@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/CramAdapter/configSchema.js

@@ -1,28 +1,50 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = (pluginManager) => {
-    return mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('CramAdapter', {
-        fetchSizeLimit: {
-            type: 'number',
-            defaultValue: 3000000,
+/**
+ * #config CramAdapter
+ * used to configure CRAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: 'number',
+        description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
+        defaultValue: 3000000,
+    },
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram',
+            locationType: 'UriLocation',
         },
-        cramLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram',
-                locationType: 'UriLocation',
-            },
+    },
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram.crai',
+            locationType: 'UriLocation',
         },
-        craiLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram.crai',
-                locationType: 'UriLocation',
-            },
-        },
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true }));
-};
+    },
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: 'frozen',
+        description: 'sequence data adapter',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true });
+exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/CramAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AACA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,OAAO,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACrB,IAAA,mCAAmB,EACjB,aAAa,EACb;QACE,cAAc,EAAE;YACd,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,OAAS;SACxB;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,kBAAkB;gBACvB,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,YAAY,EAAE;YACZ,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,uBAAuB;gBAC5B,YAAY,EAAE,aAAa;aAC5B;SACF;QACD,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,aAAa,EACb;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8FAA8F;QAChG,YAAY,EAAE,OAAS;KACxB;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,kBAAkB;YACvB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,uBAAuB;YAC5B,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uBAAuB;QACpC,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,YAAY,CAAA"}

package/dist/CramAdapter/index.js

@@ -30,10 +30,12 @@ const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'CramAdapter',
-        configSchema: pluginManager.load(configSchema_1.default),
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'CramAdapter',
+            configSchema: configSchema_1.default,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/dist/CramAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,sBAAa,CAAC;QAC/C,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,YAAY,EAAZ,sBAAY;YACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACpE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/CramAdapter/util.d.ts

@@ -0,0 +1,18 @@
+import { CramRecord } from '@gmod/cram';
+type ReadFeatures = CramRecord['readFeatures'];
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string | undefined;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
+export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
+    seq: string;
+    start: number;
+}): string;
+export {};

package/dist/CramAdapter/util.js

@@ -0,0 +1,241 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readFeaturesToCIGAR = exports.readFeaturesToMismatches = void 0;
+function readFeaturesToMismatches(readFeatures, start, qual) {
+    if (!readFeatures) {
+        return [];
+    }
+    const mismatches = new Array(readFeatures.length);
+    let j = 0;
+    let insLen = 0;
+    let refPos = 0;
+    let sublen = 0;
+    let lastPos = start;
+    for (let i = 0; i < readFeatures.length; i++) {
+        const f = readFeatures[i];
+        const { code, pos, data, sub, ref } = f;
+        sublen = refPos - lastPos;
+        lastPos = refPos;
+        if (sublen && insLen > 0) {
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${insLen}`,
+                length: 0,
+            };
+            insLen = 0;
+        }
+        refPos = f.refPos - 1 - start;
+        if (code === 'X') {
+            // substitution
+            mismatches[j++] = {
+                start: refPos,
+                length: 1,
+                base: sub,
+                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
+                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
+                type: 'mismatch',
+            };
+        }
+        else if (code === 'I') {
+            // insertion
+            mismatches[j++] = {
+                start: refPos,
+                type: 'insertion',
+                base: `${data.length}`,
+                length: 0,
+            };
+        }
+        else if (code === 'N') {
+            // reference skip
+            mismatches[j++] = {
+                type: 'skip',
+                length: data,
+                start: refPos,
+                base: 'N',
+            };
+        }
+        else if (code === 'S') {
+            // soft clip
+            const len = data.length;
+            mismatches[j++] = {
+                start: refPos,
+                type: 'softclip',
+                base: `S${len}`,
+                cliplen: len,
+                length: 1,
+            };
+        }
+        else if (code === 'P') {
+            // padding
+        }
+        else if (code === 'H') {
+            // hard clip
+            const len = data;
+            mismatches[j++] = {
+                start: refPos,
+                type: 'hardclip',
+                base: `H${len}`,
+                cliplen: len,
+                length: 1,
+            };
+        }
+        else if (code === 'D') {
+            // deletion
+            mismatches[j++] = {
+                type: 'deletion',
+                length: data,
+                start: refPos,
+                base: '*',
+            };
+        }
+        else if (code === 'b') {
+            // stretch of bases
+        }
+        else if (code === 'q') {
+            // stretch of qual scores
+        }
+        else if (code === 'B') {
+            // a pair of [base, qual]
+        }
+        else if (code === 'i') {
+            // single-base insertion, we collect these if there are multiple in a row
+            // into a single insertion entry
+            insLen++;
+        }
+        else if (code === 'Q') {
+            // single quality value
+        }
+    }
+    if (sublen && insLen > 0) {
+        mismatches[j++] = {
+            start: refPos,
+            type: 'insertion',
+            base: `${insLen}`,
+            length: 0,
+        };
+        insLen = 0;
+    }
+    return mismatches.slice(0, j);
+}
+exports.readFeaturesToMismatches = readFeaturesToMismatches;
+function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
+    let seq = '';
+    let cigar = '';
+    let op = 'M';
+    let oplen = 0;
+    if (!refRegion) {
+        return '';
+    }
+    // not sure I should access these, but...
+    const ref = refRegion.seq;
+    const refStart = refRegion.start;
+    let lastPos = alignmentStart;
+    let sublen = 0;
+    let insLen = 0;
+    if (readFeatures !== undefined) {
+        for (let i = 0; i < readFeatures.length; i++) {
+            const { code, refPos, sub, data } = readFeatures[i];
+            sublen = refPos - lastPos;
+            seq += ref.substring(lastPos - refStart, refPos - refStart);
+            lastPos = refPos;
+            if (insLen > 0 && sublen) {
+                cigar += `${insLen}I`;
+                insLen = 0;
+            }
+            if (oplen && op !== 'M') {
+                cigar += oplen + op;
+                oplen = 0;
+            }
+            if (sublen) {
+                op = 'M';
+                oplen += sublen;
+            }
+            if (code === 'b') {
+                // An array of bases stored verbatim
+                const ret = data.split(',');
+                const added = String.fromCharCode(...ret);
+                seq += added;
+                lastPos += added.length;
+                oplen += added.length;
+            }
+            else if (code === 'B') {
+                // Single base (+ qual score)
+                seq += sub;
+                lastPos++;
+                oplen++;
+            }
+            else if (code === 'X') {
+                // Substitution
+                seq += sub;
+                lastPos++;
+                oplen++;
+            }
+            else if (code === 'D' || code === 'N') {
+                // Deletion or Ref Skip
+                lastPos += data;
+                if (oplen) {
+                    cigar += oplen + op;
+                }
+                cigar += data + code;
+                oplen = 0;
+            }
+            else if (code === 'I' || code === 'S') {
+                // Insertion or soft-clip
+                seq += data;
+                if (oplen) {
+                    cigar += oplen + op;
+                }
+                cigar += data.length + code;
+                oplen = 0;
+            }
+            else if (code === 'i') {
+                // Single base insertion
+                // seq += data
+                if (oplen) {
+                    cigar += oplen + op;
+                }
+                insLen++;
+                seq += data;
+                oplen = 0;
+            }
+            else if (code === 'P') {
+                // Padding
+                if (oplen) {
+                    cigar += oplen + op;
+                }
+                cigar += `${data}P`;
+            }
+            else if (code === 'H') {
+                // Hard clip
+                if (oplen) {
+                    cigar += oplen + op;
+                }
+                cigar += `${data}H`;
+                oplen = 0;
+            } // else q or Q
+        }
+    }
+    else {
+        sublen = readLen - seq.length;
+    }
+    if (seq.length !== readLen) {
+        sublen = readLen - seq.length;
+        seq += ref.substring(lastPos - refStart, lastPos - refStart + sublen);
+        if (oplen && op !== 'M') {
+            cigar += oplen + op;
+            oplen = 0;
+        }
+        op = 'M';
+        oplen += sublen;
+    }
+    if (sublen && insLen > 0) {
+        cigar += `${insLen}I`;
+    }
+    if (oplen) {
+        cigar += oplen + op;
+    }
+    return cigar;
+}
+exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
+//# sourceMappingURL=util.js.map

package/dist/CramAdapter/util.js.map

@@ -0,0 +1 @@
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package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -2,8 +2,11 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
-    protected configure(): Promise<{
+    protected configurePre(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+        sequenceAdapter: BaseFeatureDataAdapter;
+    } | {
+        bam: BamFile;
+        sequenceAdapter?: undefined;
     }>;
 }

