@jbrowse/plugin-alignments 2.2.2 → 2.3.1

package/esm/LinearReadCloudDisplay/model.js

@@ -0,0 +1,224 @@
+import React, { lazy } from 'react';
+import { autorun } from 'mobx';
+import { addDisposer, cast, types } from 'mobx-state-tree';
+import { ConfigurationReference, ConfigurationSchema, } from '@jbrowse/core/configuration';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
+// icons
+import PaletteIcon from '@mui/icons-material/Palette';
+import FilterListIcon from '@mui/icons-material/ClearAll';
+// locals
+import { FilterModel } from '../shared';
+import { fetchChains } from '../shared/fetchChains';
+import drawFeats from './drawFeats';
+// async
+const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
+/**
+ * #stateModel LinearReadCloudDisplay
+ * extends `BaseLinearDisplay`
+ */
+function stateModelFactory(configSchema) {
+    return types
+        .compose('LinearReadCloudDisplay', BaseLinearDisplay, types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearReadCloudDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        filterBy: types.optional(FilterModel, {}),
+        /**
+         * #property
+         */
+        colorBy: types.maybe(types.model({
+            type: types.string,
+            tag: types.maybe(types.string),
+            extra: types.frozen(),
+        })),
+    }))
+        .volatile(() => ({
+        loading: false,
+        drawn: false,
+        chainData: undefined,
+        ref: null,
+        lastDrawnOffsetPx: 0,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+         */
+        reload() {
+            self.error = undefined;
+        },
+        /**
+         * #action
+         */
+        setRef(ref) {
+            self.ref = ref;
+        },
+        setColorScheme(s) {
+            self.colorBy = cast(s);
+        },
+        /**
+         * #action
+         */
+        setChainData(args) {
+            self.chainData = args;
+        },
+        /**
+         * #action
+         */
+        setLoading(f) {
+            self.loading = f;
+        },
+        /**
+         * #action
+         */
+        setDrawn(f) {
+            self.drawn = f;
+        },
+        /**
+         * #action
+         */
+        setFilterBy(filter) {
+            self.filterBy = cast(filter);
+        },
+        /**
+         * #action
+         */
+        setLastDrawnOffsetPx(n) {
+            self.lastDrawnOffsetPx = n;
+        },
+    }))
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        return {
+            /**
+             * #getter
+             */
+            get ready() {
+                return !!self.chainData;
+            },
+            // we don't use a server side renderer, but we need to provide this
+            // to avoid confusing the system currently
+            get rendererTypeName() {
+                return 'PileupRenderer';
+            },
+            // we don't use a server side renderer, so this fills in minimal
+            // info so as not to crash
+            renderProps() {
+                return {
+                    ...superRenderProps(),
+                    // never ready, we don't want to use server side render
+                    notReady: true,
+                    config: ConfigurationSchema('empty', {}).create(),
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Filter by',
+                        icon: FilterListIcon,
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                FilterByTagDlg,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Color scheme',
+                        icon: PaletteIcon,
+                        subMenu: [
+                            {
+                                label: 'Insert size ± 3σ and orientation',
+                                onClick: () => self.setColorScheme({ type: 'insertSizeAndOrientation' }),
+                            },
+                            {
+                                label: 'Insert size ± 3σ',
+                                onClick: () => self.setColorScheme({ type: 'insertSize' }),
+                            },
+                            {
+                                label: 'Orientation',
+                                onClick: () => self.setColorScheme({ type: 'orientation' }),
+                            },
+                            {
+                                label: 'Insert size gradient',
+                                onClick: () => self.setColorScheme({ type: 'gradient' }),
+                            },
+                        ],
+                    },
+                ];
+            },
+            /**
+             * #method
+             */
+            async renderSvg(opts) {
+                const view = getContainingView(self);
+                const width = view.dynamicBlocks.totalWidthPx;
+                const height = self.height;
+                let str;
+                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);
+                    await drawFeats(self, ctx);
+                    str = (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);
+                    await drawFeats(self, ctx);
+                    str = (
+                    // eslint-disable-next-line react/no-danger
+                    React.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } }));
+                }
+                return React.createElement("g", null, str);
+            },
+        };
+    })
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, autorun(() => fetchChains(self), { delay: 1000 }));
+            addDisposer(self, autorun(async () => {
+                try {
+                    const canvas = self.ref;
+                    if (!canvas) {
+                        return;
+                    }
+                    const ctx = canvas.getContext('2d');
+                    if (!ctx) {
+                        return;
+                    }
+                    ctx.clearRect(0, 0, canvas.width, self.height * 2);
+                    ctx.resetTransform();
+                    ctx.scale(2, 2);
+                    await drawFeats(self, ctx);
+                    self.setDrawn(true);
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            }, { delay: 1000 }));
+        },
+    }));
+}
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LinearReadCloudDisplay/model.js.map

