@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -8,33 +8,13 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const operators_1 = require("rxjs/operators");
+const generateCoverageBins_1 = __importDefault(require("./generateCoverageBins"));
 const util_1 = require("../util");
-const MismatchParser_1 = require("../BamAdapter/MismatchParser");
-function mismatchLen(mismatch) {
-    return !isInterbase(mismatch.type) ? mismatch.length : 1;
-}
-function isInterbase(type) {
-    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
-}
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function inc(bin, strand, type, field) {
-    let thisBin = bin[type][field];
-    if (thisBin === undefined) {
-        thisBin = bin[type][field] = {
-            total: 0,
-            '-1': 0,
-            '0': 0,
-            '1': 0,
-        };
-    }
-    thisBin.total++;
-    thisBin[strand]++;
-}
 class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a, _b;
         const subadapterConfig = this.getConf('subadapter');
-        const sequenceConf = this.getConf(['subadapter', 'sequenceAdapter']);
+        const sequenceConf = subadapterConfig.sequenceAdapter;
         const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, subadapterConfig));
         const sequenceAdapter = sequenceConf
             ? await ((_b = this.getSubAdapter) === null || _b === void 0 ? void 0 : _b.call(this, sequenceConf))
@@ -61,7 +41,7 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .getFeatures(region, opts)
                 .pipe((0, operators_1.toArray)())
                 .toPromise();
-            const { bins, skipmap } = await this.generateCoverageBins(feats, region, opts);
+            const { bins, skipmap } = await (0, generateCoverageBins_1.default)(feats, region, opts, arg => this.fetchSequence(arg));
             bins.forEach((bin, index) => {
                 const start = region.start + index;
                 observer.next(new simpleFeature_1.default({
@@ -101,165 +81,6 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return subadapter.getRefNames(opts);
     }
     freeResources( /* { region } */) { }
-    async generateCoverageBins(features, region, opts) {
-        var _a;
-        const { colorBy } = opts;
-        const binMax = Math.ceil(region.end - region.start);
-        const skipmap = {};
-        const regionSeq = features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
-            ? await this.fetchSequence(region)
-            : undefined;
-        const bins = [];
-        for (let i = 0; i < features.length; i++) {
-            const feature = features[i];
-            const fstart = feature.get('start');
-            const fend = feature.get('end');
-            const fstrand = feature.get('strand');
-            for (let j = fstart; j < fend + 1; j++) {
-                const i = j - region.start;
-                if (i >= 0 && i < binMax) {
-                    if (bins[i] === undefined) {
-                        bins[i] = {
-                            total: 0,
-                            all: 0,
-                            ref: 0,
-                            '-1': 0,
-                            '0': 0,
-                            '1': 0,
-                            lowqual: {},
-                            cov: {},
-                            delskips: {},
-                            noncov: {},
-                        };
-                    }
-                    if (j !== fend) {
-                        bins[i].total++;
-                        bins[i].all++;
-                        bins[i].ref++;
-                        bins[i][fstrand]++;
-                    }
-                }
-            }
-            if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                const seq = feature.get('seq');
-                const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                const fend = feature.get('end');
-                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                    const mod = `mod_${type}`;
-                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                        const epos = pos + fstart - region.start;
-                        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                            const bin = bins[epos];
-                            if (bin) {
-                                inc(bin, fstrand, 'cov', mod);
-                            }
-                            else {
-                                console.warn('Undefined position in modifications snpcoverage encountered');
-                            }
-                        }
-                    }
-                });
-            }
-            // methylation based coloring takes into account both reference
