx");
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
-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
+const mobx_state_tree_1 = require("mobx-state-tree");
+const rxjs_1 = require("rxjs");
+const operators_1 = require("rxjs/operators");
 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
 exports.orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -83,8 +73,6 @@ function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -92,28 +80,25 @@ async function fetchSequence(region, adapter) {
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
-        end: end + 1,
-        start: Math.max(0, start - 1),
+        end,
+        start,
     })
         .pipe((0, operators_1.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
-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
-exports.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%)',
+exports.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' },
 };
 function createAutorun(self, cb, opts) {
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
@@ -134,3 +119,7 @@ function randomColor(str) {
     }
     return `hsl(${sum * 10}, 20%, 50%)`;
 }
+function getColorForModification(str) {
+    var _a;
+    return ((_a = exports.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
+}

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 declare const AlignmentsFeatureDetails: (props: {
     model: AlignmentFeatureWidgetModel;
 }) => React.JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,29 +1,22 @@
 import React, { lazy } from 'react';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import clone from 'clone';
-import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
-// locals
-import { getTag } from './util';
-import { tags } from './tagInfo';
-// local components
 import Flags from './Flags';
-import PairLink from './PairLink';
 import Formatter from './Formatter';
-// lazies
+import PairLink from './PairLink';
+import { tags } from './tagInfo';
+import { getTag } from './util';
 const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'));
 const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'));
-const omit = ['clipPos', 'flags'];
 const AlignmentsFeatureDetails = observer(function (props) {
     const { model } = props;
     const { featureData } = model;
-    const feat = clone(featureData);
+    const feat = structuredClone(featureData);
     const SA = getTag('SA', feat);
     const { flags } = feat;
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
-        React.createElement(FeatureDetails, { ...props, omit: omit, 
-            // @ts-expect-error
-            descriptions: { ...tags, tags: tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
+        React.createElement(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
         SA !== undefined ? (React.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
         flags & 1 ? (React.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
         flags !== undefined ? React.createElement(Flags, { feature: feat, ...props }) : null));

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1,2 +1 @@
-// re-exported for react lazy
 export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1,2 +1 @@
-// re-exported for react lazy
 export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -1,8 +1,8 @@
 import React from 'react';
-import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
+import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,

package/esm/AlignmentsFeatureDetail/Formatter.js

@@ -1,8 +1,5 @@
 import React, { useState } from 'react';
 import copy from 'copy-to-clipboard';
-// this 'show more...' used specifically as a formatter on alignments feature
-// details because long SEQ or CRAM files, even a single div full of a ton of
-// data from a long read, can slow down the rest of the app
 export default function Formatter({ value }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
 }): React.JSX.Element;

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,10 +1,9 @@
 import React, { lazy } from 'react';
-import { Typography, Link } from '@mui/material';
-import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
-// lazies
+import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { Link, Typography } from '@mui/material';
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }) {
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = getSession(model);
     const f1 = {
         uniqueId: feature.uniqueId,
@@ -38,10 +37,8 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
                             BreakendMultiLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },
@@ -54,10 +51,8 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
                             BreakendSingleLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },