@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,13 +1,11 @@
-import { createJBrowseTheme } from '@jbrowse/core/ui';
-import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util';
 import { readConfObject } from '@jbrowse/core/configuration';
-import { getOrigin, getScale, WiggleBaseRenderer, YSCALEBAR_LABEL_OFFSET, } from '@jbrowse/plugin-wiggle';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { bpSpanPx, featureSpanPx } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { WiggleBaseRenderer, YSCALEBAR_LABEL_OFFSET, getOrigin, getScale, } from '@jbrowse/plugin-wiggle';
 import { alphaColor } from '../shared/util';
-// width/height of the triangle above e.g. insertion indicators
 const INTERBASE_INDICATOR_WIDTH = 7;
 const INTERBASE_INDICATOR_HEIGHT = 4.5;
-// minimum read depth to draw the insertion indicators, below this the
-// 'statistical significance' is low
 const MINIMUM_INTERBASE_INDICATOR_READ_DEPTH = 7;
 const complementBase = {
     C: 'G',
@@ -17,22 +15,16 @@ const complementBase = {
 };
 const fudgeFactor = 0.6;
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
-    // note: the snps are drawn on linear scale even if the data is drawn in log
-    // scape hence the two different scales being used
     async draw(ctx, props) {
         var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
-        const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, } = props;
+        const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
         const theme = createJBrowseTheme(configTheme);
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
-        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-        // wiggle display, and makes the height of the actual drawn area add
-        // "padding" to the top and bottom of the display
         const offset = YSCALEBAR_LABEL_OFFSET;
         const height = unadjustedHeight - offset * 2;
         const opts = { ...scaleOpts, range: [0, height] };
         const viewScale = getScale(opts);
-        // clipping and insertion indicators, uses a smaller height/2 scale
         const indicatorViewScale = getScale({
             ...opts,
             range: [0, height / 2],
@@ -44,10 +36,8 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts');
         const drawArcs = readConfObject(cfg, 'drawArcs');
         const drawIndicators = readConfObject(cfg, 'drawIndicators');
-        // get the y coordinate that we are plotting at, this can be log scale
         const toY = (n) => height - (viewScale(n) || 0) + offset;
         const toHeight = (n) => toY(originY) - toY(n);
-        // used specifically for indicator
         const toY2 = (n) => height - (indicatorViewScale(n) || 0) + offset;
         const toHeight2 = (n) => toY2(originLinear) - toY2(n);
         const { bases } = theme.palette;
@@ -65,9 +55,8 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             cpg_unmeth: 'blue',
         };
         const feats = [...features.values()];
-        // Use two pass rendering, which helps in visualizing the SNPs at higher
-        // bpPerPx First pass: draw the gray background
         ctx.fillStyle = colorForBase.total;
+        let start = performance.now();
         for (const feature of feats) {
             if (feature.get('type') === 'skip') {
                 continue;
@@ -76,29 +65,22 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');
             ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+            if (performance.now() - start > 400) {
+                checkStopToken(stopToken);
+                start = performance.now();
+            }
         }
-        // Keep track of previous total which we will use it to draw the interbase
-        // indicator (if there is a sudden clip, there will be no read coverage but
-        // there will be "clip" coverage) at that position beyond the read.
-        //
-        // if the clip is right at a block boundary then prevTotal will not be
-        // available, so this is a best attempt to plot interbase indicator at the
-        // "cliffs"
         let prevTotal = 0;
-        // extraHorizontallyFlippedOffset is used to draw interbase items, which
-        // are located to the left when forward and right when reversed
         const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0;
-        // @ts-expect-error
         const drawingModifications = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications';
-        // @ts-expect-error
         const drawingMethylation = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation';
-        const isolatedModification = 
-        // @ts-expect-error
-        (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-        // Second pass: draw the SNP data, and add a minimum feature width of 1px
-        // which can be wider than the actual bpPerPx This reduces overdrawing of
-        // the grey background over the SNPs
+        const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
+        start = performance.now();
         for (const feature of feats) {
+            const now = performance.now();
+            if (now - start > 400) {
+                checkStopToken(stopToken);
+            }
             if (feature.get('type') === 'skip') {
                 continue;
             }
@@ -121,8 +103,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                         continue;
                     }
                     const cmp = complementBase[mod.base];
-                    // this approach is inspired from the 'simplex' approach in igv
-                    // https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/java/org/broad/igv/sam/mods/BaseModificationCoverageRenderer.java#L51
                     const detectable = mod.base === 'N'
                         ? score0
                         : (((_c = snps[mod.base]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
@@ -155,8 +135,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                         continue;
                     }
                     const cmp = complementBase[mod.base];
-                    // this approach is inspired from the 'simplex' approach in igv
-                    // https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/java/org/broad/igv/sam/mods/BaseModificationCoverageRenderer.java#L51
                     const detectable = mod.base === 'N'
                         ? score0
                         : (((_g = snps[mod.base]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
@@ -235,8 +213,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                         maxBase = base;
                     }
                 }
-                // avoid drawing a bunch of indicators if coverage is very low. note:
-                // also uses the prev total in the case of the "cliff"
                 const indicatorComparatorScore = Math.max(score0, prevTotal);
                 if (accum > indicatorComparatorScore * indicatorThreshold &&
                     indicatorComparatorScore > MINIMUM_INTERBASE_INDICATOR_READ_DEPTH) {

