@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -39,5 +39,10 @@ declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configura
         description: string;
         defaultValue: boolean;
     };
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SNPCoverageRenderer;

package/dist/SNPCoverageRenderer/configSchema.js

@@ -46,6 +46,11 @@ const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverag
         description: 'draw a triangular indicator where an event has been detected',
         defaultValue: true,
     },
+    color: {
+        type: 'color',
+        description: 'Background color for the SNPCoverage renderer',
+        defaultValue: '#d3d3d3',
+    },
 }, { explicitlyTyped: true });
 exports.default = SNPCoverageRenderer;
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;IAED,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,SAAS;KACxB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}

package/dist/shared/BaseDisplayComponent.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+declare const _default: ({ model, children, }: {
+    model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
+    children?: React.ReactNode;
+}) => React.JSX.Element | null;
+export default _default;

package/dist/shared/BaseDisplayComponent.js

@@ -0,0 +1,49 @@
+"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 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 useStyles = (0, mui_1.makeStyles)()(theme => {
+    const bg = theme.palette.action.disabledBackground;
+    return {
+        loading: {
+            backgroundColor: theme.palette.background.default,
+            backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,
+            position: 'absolute',
+            bottom: 0,
+            height: 50,
+            width: 300,
+            right: 0,
+            pointerEvents: 'none',
+            textAlign: 'center',
+        },
+    };
+});
+exports.default = (0, mobx_react_1.observer)(function ({ model, children, }) {
+    const { error, regionTooLarge } = model;
+    return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : 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}` },
+        react_1.default.createElement("div", { style: { position: 'absolute', left } }, children),
+        left !== 0 || loading ? react_1.default.createElement(LoadingBar, { model: model }) : null));
+});
+const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { classes } = useStyles();
+    const { message } = model;
+    return (react_1.default.createElement("div", { className: classes.loading },
+        react_1.default.createElement(ui_1.LoadingEllipses, { message: message })));
+});
+//# sourceMappingURL=BaseDisplayComponent.js.map

package/dist/shared/BaseDisplayComponent.js.map

@@ -0,0 +1 @@
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package/dist/shared/FilterByTag.d.ts

@@ -1,17 +1,19 @@
+import React from 'react';
+interface FilterBy {
+    flagExclude: number;
+    flagInclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 declare function FilterByTagDlg(props: {
     model: {
-        filterBy?: {
-            flagExclude: number;
-            flagInclude: number;
-            readName?: string;
-            tagFilter?: {
-                tag: string;
-                value: string;
-            };
-        };
-        setFilterBy: Function;
+        filterBy: FilterBy;
+        setFilterBy: (arg: FilterBy) => void;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof FilterByTagDlg;
 export default _default;

package/dist/shared/FilterByTag.js

@@ -75,11 +75,11 @@ function FilterByTagDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { filterBy } = model;
-    const [flagInclude, setFlagInclude] = (0, react_1.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude);
-    const [flagExclude, setFlagExclude] = (0, react_1.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude);
-    const [tag, setTag] = (0, react_1.useState)(((_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
-    const [tagValue, setTagValue] = (0, react_1.useState)(((_b = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
-    const [readName, setReadName] = (0, react_1.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || '');
+    const [flagInclude, setFlagInclude] = (0, react_1.useState)(filterBy.flagInclude);
+    const [flagExclude, setFlagExclude] = (0, react_1.useState)(filterBy.flagExclude);
+    const [tag, setTag] = (0, react_1.useState)(((_a = filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
+    const [tagValue, setTagValue] = (0, react_1.useState)(((_b = filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
+    const [readName, setReadName] = (0, react_1.useState)(filterBy.readName || '');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
     const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
@@ -101,16 +101,11 @@ function FilterByTagDlg(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,
-                        'data-testid': 'color-tag-name-input',
-                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', "data-testid": "color-tag-name" }),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value", inputProps: {
-                        'data-testid': 'color-tag-name-input',
-                    }, "data-testid": "color-tag-value" })),
+                    }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '' }),
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => setTagValue(event.target.value), placeholder: "Enter tag value" })),
             react_1.default.createElement(material_1.Paper, { className: classes.paper, variant: "outlined" },
                 react_1.default.createElement(material_1.Typography, null, "Filter by read name"),
-                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name", inputProps: {
-                        'data-testid': 'color-tag-readname-input',
-                    }, "data-testid": "color-tag-readname" })),
+                react_1.default.createElement(material_1.TextField, { className: classes.field, value: readName, onChange: event => setReadName(event.target.value), placeholder: "Enter read name" })),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
                         model.setFilterBy({

package/dist/shared/FilterByTag.js.map

@@ -1 +1 @@
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package/dist/shared/afterAttach.d.ts