-            // sequence CpG detection and reads
-            else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-                if (!regionSeq) {
-                    throw new Error('no region sequence detected, need sequenceAdapter configuration');
-                }
-                const seq = feature.get('seq');
-                const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-                const methBins = new Array(region.end - region.start).fill(0);
-                const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                    // we are processing methylation
-                    if (type === 'm') {
-                        for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                            const epos = pos + fstart - region.start;
-                            if (epos >= 0 && epos < methBins.length) {
-                                methBins[epos] = 1;
-                            }
-                        }
-                    }
-                });
-                for (let j = fstart; j < fend; j++) {
-                    const i = j - region.start;
-                    if (i >= 0 && i < bins.length - 1) {
-                        const l1 = regionSeq[i].toLowerCase();
-                        const l2 = regionSeq[i + 1].toLowerCase();
-                        const bin = bins[i];
-                        const bin1 = bins[i + 1];
-                        // color
-                        if (l1 === 'c' && l2 === 'g') {
-                            if (methBins[i] || methBins[i + 1]) {
-                                inc(bin, fstrand, 'cov', 'meth');
-                                inc(bin1, fstrand, 'cov', 'meth');
-                                bins[i].ref--;
-                                bins[i][fstrand]--;
-                                bins[i + 1].ref--;
-                                bins[i + 1][fstrand]--;
-                            }
-                            else {
-                                inc(bin, fstrand, 'cov', 'unmeth');
-                                inc(bin1, fstrand, 'cov', 'unmeth');
-                                bins[i].ref--;
-                                bins[i][fstrand]--;
-                                bins[i + 1].ref--;
-                                bins[i + 1][fstrand]--;
-                            }
-                        }
-                    }
-                }
-            }
-            // normal SNP based coloring
-            const mismatches = feature.get('mismatches') || [];
-            const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-            for (let i = 0; i < mismatches.length; i++) {
-                const mismatch = mismatches[i];
-                const mstart = fstart + mismatch.start;
-                const mlen = mismatchLen(mismatch);
-                const mend = mstart + mlen;
-                for (let j = mstart; j < mstart + mlen; j++) {
-                    const epos = j - region.start;
-                    if (epos >= 0 && epos < bins.length) {
-                        const bin = bins[epos];
-                        const { base, type } = mismatch;
-                        const interbase = isInterbase(type);
-                        if (!interbase) {
-                            bin.ref--;
-                            bin[fstrand]--;
-                        }
-                        else {
-                            inc(bin, fstrand, 'noncov', type);
-                        }
-                        if (type === 'deletion' || type === 'skip') {
-                            inc(bin, fstrand, 'delskips', type);
-                            bin.total--;
-                        }
-                        else if (!interbase && colorSNPs) {
-                            inc(bin, fstrand, 'cov', base);
-                            bin.refbase = mismatch.altbase;
-                        }
-                    }
-                }
-                if (mismatch.type === 'skip') {
-                    const hash = `${mstart}_${mend}_${fstrand}`;
-                    if (skipmap[hash] === undefined) {
-                        skipmap[hash] = {
-                            feature: feature,
-                            start: mstart,
-                            end: mend,
-                            strand: fstrand,
-                            xs: (0, util_1.getTag)(feature, 'XS') || (0, util_1.getTag)(feature, 'TS'),
-                            score: 0,
-                        };
-                    }
-                    skipmap[hash].score++;
-                }
-            }
-        }
-        return { bins, skipmap };
-    }
 }
 exports.default = SNPCoverageAdapter;
 const { capabilities } = SNPCoverageAdapter;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map

