@jbrowse/plugin-alignments 2.2.2 → 2.3.1

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[]>;
+}

package/dist/PileupRPC/methods/GetVisibleModifications.js

@@ -0,0 +1,32 @@
+"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");
+// locals
+const MismatchParser_1 = require("../../MismatchParser");
+const base_1 = __importDefault(require("../base"));
+const util_1 = require("../../util");
+class PileupGetVisibleModifications extends base_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'PileupGetVisibleModifications';
+    }
+    async execute(args, rpcDriver) {
+        const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const featuresArray = await dataAdapter
+            .getFeaturesInMultipleRegions(regions)
+            .pipe((0, operators_1.toArray)())
+            .toPromise();
+        const uniqueValues = new Set();
+        featuresArray.forEach(f => {
+            (0, MismatchParser_1.getModificationTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));
+        });
+        return [...uniqueValues];
+    }
+}
+exports.default = PileupGetVisibleModifications;
+//# sourceMappingURL=GetVisibleModifications.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AAExC,SAAS;AACT,yDAA2D;AAC3D,mDAAmC;AACnC,qCAAsC;AAEtC,MAAqB,6BAA8B,SAAQ,cAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IAgCxC,CAAC;IA9BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,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,CAAC;aACrC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;aACf,SAAS,EAAE,CAAA;QAEd,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,IAAA,qCAAoB,EAAC,IAAA,gBAAS,EAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF;AAjCD,gDAiCC"}

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,34 +1,4 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { Region } from '@jbrowse/core/util';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-export declare class PileupGetGlobalValueForTag extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
-export declare class PileupGetVisibleModifications extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
+import PileupGetReducedFeatures from './methods/GetReducedFeatures';
+import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
+import PileupGetVisibleModifications from './methods/GetVisibleModifications';
+export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };

package/dist/PileupRPC/rpcMethods.js

@@ -3,81 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.PileupGetVisibleModifications = exports.PileupGetGlobalValueForTag = void 0;
-const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-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 MismatchParser_1 = require("../BamAdapter/MismatchParser");
-class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetGlobalValueForTag';
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        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, rpcDriverClassName);
-    }
-    async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
-        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions, tag } = deArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
-            .dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
-        const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
-        const uniqueValues = new Set();
-        featuresArray.forEach(feature => {
-            const tags = feature.get('tags');
-            const val = tags ? tags[tag] : feature.get(tag);
-            if (val !== undefined) {
-                uniqueValues.add(`${val}`);
-            }
-        });
-        return [...uniqueValues];
-    }
-}
-exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
-class PileupGetVisibleModifications extends RpcMethodType_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetVisibleModifications';
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        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, rpcDriverClassName);
-    }
-    async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
-        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions } = deArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
-            .dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
-        const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
-        const uniqueValues = new Set();
-        featuresArray.forEach(feature => {
-            const val = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
-            if (val !== undefined) {
-                (0, MismatchParser_1.getModificationTypes)(val).forEach(t => uniqueValues.add(t));
-            }
-        });
-        return [...uniqueValues];
-    }
-}
-exports.PileupGetVisibleModifications = PileupGetVisibleModifications;
+exports.PileupGetGlobalValueForTag = exports.PileupGetVisibleModifications = exports.PileupGetReducedFeatures = void 0;
+const GetReducedFeatures_1 = __importDefault(require("./methods/GetReducedFeatures"));
+exports.PileupGetReducedFeatures = GetReducedFeatures_1.default;
+const GetGlobalValueForTag_1 = __importDefault(require("./methods/GetGlobalValueForTag"));
+exports.PileupGetGlobalValueForTag = GetGlobalValueForTag_1.default;
+const GetVisibleModifications_1 = __importDefault(require("./methods/GetVisibleModifications"));
+exports.PileupGetVisibleModifications = GetVisibleModifications_1.default;
 //# sourceMappingURL=rpcMethods.js.map