package/esm/SNPCoverageRenderer/configSchema.d.ts

@@ -1,39 +1,24 @@
 declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     clipColor: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     indicatorThreshold: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     drawArcs: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     drawInterbaseCounts: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     drawIndicators: {
         type: string;
         description: string;

package/esm/SNPCoverageRenderer/configSchema.js

@@ -1,44 +1,26 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config SNPCoverageRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const SNPCoverageRenderer = ConfigurationSchema('SNPCoverageRenderer', {
-    /**
-     * #slot
-     */
     clipColor: {
         type: 'color',
         description: 'the color of the clipping marker',
         defaultValue: 'red',
     },
-    /**
-     * #slot
-     */
     indicatorThreshold: {
         type: 'number',
         description: 'the proportion of reads containing a insertion/clip indicator',
         defaultValue: 0.4,
     },
-    /**
-     * #slot
-     */
     drawArcs: {
         type: 'boolean',
         description: 'Draw sashimi-style arcs for intron features',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     drawInterbaseCounts: {
         type: 'boolean',
         description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
         defaultValue: true,
     },
-    /**
-     * #slot
-     */
     drawIndicators: {
         type: 'boolean',
         description: 'draw a triangular indicator where an event has been detected',

package/esm/SNPCoverageRenderer/index.d.ts

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

package/esm/SNPCoverageRenderer/index.js

@@ -1,6 +1,6 @@
-import configSchema from './configSchema';
-import SNPCoverageRenderer from './SNPCoverageRenderer';
 import { WiggleRendering } from '@jbrowse/plugin-wiggle';
+import SNPCoverageRenderer from './SNPCoverageRenderer';
+import configSchema from './configSchema';
 export default function register(pluginManager) {
     pluginManager.addRendererType(() => new SNPCoverageRenderer({
         name: 'SNPCoverageRenderer',

package/esm/index.d.ts

@@ -1,9 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
-export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, SharedLinearPileupDisplayMixin, } from './LinearPileupDisplay';
+export { SharedLinearPileupDisplayMixin, linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, } from './LinearPileupDisplay';
 export { type LinearPileupDisplayModel } from './LinearPileupDisplay/model';
 export * as MismatchParser from './MismatchParser';