@@ -0,0 +1,2 @@
+import { 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

@@ -0,0 +1,44 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doAfterAttach = void 0;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("../util");
+const fetchChains_1 = require("./fetchChains");
+function doAfterAttach(self, cb) {
+    (0, util_2.createAutorun)(self, async () => {
+        await (0, fetchChains_1.fetchChains)(self);
+    }, { delay: 1000 });
+    function draw(view) {
+        const canvas = self.ref;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        if (!self.chainData) {
+            return;
+        }
+        ctx.clearRect(0, 0, canvas.width, self.height * 2);
+        ctx.resetTransform();
+        ctx.scale(2, 2);
+        cb(self, ctx, canvas.width, self.height);
+        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);
+    }, { delay: 1000 });
+}
+exports.doAfterAttach = doAfterAttach;
+//# sourceMappingURL=afterAttach.js.map

package/dist/shared/afterAttach.js.map

@@ -0,0 +1 @@
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package/dist/shared/color.d.ts

@@ -1,17 +1,55 @@
 import { ChainStats } from './fetchChains';
-export declare function getInsertSizeColor(f1: {
+export declare const fillColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare const strokeColor: {
+    color_fwd_strand_not_proper: string;
+    color_rev_strand_not_proper: string;
+    color_fwd_strand: string;
+    color_rev_strand: string;
+    color_fwd_missing_mate: string;
+    color_rev_missing_mate: string;
+    color_fwd_diff_chr: string;
+    color_rev_diff_chr: string;
+    color_pair_lr: string;
+    color_pair_rr: string;
+    color_pair_rl: string;
+    color_pair_ll: string;
+    color_nostrand: string;
+    color_interchrom: string;
+    color_longinsert: string;
+    color_shortinsert: string;
+    color_unknown: string;
+};
+export declare function getPairedInsertSizeColor(f1: {
     refName: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): "" | "red" | "purple" | "#f0f";
-export declare function getInsertSizeAndOrientationColor(f1: {
+}, stats?: ChainStats): readonly [string, string] | undefined;
+export declare function getPairedInsertSizeAndOrientationColor(f1: {
     refName: string;
     pair_orientation?: string;
     tlen?: number;
 }, f2: {
     refName: string;
-}, stats?: ChainStats): string;
-export declare function getOrientationColor(f: {
+}, stats?: ChainStats): readonly [string, string];
+export declare function getPairedOrientationColor(f: {
     pair_orientation?: string;
-}): string;
+}): readonly [string, string];