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,sFAAmE;AAKjE,mCALK,4BAAwB,CAKL;AAJ1B,0FAAuE;AAMrE,qCANK,8BAA0B,CAML;AAL5B,gGAA6E;AAI3E,wCAJK,iCAA6B,CAIL"}

package/dist/PileupRPC/util.d.ts

@@ -0,0 +1,8 @@
+import { ReducedFeature } from '../shared/fetchChains';
+export declare function getInsertSizeStats(features: ReducedFeature[]): {
+    upper: number;
+    lower: number;
+    avg: number;
+    sd: number;
+};
+export declare function filterForPairs(features: ReducedFeature[]): ReducedFeature[];

package/dist/PileupRPC/util.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.filterForPairs = exports.getInsertSizeStats = void 0;
+function getInsertSizeStats(features) {
+    const filtered = features.map(f => Math.abs(f.tlen));
+    const sum = filtered.reduce((a, b) => a + b, 0);
+    const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0);
+    const total = filtered.length;
+    const avg = sum / total;
+    const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total));
+    const upper = avg + 4 * sd;
+    const lower = avg - 3 * sd;
+    return { upper, lower, avg, sd };
+}
+exports.getInsertSizeStats = getInsertSizeStats;
+function filterForPairs(features) {
+    return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
+}
+exports.filterForPairs = filterForPairs;
+//# sourceMappingURL=util.js.map

package/dist/PileupRPC/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/PileupRPC/util.ts"],"names":[],"mappings":";;;AAEA,SAAgB,kBAAkB,CAAC,QAA0B;IAC3D,MAAM,QAAQ,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;IACpD,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;IAC/C,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAA;IAC7B,MAAM,GAAG,GAAG,GAAG,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,GAAG,KAAK,CAAC,CAAC,CAAA;IAClE,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,GAAG,EAAE,CAAA;IAC1B,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,GAAG,EAAE,CAAA;IAC1B,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;AAClC,CAAC;AAVD,gDAUC;AAED,SAAgB,cAAc,CAAC,QAA0B;IACvD,OAAO,QAAQ,CAAC,MAAM,CACpB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAC1D,CAAA;AACH,CAAC;AAJD,wCAIC"}

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -57,8 +57,8 @@ export default class PileupRenderer extends BoxRendererType {
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
-        reversed?: boolean | undefined;
         refName: string;
+        reversed?: boolean | undefined;
         assemblyName: string;
     };
     colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;

package/dist/PileupRenderer/PileupRenderer.js

@@ -33,7 +33,7 @@ const offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils"
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const configuration_1 = require("@jbrowse/core/configuration");
 // locals
-const MismatchParser_1 = require("../BamAdapter/MismatchParser");
+const MismatchParser_1 = require("../MismatchParser");
 const sortUtil_1 = require("./sortUtil");
 const util_2 = require("../util");
 const PileupLayoutSession_1 = require("./PileupLayoutSession");
@@ -169,7 +169,7 @@ class PileupRenderer extends BoxRendererType_1.default {
     }
     colorByInsertSize(feature, _config) {
         return feature.get('is_paired') &&
-            feature.get('seq_id') !== feature.get('next_seq_id')
+            feature.get('refName') !== feature.get('next_ref')
             ? '#555'
             : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`;
     }
@@ -189,7 +189,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                     ? 'color_rev_missing_mate'
                     : 'color_fwd_missing_mate';
             }
-            if (feature.get('seq_id') === feature.get('next_seq_id')) {
+            if (feature.get('refName') === feature.get('next_refName')) {
                 return strand * flipper === 1
                     ? 'color_rev_strand_not_proper'
                     : 'color_fwd_strand_not_proper';
@@ -586,7 +586,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 }
             }
             else if (mismatch.type === 'deletion' && drawIndels) {
-                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth, colorForBase.deletion);
+                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
                 const txt = `${mismatch.length}`;
                 const rwidth = (0, util_1.measureText)(txt, 10);
                 if (widthPx >= rwidth && heightPx >= heightLim) {
@@ -598,7 +598,7 @@ class PileupRenderer extends BoxRendererType_1.default {
                 ctx.fillStyle = 'purple';
                 const pos = leftPx + extraHorizontallyFlippedOffset;
                 const len = +mismatch.base || mismatch.length;
-                const insW = Math.max(minSubfeatureWidth / 2, Math.min(1.2, 1 / bpPerPx));
+                const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
                 if (len < 10) {
                     fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
                     if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {