@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -1,15 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const util_2 = require("../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',
@@ -19,22 +17,16 @@ const complementBase = {
 };
 const fudgeFactor = 0.6;
 class SNPCoverageRenderer extends plugin_wiggle_1.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 = (0, ui_1.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 = plugin_wiggle_1.YSCALEBAR_LABEL_OFFSET;
         const height = unadjustedHeight - offset * 2;
         const opts = { ...scaleOpts, range: [0, height] };
         const viewScale = (0, plugin_wiggle_1.getScale)(opts);
-        // clipping and insertion indicators, uses a smaller height/2 scale
         const indicatorViewScale = (0, plugin_wiggle_1.getScale)({
             ...opts,
             range: [0, height / 2],
@@ -46,10 +38,8 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
         const drawInterbaseCounts = (0, configuration_1.readConfObject)(cfg, 'drawInterbaseCounts');
         const drawArcs = (0, configuration_1.readConfObject)(cfg, 'drawArcs');
         const drawIndicators = (0, configuration_1.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;
@@ -67,9 +57,8 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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;
@@ -78,29 +67,22 @@ class SNPCoverageRenderer extends plugin_wiggle_1.WiggleBaseRenderer {
             const w = rightPx - leftPx + fudgeFactor;
             const score = feature.get('score');
             ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+            if (performance.now() - start > 400) {
+                (0, stopToken_1.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) {
+                (0, stopToken_1.checkStopToken)(stopToken);
+            }
             if (feature.get('type') === 'skip') {
                 continue;
             }
@@ -123,8 +105,6 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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) +
@@ -157,8 +137,6 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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) +
@@ -237,8 +215,6 @@ class SNPCoverageRenderer extends plugin_wiggle_1.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/dist/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/dist/SNPCoverageRenderer/configSchema.js

@@ -1,46 +1,28 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config SNPCoverageRenderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const SNPCoverageRenderer = (0, configuration_1.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/dist/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/dist/SNPCoverageRenderer/index.js

@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = register;
-const configSchema_1 = __importDefault(require("./configSchema"));
-const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 function register(pluginManager) {
     pluginManager.addRendererType(() => new SNPCoverageRenderer_1.default({
         name: 'SNPCoverageRenderer',

package/dist/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/dist/index.js

@@ -26,23 +26,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MismatchParser = exports.SharedLinearPileupDisplayMixin = exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
+exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = exports.SharedLinearPileupDisplayMixin = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const CramAdapter_1 = __importDefault(require("./CramAdapter"));
+const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
+const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
 const BamAdapter_1 = __importDefault(require("./BamAdapter"));
+const CramAdapter_1 = __importDefault(require("./CramAdapter"));
+const GuessAlignmentsTypes_1 = __importDefault(require("./GuessAlignmentsTypes"));
 const HtsgetBamAdapter_1 = __importDefault(require("./HtsgetBamAdapter"));
-const SNPCoverageAdapter_1 = __importDefault(require("./SNPCoverageAdapter"));
-const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
-const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
-const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
+const LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
 const LinearReadArcsDisplay_1 = __importDefault(require("./LinearReadArcsDisplay"));
 const LinearReadCloudDisplay_1 = __importDefault(require("./LinearReadCloudDisplay"));
-const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
-const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
+const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
 const PileupRPC_1 = __importDefault(require("./PileupRPC"));
-const GuessAlignmentsTypes_1 = __importDefault(require("./GuessAlignmentsTypes"));
-const LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
+const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
+const SNPCoverageAdapter_1 = __importDefault(require("./SNPCoverageAdapter"));
+const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 class AlignmentsPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -73,7 +73,7 @@ class AlignmentsPlugin extends Plugin_1.default {
 }
 exports.default = AlignmentsPlugin;
 var LinearPileupDisplay_2 = require("./LinearPileupDisplay");
-Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayStateModelFactory; } });
-Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayConfigSchemaFactory; } });
 Object.defineProperty(exports, "SharedLinearPileupDisplayMixin", { enumerable: true, get: function () { return LinearPileupDisplay_2.SharedLinearPileupDisplayMixin; } });
+Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayConfigSchemaFactory; } });
+Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_2.linearPileupDisplayStateModelFactory; } });
 exports.MismatchParser = __importStar(require("./MismatchParser"));

package/dist/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/dist/shared/afterAttach.js