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package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -0,0 +1,53 @@
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default function generateCoverageBins(features: Feature[], region: Region, opts: {
+    bpPerPx?: number;
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
+    bins: {
+        refbase?: string | undefined;
+        total: number;
+        all: number;
+        ref: number;
+        '-1': 0;
+        '0': 0;
+        '1': 0;
+        lowqual: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        cov: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        delskips: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+        noncov: {
+            total: number;
+            strands: {
+                [key: string]: number;
+            };
+        };
+    }[];
+    skipmap: {
+        [key: string]: {
+            score: number;
+            feature: unknown;
+            start: number;
+            end: number;
+            strand: number;
+            xs: string;
+        };
+    };
+}>;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -0,0 +1,185 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const util_1 = require("../util");
+const MismatchParser_1 = require("../MismatchParser");
+function mismatchLen(mismatch) {
+    return !isInterbase(mismatch.type) ? mismatch.length : 1;
+}
+function isInterbase(type) {
+    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function inc(bin, strand, type, field) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            total: 0,
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.total++;
+    thisBin[strand]++;
+}
+async function generateCoverageBins(features, region, opts, fetchSequence) {
+    var _a;
+    const { colorBy } = opts;
+    const binMax = Math.ceil(region.end - region.start);
+    const skipmap = {};
+    const regionSeq = features.length && (0, util_1.shouldFetchReferenceSequence)((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
+        ? await fetchSequence(region)
+        : undefined;
+    const bins = [];
+    for (let i = 0; i < features.length; i++) {
+        const feature = features[i];
+        const fstart = feature.get('start');
+        const fend = feature.get('end');
+        const fstrand = feature.get('strand');
+        for (let j = fstart; j < fend + 1; j++) {
+            const i = j - region.start;
+            if (i >= 0 && i < binMax) {
+                if (bins[i] === undefined) {
+                    bins[i] = {
+                        total: 0,
+                        all: 0,
+                        ref: 0,
+                        '-1': 0,
+                        '0': 0,
+                        '1': 0,
+                        lowqual: {},
+                        cov: {},
+                        delskips: {},
+                        noncov: {},
+                    };
+                }
+                if (j !== fend) {
+                    bins[i].total++;
+                    bins[i].all++;
+                    bins[i].ref++;
+                    bins[i][fstrand]++;
+                }
+            }
+        }
+        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+            const seq = feature.get('seq');
+            const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+            const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+            const fend = feature.get('end');
+            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                const mod = `mod_${type}`;
+                for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                    const epos = pos + fstart - region.start;
+                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                        const bin = bins[epos];
+                        if (bin) {
+                            inc(bin, fstrand, 'cov', mod);
+                        }
+                        else {
+                            console.warn('Undefined position in modifications snpcoverage encountered');
+                        }
+                    }
+                }
+            });
+        }
+        // methylation based coloring takes into account both reference
+        // sequence CpG detection and reads
+        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+            if (!regionSeq) {
+                throw new Error('no region sequence detected, need sequenceAdapter configuration');
+            }
+            const seq = feature.get('seq');
+            const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
+            const methBins = new Array(region.end - region.start).fill(0);
+            const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                // we are processing methylation
+                if (type === 'm') {
+                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
+                        const epos = pos + fstart - region.start;
+                        if (epos >= 0 && epos < methBins.length) {
+                            methBins[epos] = 1;
+                        }
+                    }
+                }
+            });
+            for (let j = fstart; j < fend; j++) {
+                const i = j - region.start;
+                if (i >= 0 && i < bins.length - 1) {
+                    const l1 = regionSeq[i].toLowerCase();
+                    const l2 = regionSeq[i + 1].toLowerCase();
+                    const bin = bins[i];
+                    const bin1 = bins[i + 1];
+                    // color
+                    if (l1 === 'c' && l2 === 'g') {
+                        if (methBins[i] || methBins[i + 1]) {
+                            inc(bin, fstrand, 'cov', 'meth');
+                            inc(bin1, fstrand, 'cov', 'meth');
+                            bins[i].ref--;
+                            bins[i][fstrand]--;
+                            bins[i + 1].ref--;
+                            bins[i + 1][fstrand]--;
+                        }
+                        else {
+                            inc(bin, fstrand, 'cov', 'unmeth');
+                            inc(bin1, fstrand, 'cov', 'unmeth');
+                            bins[i].ref--;
+                            bins[i][fstrand]--;
+                            bins[i + 1].ref--;
+                            bins[i + 1][fstrand]--;
+                        }
+                    }
+                }
+            }
+        }
+        // normal SNP based coloring
+        const mismatches = feature.get('mismatches') || [];
+        const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
+        for (let i = 0; i < mismatches.length; i++) {
+            const mismatch = mismatches[i];
+            const mstart = fstart + mismatch.start;
+            const mlen = mismatchLen(mismatch);
+            const mend = mstart + mlen;
+            for (let j = mstart; j < mstart + mlen; j++) {
+                const epos = j - region.start;
+                if (epos >= 0 && epos < bins.length) {
+                    const bin = bins[epos];
+                    const { base, type } = mismatch;
+                    const interbase = isInterbase(type);
+                    if (!interbase) {
+                        bin.ref--;
+                        bin[fstrand]--;
+                    }
+                    else {
+                        inc(bin, fstrand, 'noncov', type);
+                    }
+                    if (type === 'deletion' || type === 'skip') {
+                        inc(bin, fstrand, 'delskips', type);
+                        bin.total--;
+                    }
+                    else if (!interbase && colorSNPs) {
+                        inc(bin, fstrand, 'cov', base);
+                        bin.refbase = mismatch.altbase;
+                    }
+                }
+            }
+            if (mismatch.type === 'skip') {
+                const hash = `${mstart}_${mend}_${fstrand}`;
+                if (skipmap[hash] === undefined) {
+                    skipmap[hash] = {
+                        feature: feature,
+                        start: mstart,
+                        end: mend,
+                        strand: fstrand,
+                        xs: (0, util_1.getTag)(feature, 'XS') || (0, util_1.getTag)(feature, 'TS'),
+                        score: 0,
+                    };
+                }
+                skipmap[hash].score++;
+            }
+        }
+    }
+    return { bins, skipmap };
+}
+exports.default = generateCoverageBins;
+//# sourceMappingURL=generateCoverageBins.js.map