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -4,29 +4,24 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bam_1 = require("@gmod/bam");
-const configuration_1 = require("@jbrowse/core/configuration");
 const BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
 class HtsgetBamAdapter extends BamAdapter_1.default {
-    async configure() {
-        if (!this.configured) {
-            const htsgetBase = (0, configuration_1.readConfObject)(this.config, 'htsgetBase');
-            const htsgetTrackId = (0, configuration_1.readConfObject)(this.config, 'htsgetTrackId');
-            const bam = new bam_1.HtsgetFile({
-                baseUrl: htsgetBase,
-                trackId: htsgetTrackId,
-            });
-            const adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-            if (adapterConfig && this.getSubAdapter) {
-                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => {
-                    return {
-                        bam,
-                        sequenceAdapter: dataAdapter,
-                    };
-                });
-            }
-            this.configured = Promise.resolve({ bam });
+    async configurePre() {
+        const htsgetBase = this.getConf('htsgetBase');
+        const htsgetTrackId = this.getConf('htsgetTrackId');
+        const bam = new bam_1.HtsgetFile({
+            baseUrl: htsgetBase,
+            trackId: htsgetTrackId,
+        });
+        const adapterConfig = this.getConf('sequenceAdapter');
+        if (adapterConfig && this.getSubAdapter) {
+            const adapter = await this.getSubAdapter(adapterConfig);
+            return {
+                bam,
+                sequenceAdapter: adapter.dataAdapter,
+            };
         }
-        return this.configured;
+        return { bam };
     }
 }
 exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAA+C;AAE/C,0EAAiD;AAEjD,MAAqB,gBAAiB,SAAQ,oBAAU;IAC5C,KAAK,CAAC,YAAY;QAC1B,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,GAAG,GAAG,IAAI,gBAAU,CAAC;YACzB,OAAO,EAAE,UAAU;YACnB,OAAO,EAAE,aAAa;SACvB,CAAuB,CAAA;QAExB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YACvD,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,OAAO,CAAC,WAAqC;aAC/D,CAAA;SACF;QACD,OAAO,EAAE,GAAG,EAAE,CAAA;IAChB,CAAC;CACF;AAnBD,mCAmBC"}

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,19 +1,36 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
+/**
+ * #config HtsgetBamAdapter
+ * Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
+    /**
+     * #slot
+     */
     htsgetBase: {
         type: 'string',
+        description: 'the base URL to fetch from',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     htsgetTrackId: {
         type: 'string',
+        description: 'the trackId, which is appended to the base URL',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
         type: 'frozen',
+        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+exports.default = HtsgetBamAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/HtsgetBamAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,gBAAgB,GAAG,IAAA,mCAAmB,EAC1C,kBAAkB,EAClB;IACE;;OAEG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4BAA4B;QACzC,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,gDAAgD;QAC7D,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,gBAAgB,CAAA"}

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
-const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     resizeHandle: {
         height: 2,

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
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package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -1,4 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
+declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
 export default configModelFactory;

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -2,13 +2,30 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const configModelFactory = (pluginManager) => {
-    const PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
-    const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
+/**
+ * #config LinearAlignmentsDisplay
+ * has a "pileup" sub-display, where you can see individual reads and a
+ * quantitative "snpcoverage" sub-display track showing SNP frequencies
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configModelFactory = (pm) => {
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
-        pileupDisplay: PileupDisplayConfigSchema,
-        snpCoverageDisplay: SNPCoverageDisplayConfigSchema,
-    }, { baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema, explicitlyTyped: true });
+        /**
+         * #slot
+         */
+        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
+        /**
+         * #slot
+         */
+        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+            .configSchema,
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
 };
 exports.default = configModelFactory;
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearAlignmentsDisplay/models/configSchema.js.map

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