@jbrowse/plugin-alignments 2.2.1 → 2.3.0

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

@@ -1,6 +1,6 @@
 /// <reference types="react" />
-import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
+import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
 /**
  * #stateModel LinearSNPCoverageDisplay
  * extends `LinearWiggleDisplay`
@@ -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;
@@ -43,9 +47,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
-         * #action
-         */
+        setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
@@ -54,7 +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;
@@ -68,9 +72,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
-     * #getter
-     */
+    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -150,7 +152,9 @@ 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>>;
         }, {
@@ -172,10 +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;
 } & {
@@ -243,12 +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: {
@@ -289,14 +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;
@@ -310,7 +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;
@@ -343,7 +346,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
-    modificationTagMap: import("mobx").ObservableMap<any, any>;
+    modificationTagMap: Record<string, string> | undefined;
 } & {
     /**
      * #action

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
+const clone_1 = __importDefault(require("clone"));
 const mobx_1 = require("mobx");
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
@@ -39,12 +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
          */
@@ -54,7 +50,7 @@ function stateModelFactory(pluginManager, configSchema) {
         })),
     }))
         .volatile(() => ({
-        modificationTagMap: mobx_1.observable.map({}),
+        modificationTagMap: undefined,
     }))
         .actions(self => ({
         /**
@@ -81,12 +77,14 @@ function stateModelFactory(pluginManager, configSchema) {
         updateModificationColorMap(uniqueModifications) {
             const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
             let i = 0;
+            const newMap = (0, clone_1.default)(self.modificationTagMap) || {};
             uniqueModifications.forEach(value => {
-                if (!self.modificationTagMap.has(value)) {
+                if (!newMap[value]) {
                     const newColor = colorPalette[i++];
-                    self.modificationTagMap.set(value, newColor);
+                    newMap[value] = newColor;
                 }
             });
+            self.modificationTagMap = newMap;
         },
     }))
         .views(self => {
@@ -132,8 +130,7 @@ function stateModelFactory(pluginManager, configSchema) {
             get modificationsReady() {
                 var _a;
                 return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
-                    ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
-                        .length > 0
+                    ? self.modificationTagMap !== undefined
                     : true;
             },
             /**
@@ -145,7 +142,7 @@ function stateModelFactory(pluginManager, configSchema) {
                 return {
                     ...superProps,
                     notReady: superProps.notReady || !this.modificationsReady,
-                    modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
+                    modificationTagMap: modificationTagMap,
                     // must use getSnapshot because otherwise changes to e.g. just the
                     // colorBy.type are not read
                     colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,

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<{}>;
+}

package/dist/PileupRPC/base.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const util_1 = require("@jbrowse/core/util");
+// specialized get features to return limited data about alignments
+class PileupBaseRPC extends RpcMethodType_1.default {
+    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 (0, util_1.renameRegionsIfNeeded)(assemblyManager, args);
+        return super.serializeArguments(renamedArgs, rpcDriver);
+    }
+}
+exports.default = PileupBaseRPC;
+//# sourceMappingURL=base.js.map

package/dist/PileupRPC/base.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"base.js","sourceRoot":"","sources":["../../src/PileupRPC/base.ts"],"names":[],"mappings":";;;;;AAAA,sGAA6E;AAC7E,6CAA0D;AAG1D,mEAAmE;AACnE,MAA8B,aAAc,SAAQ,uBAAa;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,IAAA,4BAAqB,EAAC,eAAe,EAAE,IAAI,CAAC,CAAA;QAEtE,OAAO,KAAK,CAAC,kBAAkB,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;IACzD,CAAC;CACF;AAlBD,gCAkBC"}

package/dist/PileupRPC/index.d.ts

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

package/dist/PileupRPC/index.js

@@ -0,0 +1,9 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const rpcMethods_1 = require("./rpcMethods");
+exports.default = (pm) => {
+    pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
+    pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
+    pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
+};
+//# sourceMappingURL=index.js.map

package/dist/PileupRPC/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRPC/index.ts"],"names":[],"mappings":";;AACA,6CAIqB;AAErB,kBAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,uCAA0B,CAAC,EAAE,CAAC,CAAC,CAAA;IACzD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,0CAA6B,CAAC,EAAE,CAAC,CAAC,CAAA;IAC5D,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC,IAAI,qCAAwB,CAAC,EAAE,CAAC,CAAC,CAAA;AACzD,CAAC,CAAA"}

package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts

@@ -0,0 +1,14 @@
+import { Region } from '@jbrowse/core/util';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import PileupBaseRPC from '../base';
+export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
+    name: string;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriver: string): Promise<string[]>;
+}