@@ -0,0 +1 @@
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package/esm/LinearSNPCoverageDisplay/index.js

@@ -7,6 +7,7 @@ export default function register(pluginManager) {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'LinearSNPCoverageDisplay',
+            displayName: 'SNPCoverage display',
             configSchema,
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',

package/esm/LinearSNPCoverageDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,iCAAiC,EAAE,MAAM,wBAAwB,CAAA;AAC1E,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iCAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,EAAE,iCAAiC,EAAE,MAAM,wBAAwB,CAAA;AAC1E,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,WAAW,EAAE,qBAAqB;YAClC,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iCAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/LinearSNPCoverageDisplay/models/model.d.ts

@@ -14,7 +14,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
+            refName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -35,7 +37,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean;
+        maxHeightReached: boolean; /**
+         * #action
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -52,7 +56,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
-        } | undefined): void;
+        } | undefined): void; /**
+         * #getter
+         */
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -146,22 +152,19 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+             * #getter
+             */
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
-         * #getter
-         */
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    /**
-     * #method
-     */
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
@@ -173,10 +176,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
@@ -244,12 +247,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
-    statsReady: boolean;
     message: string | undefined;
     stats: {
         scoreMin: number;
         scoreMax: number;
-    };
+    } | undefined;
     statsFetchInProgress: AbortController | undefined;
 } & {
     updateStats(stats: {
@@ -290,14 +292,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     readonly filled: any;
     readonly summaryScoreModeSetting: any;
-    readonly domain: number[];
+    readonly domain: number[] | undefined;
     readonly needsScalebar: boolean;
     readonly scaleOpts: {
-        domain: number[];
+        domain: number[] | undefined;
         stats: {
             scoreMin: number;
             scoreMax: number;
-        };
+        } | undefined;
         autoscaleType: any;
         scaleType: any;
         inverted: any;
@@ -311,7 +313,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         values: number[];
         format: (d: import("d3-scale").NumberValue) => string;
         position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
-    };
+    } | undefined;
     readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
@@ -425,9 +427,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             featureUnderMouse: import("@jbrowse/core/util").Feature;
         };
         height: number;
-        /**
-         * #action
-         */
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];
         clientRect?: DOMRect | undefined;

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -6,7 +6,7 @@ import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
 import { getContainingView } from '@jbrowse/core/util';
 // locals
 import Tooltip from '../components/Tooltip';
-import { getUniqueModificationValues } from '../../shared';
+import { FilterModel, getUniqueModificationValues } from '../../shared';
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
 /**
@@ -35,12 +35,7 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #property
          */
-        filterBy: types.optional(types.model({
-            flagInclude: types.optional(types.number, 0),
-            flagExclude: types.optional(types.number, 1540),
-            readName: types.maybe(types.string),
-            tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
-        }), {}),
+        filterBy: types.optional(FilterModel, {}),
         /**
          * #property
          */

package/esm/LinearSNPCoverageDisplay/models/model.js.map

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package/esm/{BamAdapter/MismatchParser.d.ts → MismatchParser/index.d.ts}