package/dist/SNPCoverageAdapter/generateCoverageBins.js.map

@@ -0,0 +1 @@
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package/dist/SNPCoverageAdapter/index.js

@@ -33,11 +33,9 @@ function default_1(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'SNPCoverageAdapter',
+            displayName: 'SNPCoverage adapter',
             adapterMetadata: {
-                category: null,
-                displayName: null,
                 hiddenFromGUI: true,
-                description: null,
             },
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
             configSchema: configSchema_1.default,

package/dist/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AACzC,6DAAmD;AAEnD,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,eAAe,EAAE;gBACf,QAAQ,EAAE,IAAI;gBACd,WAAW,EAAE,IAAI;gBACjB,aAAa,EAAE,IAAI;gBACnB,WAAW,EAAE,IAAI;aAClB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,sBAAsB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY,EAAZ,sBAAY;YACZ,mBAAmB,EAAE,iCAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,4BAgBC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AACzC,6DAAmD;AAEnD,mBAAyB,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,qBAAqB;YAClC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,sBAAsB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY,EAAZ,sBAAY;YACZ,mBAAmB,EAAE,iCAAY;SAClC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,4BAcC"}

package/dist/index.d.ts

@@ -1,8 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import * as MismatchParser from './BamAdapter/MismatchParser';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
 import { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory } from './LinearPileupDisplay';
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+import * as MismatchParser from './MismatchParser';
 export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -28,8 +28,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MismatchParser = exports.linearPileupDisplayStateModelFactory = exports.linearPileupDisplayConfigSchemaFactory = void 0;
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const MismatchParser = __importStar(require("./BamAdapter/MismatchParser"));
-exports.MismatchParser = MismatchParser;
 const CramAdapter_1 = __importDefault(require("./CramAdapter"));
 const BamAdapter_1 = __importDefault(require("./BamAdapter"));
 const HtsgetBamAdapter_1 = __importDefault(require("./HtsgetBamAdapter"));
@@ -38,13 +36,17 @@ const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
 const LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
+const LinearReadArcsDisplay_1 = __importDefault(require("./LinearReadArcsDisplay"));
+const LinearReadCloudDisplay_1 = __importDefault(require("./LinearReadCloudDisplay"));
+const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
+const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
+const PileupRPC_1 = __importDefault(require("./PileupRPC"));
+const GuessAlignmentsTypes_1 = __importDefault(require("./GuessAlignmentsTypes"));
 const LinearPileupDisplay_1 = __importStar(require("./LinearPileupDisplay"));
 Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayStateModelFactory; } });
 Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return LinearPileupDisplay_1.linearPileupDisplayConfigSchemaFactory; } });
-const AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
-const AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
-const rpcMethods_1 = require("./PileupRPC/rpcMethods");
-const tracks_1 = require("@jbrowse/core/util/tracks");
+const MismatchParser = __importStar(require("./MismatchParser"));
+exports.MismatchParser = MismatchParser;
 class AlignmentsPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -61,62 +63,14 @@ class AlignmentsPlugin extends Plugin_1.default {
             SNPCoverageAdapter_1.default,
             HtsgetBamAdapter_1.default,
             PileupRenderer_1.default,
+            PileupRPC_1.default,
             SNPCoverageRenderer_1.default,
+            LinearReadArcsDisplay_1.default,
+            LinearReadCloudDisplay_1.default,
             LinearAlignmentsDisplay_1.default,
             AlignmentsFeatureDetail_1.default,
+            GuessAlignmentsTypes_1.default,
         ].map(f => f(pluginManager));
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.cram$/i;
-                const adapterName = 'CramAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const obj = {
-                    type: adapterName,
-                    cramLocation: file,
-                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.bam$/i;
-                const adapterName = 'BamAdapter';
-                const fileName = (0, tracks_1.getFileName)(file);
-                const indexName = index && (0, tracks_1.getFileName)(index);
-                const obj = {
-                    type: adapterName,
-                    bamLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                    },
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => {
-                if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
-                    return 'AlignmentsTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pluginManager));
-        pluginManager.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pluginManager));
     }
 }
 exports.default = AlignmentsPlugin;

package/dist/index.js.map

@@ -1 +1 @@
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