package/dist/PileupRPC/methods/GetGlobalValueForTag.js

@@ -0,0 +1,29 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const operators_1 = require("rxjs/operators");
+const base_1 = __importDefault(require("../base"));
+const util_1 = require("../../util");
+class PileupGetGlobalValueForTag extends base_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetGlobalValueForTag';
+    }
+    async execute(args, rpcDriver) {
+        const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
+        const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
+        return [
+            ...new Set(featuresArray
+                .map(feature => (0, util_1.getTag)(feature, tag))
+                .filter(f => f !== undefined)
+                .map(f => `${f}`)),
+        ];
+    }
+}
+exports.default = PileupGetGlobalValueForTag;
+//# sourceMappingURL=GetGlobalValueForTag.js.map

package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,mDAAmC;AACnC,qCAAmC;AAEnC,MAAqB,0BAA2B,SAAQ,cAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,SAAS,EAAE,CAAA;QAChE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,IAAA,aAAM,EAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF;AAhCD,6CAgCC"}

package/dist/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -0,0 +1,25 @@
+import { Region } from '@jbrowse/core/util';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import { ReducedFeature } from '../../shared/fetchChains';
+import PileupBaseRPC from '../base';
+export default class PileupGetReducedFeatures extends PileupBaseRPC {
+    name: string;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriver: string): Promise<{
+        chains: ReducedFeature[][];
+        stats: {
+            upper: number;
+            lower: number;
+            avg: number;
+            sd: number;
+        } | undefined;
+        hasPaired: boolean;
+        containsNoTransferables: boolean;
+    }>;
+}

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -0,0 +1,61 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const util_1 = require("@jbrowse/core/util");
+const operators_1 = require("rxjs/operators");
+// locals
+const util_2 = require("../util");
+const base_1 = __importDefault(require("../base"));
+const util_3 = require("../../util");
+// specialized get features to return limited data about alignments
+class PileupGetReducedFeatures extends base_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetReducedFeatures';
+    }
+    async execute(args, rpcDriver) {
+        const des = await this.deserializeArguments(args, rpcDriver);
+        const { adapterConfig, sessionId, regions } = des;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const featuresArray = await dataAdapter
+            .getFeaturesInMultipleRegions(regions, des)
+            .pipe((0, operators_1.toArray)())
+            .toPromise();
+        const reduced = (0, util_1.dedupe)(featuresArray.map(f => ({
+            id: f.id(),
+            refName: f.get('refName'),
+            name: f.get('name'),
+            start: f.get('start'),
+            strand: f.get('strand'),
+            end: f.get('end'),
+            flags: f.get('flags'),
+            tlen: f.get('template_length'),
+            pair_orientation: f.get('pair_orientation'),
+            next_ref: f.get('next_ref'),
+            next_pos: f.get('next_pos'),
+            clipPos: f.get('clipPos'),
+            SA: (0, util_3.getTag)(f, 'SA'),
+        })), f => f.id);
+        const filtered = (0, util_2.filterForPairs)(reduced);
+        const stats = filtered.length ? (0, util_2.getInsertSizeStats)(filtered) : undefined;
+        const chains = {};
+        // pair features
+        reduced.forEach(f => {
+            if (!chains[f.name]) {
+                chains[f.name] = [];
+            }
+            chains[f.name].push(f);
+        });
+        return {
+            chains: Object.values(chains),
+            stats,
+            hasPaired: !!stats,
+            containsNoTransferables: true,
+        };
+    }
+}
+exports.default = PileupGetReducedFeatures;
+//# sourceMappingURL=GetReducedFeatures.js.map

package/dist/PileupRPC/methods/GetReducedFeatures.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AACzE,6CAAmD;AAGnD,8CAAwC;AAExC,SAAS;AACT,kCAA4D;AAE5D,mDAAmC;AACnC,qCAAmC;AAEnC,mEAAmE;AACnE,MAAqB,wBAAyB,SAAQ,cAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA6DnC,CAAC;IA3DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,WAAW;aACpC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC;aAC1C,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;aACf,SAAS,EAAE,CAAA;QAEd,MAAM,OAAO,GAAG,IAAA,aAAM,EACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,IAAA,aAAM,EAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,IAAA,qBAAc,EAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,IAAA,yBAAkB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF;AA9DD,2CA8DC"}

package/dist/PileupRPC/methods/GetVisibleModifications.d.ts

@@ -0,0 +1,14 @@
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import { Region } from '@jbrowse/core/util';
+import PileupBaseRPC from '../base';
+export default class PileupGetVisibleModifications extends PileupBaseRPC {
+    name: string;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriver: string): Promise<string[]>;
+}