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import { Feature } from '@jbrowse/core/util';
 export interface Mismatch {
     qual?: number;
     start: number;
@@ -23,3 +24,25 @@ export declare function getModificationPositions(mm: string, fseq: string, fstra
     positions: number[];
 }[];
 export declare function getModificationTypes(mm: string): string[];
+export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
+export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
+export declare function getLengthOnRef(cigar: string): number;
+export declare function getLength(cigar: string): number;
+export declare function getLengthSansClipping(cigar: string): number;
+export declare function getClip(cigar: string, strand: number): number;
+export declare function getTag(f: Feature, tag: string): any;
+export declare function featurizeSA(SA: string | undefined, id: string, strand: number, readName: string, normalize?: boolean): {
+    refName: string;
+    start: number;
+    end: number;
+    seqLength: number;
+    clipPos: number;
+    CIGAR: string;
+    strand: number;
+    uniqueId: string;
+    mate: {
+        start: number;
+        end: number;
+        refName: string;
+    };
+}[];

package/esm/{BamAdapter/MismatchParser.js → MismatchParser/index.js}

@@ -1,8 +1,11 @@
 import { revcom } from '@jbrowse/core/util';
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
+const cigarRegex = new RegExp(/([MIDNSHPX=])/);
+const startClip = new RegExp(/(\d+)[SH]$/);
+const endClip = new RegExp(/^(\d+)([SH])/);
 export function parseCigar(cigar = '') {
-    return cigar.split(/([MIDNSHPX=])/).slice(0, -1);
+    return cigar.split(cigarRegex).slice(0, -1);
 }
 export function cigarToMismatches(ops, seq, ref, qual) {
     let roffset = 0; // reference offset
@@ -288,4 +291,106 @@ export function getModificationTypes(mm) {
     })
         .flat();
 }
-//# sourceMappingURL=MismatchParser.js.map
+export function getOrientedCigar(flip, cigar) {
+    if (flip) {
+        const ret = [];
+        for (let i = 0; i < cigar.length; i += 2) {
+            const len = cigar[i];
+            let op = cigar[i + 1];
+            if (op === 'D') {
+                op = 'I';
+            }
+            else if (op === 'I') {
+                op = 'D';
+            }
+            ret.push(len);
+            ret.push(op);
+        }
+        return ret;
+    }
+    else {
+        return cigar;
+    }
+}
+export function getOrientedMismatches(flip, cigar) {
+    const p = parseCigar(cigar);
+    return cigarToMismatches(flip ? getOrientedCigar(flip, p) : p);
+}
+export function getLengthOnRef(cigar) {
+    const cigarOps = parseCigar(cigar);
+    let lengthOnRef = 0;
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
+        if (op !== 'H' && op !== 'S' && op !== 'I') {
+            lengthOnRef += len;
+        }
+    }
+    return lengthOnRef;
+}
+export function getLength(cigar) {
+    const cigarOps = parseCigar(cigar);
+    let length = 0;
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
+        if (op !== 'D' && op !== 'N') {
+            length += len;
+        }
+    }
+    return length;
+}
+export function getLengthSansClipping(cigar) {
+    const cigarOps = parseCigar(cigar);
+    let length = 0;
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
+        if (op !== 'H' && op !== 'S' && op !== 'D' && op !== 'N') {
+            length += len;
+        }
+    }
+    return length;
+}
+export function getClip(cigar, strand) {
+    return strand === -1
+        ? +(cigar.match(startClip) || [])[1] || 0
+        : +(cigar.match(endClip) || [])[1] || 0;
+}
+export function getTag(f, tag) {
+    const tags = f.get('tags');
+    return tags ? tags[tag] : f.get(tag);
+}
+// produces a list of "feature-like" object from parsing supplementary
+// alignments in the SA tag
+//
+// @param normalize - used specifically in the linear-read-vs-ref context, it
+// flips features around relative to the original feature. other contexts of
+// usage can keep this false
+export function featurizeSA(SA, id, strand, readName, normalize) {
+    return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
+        const [saRef, saStart, saStrand, saCigar] = aln.split(',');
+        const saLengthOnRef = getLengthOnRef(saCigar);
+        const saLength = getLength(saCigar);
+        const saLengthSansClipping = getLengthSansClipping(saCigar);
+        const saStrandNormalized = saStrand === '-' ? -1 : 1;
+        const saClipPos = getClip(saCigar, (normalize ? strand : 1) * saStrandNormalized);
+        const saRealStart = +saStart - 1;
+        return {
+            refName: saRef,
+            start: saRealStart,
+            end: saRealStart + saLengthOnRef,
+            seqLength: saLength,
+            clipPos: saClipPos,
+            CIGAR: saCigar,
+            strand: (normalize ? strand : 1) * saStrandNormalized,
+            uniqueId: `${id}_SA${index}`,
+            mate: {
+                start: saClipPos,
+                end: saClipPos + saLengthSansClipping,
+                refName: readName,
+            },
+        };
+    })) || []);
+}
+//# sourceMappingURL=index.js.map