package/dist/shared/color.js

@@ -1,43 +1,77 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getOrientationColor = exports.getInsertSizeAndOrientationColor = exports.getInsertSizeColor = void 0;
+exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
 const util_1 = require("../util");
-const alignmentColoring = {
+exports.fillColor = {
+    color_fwd_strand_not_proper: '#ECC8C8',
+    color_rev_strand_not_proper: '#BEBED8',
+    color_fwd_strand: '#EC8B8B',
+    color_rev_strand: '#8F8FD8',
+    color_fwd_missing_mate: '#D11919',
+    color_rev_missing_mate: '#1919D1',
+    color_fwd_diff_chr: '#000',
+    color_rev_diff_chr: '#969696',
     color_pair_lr: '#c8c8c8',
     color_pair_rr: 'navy',
     color_pair_rl: 'teal',
     color_pair_ll: 'green',
+    color_nostrand: '#c8c8c8',
+    color_interchrom: 'purple',
+    color_longinsert: 'red',
+    color_shortinsert: 'pink',
+    color_unknown: 'grey',
 };
-function getInsertSizeColor(f1, f2, stats) {
+// 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',
+    color_fwd_strand: '#DC2A2A',
+    color_rev_strand: '#4141BA',
+    color_fwd_missing_mate: '#921111',
+    color_rev_missing_mate: '#111192',
+    color_fwd_diff_chr: '#000000',
+    color_rev_diff_chr: '#696969',
+    color_pair_lr: '#8C8C8C',
+    color_pair_rr: '#00005A',
+    color_pair_rl: '#005A5A',
+    color_pair_ll: '#005A00',
+    color_nostrand: '#8C8C8C',
+    color_interchrom: '#5A005A',
+    color_longinsert: '#B30000',
+    color_shortinsert: '#FF3A5C',
+    color_unknown: 'grey',
+};
+function getPairedInsertSizeColor(f1, f2, stats) {
     const sameRef = f1.refName === f2.refName;
     const tlen = Math.abs(f1.tlen || 0);
     if (sameRef && tlen > ((stats === null || stats === void 0 ? void 0 : stats.upper) || 0)) {
-        return 'red';
+        return [exports.fillColor.color_longinsert, exports.strokeColor.color_longinsert];
     }
     else if (sameRef && tlen < ((stats === null || stats === void 0 ? void 0 : stats.lower) || 0)) {
-        return '#f0f';
+        return [exports.fillColor.color_shortinsert, exports.strokeColor.color_shortinsert];
     }
     else if (!sameRef) {
-        return 'purple';
+        return [exports.fillColor.color_interchrom, exports.strokeColor.color_interchrom];
     }
-    return '';
+    return undefined;
 }
-exports.getInsertSizeColor = getInsertSizeColor;
-function getInsertSizeAndOrientationColor(f1, f2, stats) {
-    return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1);
+exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
+function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
+    return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-exports.getInsertSizeAndOrientationColor = getInsertSizeAndOrientationColor;
-function getOrientationColor(f) {
-    const type = util_1.orientationTypes['fr'];
-    const orientation = type[f.pair_orientation || ''];
-    const map = {
-        LR: 'color_pair_lr',
-        RR: 'color_pair_rr',
-        RL: 'color_pair_rl',
-        LL: 'color_pair_ll',
-    };
-    const val = map[orientation];
-    return alignmentColoring[val] || 'grey';
+exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
+function getPairedOrientationColor(f) {
+    const type = util_1.orientationTypes.fr;
+    const type2 = util_1.pairMap[type[f.pair_orientation || '']];
+    return [
+        exports.fillColor[type2] || exports.fillColor.color_unknown,
+        exports.strokeColor[type2] || exports.strokeColor.color_unknown,
+    ];
 }
-exports.getOrientationColor = getOrientationColor;
+exports.getPairedOrientationColor = getPairedOrientationColor;
 //# sourceMappingURL=color.js.map

package/dist/shared/color.js.map

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package/dist/shared/fetchChains.d.ts

@@ -1,4 +1,5 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
+import { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
 export interface ReducedFeature {
     name: string;
     strand: number;
@@ -24,4 +25,4 @@ export interface ChainData {
     chains: ReducedFeature[][];
     stats?: ChainStats;
 }
-export declare function fetchChains(self: IAnyStateTreeNode): Promise<void>;
+export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/dist/shared/fetchChains.js

@@ -4,27 +4,21 @@ exports.fetchChains = void 0;
 const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 async function fetchChains(self) {
-    try {
-        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) {
-            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),
-            adapterConfig: self.adapterConfig,
-        }));
-        self.setChainData(ret);
-        self.setLoading(false);
-    }
-    catch (e) {
-        console.error(e);
-        self.setError(e);
+    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) {
+        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),
+        adapterConfig: self.adapterConfig,
+    }));
+    self.setChainData(ret);
+    self.setLoading(false);
 }
 exports.fetchChains = fetchChains;
 //# sourceMappingURL=fetchChains.js.map

package/dist/shared/fetchChains.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fetchChains.js","sourceRoot":"","sources":["../../src/shared/fetchChains.ts"],"names":[],"mappings":";;;AAAA,6CAI2B;AAC3B,qDAA6C;AAmCtC,KAAK,UAAU,WAAW,CAC/B,IAA8D;IAE9D,MAAM,EAAE,YAAY,EAAE,SAAS,EAAE,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IACvC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;IAE3C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,cAAc,EAAE;QAC1D,OAAM;KACP;IAED,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;IACrB,MAAM,GAAG,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,0BAA0B,EAAE;QACxE,SAAS;QACT,OAAO,EAAE,IAAI,CAAC,YAAY,CAAC,aAAa;QACxC,QAAQ,EAAE,IAAA,6BAAW,EAAC,IAAI,CAAC,QAAQ,CAAC;QACpC,aAAa,EAAE,IAAI,CAAC,aAAa;KAClC,CAAC,CAAc,CAAA;IAEhB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;IACtB,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;AACxB,CAAC;AArBD,kCAqBC"}

