@jbrowse/plugin-alignments 2.2.2 → 2.3.1

package/dist/LinearReadCloudDisplay/model.js

@@ -0,0 +1,252 @@
+"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 });
+const react_1 = __importStar(require("react"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+// icons
+const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
+const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+// locals
+const shared_1 = require("../shared");
+const fetchChains_1 = require("../shared/fetchChains");
+const drawFeats_1 = __importDefault(require("./drawFeats"));
+// async
+const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
+/**
+ * #stateModel LinearReadCloudDisplay
+ * extends `BaseLinearDisplay`
+ */
+function stateModelFactory(configSchema) {
+    return mobx_state_tree_1.types
+        .compose('LinearReadCloudDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('LinearReadCloudDisplay'),
+        /**
+         * #property
+         */
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
+        /**
+         * #property
+         */
+        filterBy: mobx_state_tree_1.types.optional(shared_1.FilterModel, {}),
+        /**
+         * #property
+         */
+        colorBy: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
+            type: mobx_state_tree_1.types.string,
+            tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+            extra: mobx_state_tree_1.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 = (0, mobx_state_tree_1.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 = (0, mobx_state_tree_1.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: (0, configuration_1.ConfigurationSchema)('empty', {}).create(),
+                };
+            },
+            /**
+             * #method
+             */
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Filter by',
+                        icon: ClearAll_1.default,
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                FilterByTagDlg,
+                                { model: self, handleClose },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Color scheme',
+                        icon: Palette_1.default,
+                        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 = (0, util_1.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 (0, drawFeats_1.default)(self, ctx);
+                    str = (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);
+                    await (0, drawFeats_1.default)(self, ctx);
+                    str = (
+                    // eslint-disable-next-line react/no-danger
+                    react_1.default.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } }));
+                }
+                return react_1.default.createElement("g", null, str);
+            },
+        };
+    })
+        .actions(self => ({
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => (0, fetchChains_1.fetchChains)(self), { delay: 1000 }));
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.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 (0, drawFeats_1.default)(self, ctx);
+                    self.setDrawn(true);
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            }, { delay: 1000 }));
+        },
+    }));
+}
+exports.default = stateModelFactory;
+//# sourceMappingURL=model.js.map

package/dist/LinearReadCloudDisplay/model.js.map

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package/dist/LinearSNPCoverageDisplay/index.js

@@ -12,6 +12,7 @@ function register(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearSNPCoverageDisplay',
+            displayName: 'SNPCoverage display',
             configSchema,
             stateModel: (0, model_1.default)(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',

package/dist/LinearSNPCoverageDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,yEAAuD;AACvD,2DAAyC;AACzC,0DAA0E;AAC1E,kGAAyE;AAEzE,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iDAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,yEAAuD;AACvD,2DAAyC;AACzC,0DAA0E;AAC1E,kGAAyE;AAEzE,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,WAAW,EAAE,qBAAqB;YAClC,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iDAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAbD,2BAaC"}

package/dist/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/dist/LinearSNPCoverageDisplay/models/model.js

@@ -40,12 +40,7 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #property
          */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-            flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-            flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-            readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-            tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
-        }), {}),
+        filterBy: mobx_state_tree_1.types.optional(shared_1.FilterModel, {}),
         /**
          * #property
          */

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

@@ -1 +1 @@
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package/dist/{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/dist/{BamAdapter/MismatchParser.js → MismatchParser/index.js}

@@ -1,11 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getModificationTypes = exports.getModificationPositions = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
+exports.featurizeSA = exports.getTag = exports.getClip = exports.getLengthSansClipping = exports.getLength = exports.getLengthOnRef = exports.getOrientedMismatches = exports.getOrientedCigar = exports.getModificationTypes = exports.getModificationPositions = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
 const util_1 = require("@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])/);
 function parseCigar(cigar = '') {
-    return cigar.split(/([MIDNSHPX=])/).slice(0, -1);
+    return cigar.split(cigarRegex).slice(0, -1);
 }
 exports.parseCigar = parseCigar;
 function cigarToMismatches(ops, seq, ref, qual) {
@@ -298,4 +301,114 @@ function getModificationTypes(mm) {
         .flat();
 }
 exports.getModificationTypes = getModificationTypes;
-//# sourceMappingURL=MismatchParser.js.map
+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;
+    }
+}
+exports.getOrientedCigar = getOrientedCigar;
+function getOrientedMismatches(flip, cigar) {
+    const p = parseCigar(cigar);
+    return cigarToMismatches(flip ? getOrientedCigar(flip, p) : p);
+}
+exports.getOrientedMismatches = getOrientedMismatches;
+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;
+}
+exports.getLengthOnRef = getLengthOnRef;
+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;
+}
+exports.getLength = getLength;
+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;
+}
+exports.getLengthSansClipping = getLengthSansClipping;
+function getClip(cigar, strand) {
+    return strand === -1
+        ? +(cigar.match(startClip) || [])[1] || 0
+        : +(cigar.match(endClip) || [])[1] || 0;
+}
+exports.getClip = getClip;
+function getTag(f, tag) {
+    const tags = f.get('tags');
+    return tags ? tags[tag] : f.get(tag);
+}
+exports.getTag = getTag;
+// 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
+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,
+            },
+        };
+    })) || []);
+}
+exports.featurizeSA = featurizeSA;
+//# sourceMappingURL=index.js.map

package/dist/MismatchParser/index.js.map

@@ -0,0 +1 @@
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package/dist/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<{}>;
+}