package/esm/MismatchParser/index.js.map

@@ -0,0 +1 @@
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package/esm/PileupRPC/base.d.ts

@@ -0,0 +1,8 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+export default abstract class PileupBaseRPC extends RpcMethodType {
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: (arg: string) => void;
+    }, rpcDriver: string): Promise<{}>;
+}

package/esm/PileupRPC/base.js

@@ -0,0 +1,16 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { renameRegionsIfNeeded } from '@jbrowse/core/util';
+// specialized get features to return limited data about alignments
+export default class PileupBaseRPC extends RpcMethodType {
+    async serializeArguments(args, rpcDriver) {
+        var _a;
+        const { rootModel } = this.pluginManager;
+        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
+        if (!assemblyManager) {
+            throw new Error('no assembly manager available');
+        }
+        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriver);
+    }
+}
+//# sourceMappingURL=base.js.map

package/esm/PileupRPC/base.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"base.js","sourceRoot":"","sources":["../../src/PileupRPC/base.ts"],"names":[],"mappings":"AAAA,OAAO,aAAa,MAAM,mDAAmD,CAAA;AAC7E,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAA;AAG1D,mEAAmE;AACnE,MAAM,CAAC,OAAO,OAAgB,aAAc,SAAQ,aAAa;IAC/D,KAAK,CAAC,kBAAkB,CACtB,IAGC,EACD,SAAiB;;QAEjB,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,MAAM,eAAe,GAAG,MAAA,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,OAAO,0CAAE,eAAe,CAAA;QAC3D,IAAI,CAAC,eAAe,EAAE;YACpB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QAED,MAAM,WAAW,GAAG,MAAM,qBAAqB,CAAC,eAAe,EAAE,IAAI,CAAC,CAAA;QAEtE,OAAO,KAAK,CAAC,kBAAkB,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;IACzD,CAAC;CACF"}

package/esm/PileupRPC/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pm: PluginManager) => void;
+export default _default;

package/esm/PileupRPC/index.js

@@ -0,0 +1,7 @@
+import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, PileupGetReducedFeatures, } from './rpcMethods';
+export default (pm) => {
+    pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
+    pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));
+    pm.addRpcMethod(() => new PileupGetReducedFeatures(pm));
+};
+//# sourceMappingURL=index.js.map

package/esm/PileupRPC/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRPC/index.ts"],"names":[],"mappings":"AACA,OAAO,EACL,0BAA0B,EAC1B,6BAA6B,EAC7B,wBAAwB,GACzB,MAAM,cAAc,CAAA;AAErB,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,0BAA0B,CAAC,EAAE,CAAC,CAAC,CAAA;IACzD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,6BAA6B,CAAC,EAAE,CAAC,CAAC,CAAA;IAC5D,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,wBAAwB,CAAC,EAAE,CAAC,CAAC,CAAA;AACzD,CAAC,CAAA"}