package/dist/shared/renderSvg.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+export declare function renderSvg<T extends {
+    id: string;
+    height: number;
+}>(self: T, opts: {
+    rasterizeLayers?: boolean;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<React.JSX.Element | undefined>;

package/dist/shared/renderSvg.js

@@ -0,0 +1,69 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderSvg = void 0;
+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-${isJest ? id : 'jest'}`;
+}
+async function renderSvg(self, opts, cb) {
+    const view = (0, util_1.getContainingView)(self);
+    const width = view.dynamicBlocks.totalWidthPx;
+    const height = self.height;
+    if (opts.rasterizeLayers) {
+        const canvas = document.createElement('canvas');
+        canvas.width = width * 2;
+        canvas.height = height * 2;
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        ctx.scale(2, 2);
+        cb(self, ctx, width, height);
+        return (react_1.default.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+    }
+    else {
+        // @ts-ignore
+        const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
+        const ctx = new C2S.default(width, height);
+        cb(self, ctx, width, height);
+        const clipid = getId(self.id);
+        return (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement("defs", null,
+                react_1.default.createElement("clipPath", { id: clipid },
+                    react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+            react_1.default.createElement("g", { 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+    }
+}
+exports.renderSvg = renderSvg;
+//# sourceMappingURL=renderSvg.js.map

package/dist/shared/renderSvg.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/shared/renderSvg.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kDAAyB;AACzB,6CAAsD;AAGtD,2CAA2C;AAC3C,SAAS,KAAK,CAAC,EAAU;IACvB,MAAM,MAAM,GAAG,OAAO,IAAI,KAAK,WAAW,CAAA;IAC1C,OAAO,YAAY,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;AAC3C,CAAC;AAIM,KAAK,UAAU,SAAS,CAC7B,IAAO,EACP,IAAmC,EACnC,EAKS;IAET,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,KAAK,GAAG,IAAI,CAAC,aAAa,CAAC,YAAY,CAAA;IAC7C,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;IAC1B,IAAI,IAAI,CAAC,eAAe,EAAE;QACxB,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAA;QAC/C,MAAM,CAAC,KAAK,GAAG,KAAK,GAAG,CAAC,CAAA;QACxB,MAAM,CAAC,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QAC1B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE;YACR,OAAM;SACP;QACD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,OAAO,CACL,yCACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,CAAC,SAAS,CAAC,WAAW,CAAC,GACxC,CACH,CAAA;KACF;SAAM;QACL,aAAa;QACb,MAAM,GAAG,GAAG,wDAAa,YAAY,GAAC,CAAA;QACtC,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1C,EAAE,CAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;QAC5B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QAC7B,OAAO,CACL;YACE;gBACE,4CAAU,EAAE,EAAE,MAAM;oBAClB,wCAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;YACP;gBACE,8CAA8C;gBAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,EAC3D,QAAQ,EAAE,QAAQ,MAAM,GAAG,GAC3B,CACD,CACJ,CAAA;KACF;AACH,CAAC;AAnDD,8BAmDC"}

package/dist/shared/util.d.ts

@@ -0,0 +1,2 @@
+import { ChainData } from './fetchChains';
+export declare function hasPairedReads(features: ChainData): boolean;

package/dist/shared/util.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.hasPairedReads = void 0;
+function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+exports.hasPairedReads = hasPairedReads;
+//# sourceMappingURL=util.js.map

package/dist/shared/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/shared/util.ts"],"names":[],"mappings":";;;AAEA,SAAgB,cAAc,CAAC,QAAmB;IAChD,KAAK,MAAM,CAAC,IAAI,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE;QACxC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,EAAE;YAClB,OAAO,IAAI,CAAA;SACZ;KACF;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAPD,wCAOC"}

package/dist/util.d.ts

@@ -1,6 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AugmentedRegion } from '@jbrowse/core/util';
+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: {
@@ -14,6 +15,19 @@ export declare const orientationTypes: {
         [key: string]: string;
     };
 };
+export declare const pairMap: {
+    readonly LR: "color_pair_lr";
+    readonly LL: "color_pair_ll";
+    readonly RR: "color_pair_rr";
+    readonly RL: "color_pair_rl";
+};
 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): boolean;
+export declare const modificationColors: Record<string, string | undefined>;
+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 {};