package/esm/index.js

@@ -1,19 +1,19 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BamAdapterF from './CramAdapter';
+import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
+import AlignmentsTrackF from './AlignmentsTrack';
 import CramAdapterF from './BamAdapter';
+import BamAdapterF from './CramAdapter';
+import GuessAlignmentsTypesF from './GuessAlignmentsTypes';
 import HtsgetBamAdapterF from './HtsgetBamAdapter';
-import SNPCoverageAdapterF from './SNPCoverageAdapter';
-import SNPCoverageRendererF from './SNPCoverageRenderer';
-import PileupRendererF from './PileupRenderer';
 import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay';
-import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay';
+import LinearPileupDisplayF from './LinearPileupDisplay';
 import LinearReadArcsDisplayF from './LinearReadArcsDisplay';
 import LinearReadCloudDisplayF from './LinearReadCloudDisplay';
-import AlignmentsTrackF from './AlignmentsTrack';
-import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail';
+import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay';
 import PileupRPCMethodsF from './PileupRPC';
-import GuessAlignmentsTypesF from './GuessAlignmentsTypes';
-import LinearPileupDisplayF from './LinearPileupDisplay';
+import PileupRendererF from './PileupRenderer';
+import SNPCoverageAdapterF from './SNPCoverageAdapter';
+import SNPCoverageRendererF from './SNPCoverageRenderer';
 export default class AlignmentsPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -42,5 +42,5 @@ export default class AlignmentsPlugin extends Plugin {
         });
     }
 }
-export { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory, SharedLinearPileupDisplayMixin, } from './LinearPileupDisplay';
+export { SharedLinearPileupDisplayMixin, linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, } from './LinearPileupDisplay';
 export * as MismatchParser from './MismatchParser';

package/esm/shared/afterAttach.d.ts

@@ -1,2 +1,2 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function doAfterAttach<T extends IAnyStateTreeNode>(self: T, cb: (self: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): void;

package/esm/shared/afterAttach.js

@@ -24,14 +24,12 @@ export function doAfterAttach(self, cb) {
         self.setLastDrawnOffsetPx(view.offsetPx);
         self.setLastDrawnBpPerPx(view.bpPerPx);
     }
-    // first autorun instantly draws if bpPerPx changes
     createAutorun(self, async () => {
         const view = getContainingView(self);
         if (view.bpPerPx !== self.lastDrawnBpPerPx) {
             draw(view);
         }
     });
-    // second autorun draws after delay 1000 e.g. if offsetPx changes
     createAutorun(self, async () => {
         const view = getContainingView(self);
         draw(view);

package/esm/shared/color.d.ts

@@ -1,4 +1,4 @@
-import { ChainStats } from './fetchChains';
+import type { ChainStats } from './fetchChains';
 export declare const fillColor: {
     color_fwd_strand_not_proper: string;
     color_rev_strand_not_proper: string;

package/esm/shared/color.js

@@ -18,12 +18,6 @@ export const fillColor = {
     color_shortinsert: 'pink',
     color_unknown: 'grey',
 };
-// manually calculated by running
-// const color = require('color')
-// Object.fromEntries(Object.entries(fillColor).map(([key,val])=>{
-//   return [key, color(val).darken('0.3').hex()]
-// }))
-// this avoids (expensive) use of Color module at runtime
 export const strokeColor = {
     color_fwd_strand_not_proper: '#CA6767',
     color_rev_strand_not_proper: '#7272AA',
@@ -60,8 +54,6 @@ export function getPairedInsertSizeColor(f1, f2, stats) {
     }
 }
 const defaultColor = [fillColor.color_unknown, fillColor.color_unknown];
-// return color scheme with both insert size and orientation coloring,
-// prioritzing orientation coloring
 export function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
     return (getPairedOrientationColorOrDefault(f1) ||
         getPairedInsertSizeColor(f1, f2, stats) ||

package/esm/shared/components/BaseDisplayComponent.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { LinearReadCloudDisplayModel } from '../../LinearReadCloudDisplay/model';
-import { LinearReadArcsDisplayModel } from '../../LinearReadArcsDisplay/model';
+import type { LinearReadArcsDisplayModel } from '../../LinearReadArcsDisplay/model';
+import type { LinearReadCloudDisplayModel } from '../../LinearReadCloudDisplay/model';
 declare const BaseDisplayComponent: ({ model, children, }: {
     model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
     children?: React.ReactNode;