@@ -27,14 +27,12 @@ function doAfterAttach(self, cb) {
         self.setLastDrawnOffsetPx(view.offsetPx);
         self.setLastDrawnBpPerPx(view.bpPerPx);
     }
-    // first autorun instantly draws if bpPerPx changes
     (0, util_2.createAutorun)(self, async () => {
         const view = (0, util_1.getContainingView)(self);
         if (view.bpPerPx !== self.lastDrawnBpPerPx) {
             draw(view);
         }
     });
-    // second autorun draws after delay 1000 e.g. if offsetPx changes
     (0, util_2.createAutorun)(self, async () => {
         const view = (0, util_1.getContainingView)(self);
         draw(view);

package/dist/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/dist/shared/color.js

@@ -25,12 +25,6 @@ exports.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
 exports.strokeColor = {
     color_fwd_strand_not_proper: '#CA6767',
     color_rev_strand_not_proper: '#7272AA',
@@ -67,8 +61,6 @@ function getPairedInsertSizeColor(f1, f2, stats) {
     }
 }
 const defaultColor = [exports.fillColor.color_unknown, exports.fillColor.color_unknown];
-// return color scheme with both insert size and orientation coloring,
-// prioritzing orientation coloring
 function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
     return (getPairedOrientationColorOrDefault(f1) ||
         getPairedInsertSizeColor(f1, f2, stats) ||

package/dist/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/dist/shared/components/BaseDisplayComponent.js

@@ -5,11 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const ui_1 = require("@jbrowse/core/ui");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 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 => ({
     loading: {
         backgroundColor: theme.palette.background.default,
@@ -23,21 +23,22 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         textAlign: 'center',
     },
 }));
-const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
-    const { error, regionTooLarge } = model;
-    return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
+const BlockError = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { error } = model;
+    return (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
             react_1.default.createElement(material_1.Button, { "data-testid": "reload_button", onClick: () => {
                     model.reload();
-                } }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
+                } }, "Reload")) }));
+});
+const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
+    const { error, regionTooLarge } = model;
+    return error ? (react_1.default.createElement(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
 });
 const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { drawn, loading } = model;
     const view = (0, util_1.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_1.default.createElement("div", { "data-testid": `drawn-${drawn}` },
+    return (react_1.default.createElement("div", { "data-testid": `drawn-${drawn}` },
         react_1.default.createElement("div", { style: { position: 'absolute', left } }, children),
         left !== 0 || loading ? react_1.default.createElement(LoadingBar, { model: model }) : null));
 });

package/dist/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/dist/shared/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: {

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

@@ -3,11 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
 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);

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

@@ -1,9 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getMaxProbModAtEachPosition = getMaxProbModAtEachPosition;
-// locals
-const ModificationParser_1 = require("../ModificationParser");
 const MismatchParser_1 = require("../MismatchParser");
+const ModificationParser_1 = require("../ModificationParser");
 const util_1 = require("../util");
 function getMaxProbModAtEachPosition(feature, cigarOps) {
     const fstrand = feature.get('strand');

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

@@ -1,9 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.defaultFilterFlags = void 0;
+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()) {
@@ -24,6 +26,14 @@ 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;
@@ -35,3 +45,19 @@ function cacheGetter(ctor, prop) {
         },
     });
 }
+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

@@ -1,7 +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/dist/util.js

@@ -7,19 +7,15 @@ exports.fetchSequence = fetchSequence;
 exports.createAutorun = createAutorun;
 exports.randomColor = randomColor;
 exports.getColorForModification = getColorForModification;
-const operators_1 = require("rxjs/operators");
-const rxjs_1 = require("rxjs");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-// 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;
     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',
@@ -90,8 +86,6 @@ async function fetchSequence(region, adapter) {
         .pipe((0, operators_1.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
 exports.modificationData = {
     m: { color: 'rgb(255,0,0)', name: '5mC' },
     h: { color: 'rgb(255,0,255)', name: '5hmC' },