package/esm/shared/components/BaseDisplayComponent.js

@@ -1,10 +1,10 @@
 import React from 'react';
 import { LoadingEllipses } from '@jbrowse/core/ui';
-import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
-import { makeStyles } from 'tss-react/mui';
-import { observer } from 'mobx-react';
 import { getContainingView } from '@jbrowse/core/util';
+import { BlockMsg } from '@jbrowse/plugin-linear-genome-view';
 import { Button, Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     loading: {
         backgroundColor: theme.palette.background.default,
@@ -18,21 +18,22 @@ const useStyles = makeStyles()(theme => ({
         textAlign: 'center',
     },
 }));
-const BaseDisplayComponent = observer(function ({ model, children, }) {
-    const { error, regionTooLarge } = model;
-    return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(Tooltip, { title: "Reload" },
+const BlockError = observer(function ({ model, }) {
+    const { error } = model;
+    return (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(Tooltip, { title: "Reload" },
             React.createElement(Button, { "data-testid": "reload_button", onClick: () => {
                     model.reload();
-                } }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
+                } }, "Reload")) }));
+});
+const BaseDisplayComponent = observer(function ({ model, children, }) {
+    const { error, regionTooLarge } = model;
+    return error ? (React.createElement(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
 });
 const DataDisplay = observer(function ({ model, children, }) {
     const { drawn, loading } = model;
     const view = getContainingView(model);
     const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
-    return (
-    // this data-testid is located here because changing props on the canvas
-    // itself is very sensitive to triggering ref invalidation
-    React.createElement("div", { "data-testid": `drawn-${drawn}` },
+    return (React.createElement("div", { "data-testid": `drawn-${drawn}` },
         React.createElement("div", { style: { position: 'absolute', left } }, children),
         left !== 0 || loading ? React.createElement(LoadingBar, { model: model }) : null));
 });

package/esm/shared/components/FilterByTagDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { FilterBy } from '../types';
+import type { FilterBy } from '../types';
 declare const FilterByTagDialog: (props: {
     model: {
         filterBy: FilterBy;

package/esm/shared/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: {

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

@@ -1,10 +1,9 @@
 import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
 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);

package/esm/shared/getMaximumModificationAtEachPosition.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 interface MaximumProbabilityMod {
     type: string;
     prob: number;

package/esm/shared/getMaximumModificationAtEachPosition.js

@@ -1,6 +1,5 @@
-// locals
-import { getModPositions, getModProbabilities } from '../ModificationParser';
 import { getNextRefPos, parseCigar } from '../MismatchParser';
+import { getModPositions, getModProbabilities } from '../ModificationParser';
 import { getTagAlt } from '../util';
 export function getMaxProbModAtEachPosition(feature, cigarOps) {
     const fstrand = feature.get('strand');

package/esm/shared/getUniqueModifications.d.ts

@@ -1,14 +1,14 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { ModificationType } from './types';
+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>;
-        signal?: AbortSignal;
+        stopToken?: string;
         filters: string[];
     };
 }): Promise<ModificationType[]>;

package/esm/shared/getUniqueTags.d.ts

@@ -1,6 +1,6 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+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;
@@ -9,7 +9,7 @@ export declare function getUniqueTags({ self, tag, blocks, opts, }: {
     blocks: BlockSet;
     opts?: {
         headers?: Record<string, string>;
-        signal?: AbortSignal;
+        stopToken?: string;
         filters: string[];
     };
 }): Promise<string[]>;

package/esm/shared/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/util.d.ts

@@ -1,10 +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

@@ -18,6 +18,14 @@ 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;
@@ -29,3 +37,19 @@ export function cacheGetter(ctor, prop) {
         },
     });
 }
+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

@@ -1,7 +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';
+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>;

package/esm/util.js

@@ -1,16 +1,12 @@
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-// 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;
     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',
@@ -81,8 +77,6 @@ export async function fetchSequence(region, adapter) {
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// adapted from IGV
-// 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' },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,9 @@
   "dependencies": {
     "@gmod/bam": "^4.0.1",
     "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.17.0",
+    "@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": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }