@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/dist/PileupRenderer/PileupRenderer.js

@@ -95,7 +95,7 @@ class PileupRenderer extends BoxRendererType_1.default {
     }
     // get width and height of chars the height is an approximation: width
     // letter M is approximately the height
-    getCharWidthHeight(ctx) {
+    getCharWidthHeight() {
         const charWidth = (0, util_1.measureText)('A');
         const charHeight = (0, util_1.measureText)('M') - 2;
         return { charWidth, charHeight };
@@ -107,7 +107,7 @@ class PileupRenderer extends BoxRendererType_1.default {
         if (showSoftClip) {
             const mismatches = feature.get('mismatches');
             const seq = feature.get('seq');
-            if (seq) {
+            if (seq && mismatches) {
                 for (let i = 0; i < mismatches.length; i += 1) {
                     const { type, start, cliplen = 0 } = mismatches[i];
                     if (type === 'softclip') {
@@ -144,8 +144,7 @@ class PileupRenderer extends BoxRendererType_1.default {
         const { config, showSoftClip } = renderArgs;
         const maxClippingSize = (0, configuration_1.readConfObject)(config, 'maxClippingSize');
         const { start, end } = region;
-        const len = end - start;
-        const bpExpansion = Math.max(len, showSoftClip ? Math.round(maxClippingSize) : 0);
+        const bpExpansion = showSoftClip ? Math.round(maxClippingSize) : 0;
         return {
             // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
             ...region,
@@ -544,6 +543,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const extraHorizontallyFlippedOffset = region.reversed
             ? 1 / bpPerPx + 1
             : -1;
+        if (!mismatches) {
+            return;
+        }
         // two pass rendering: first pass, draw all the mismatches except wide
         // insertion markers
         for (let i = 0; i < mismatches.length; i += 1) {
@@ -662,7 +664,7 @@ class PileupRenderer extends BoxRendererType_1.default {
         const minFeatWidth = (0, configuration_1.readConfObject)(config, 'minSubfeatureWidth');
         const mismatches = feature.get('mismatches');
         const seq = feature.get('seq');
-        const { charWidth, charHeight } = this.getCharWidthHeight(ctx);
+        const { charWidth, charHeight } = this.getCharWidthHeight();
         const { bases } = theme.palette;
         const colorForBase = {
             A: bases.A.main,
@@ -672,34 +674,35 @@ class PileupRenderer extends BoxRendererType_1.default {
             deletion: '#808080', // gray
         };
         // Display all bases softclipped off in lightened colors
-        if (seq) {
-            mismatches
-                .filter(mismatch => mismatch.type === 'softclip')
-                .forEach(mismatch => {
-                const softClipLength = mismatch.cliplen || 0;
-                const s = feature.get('start');
-                const softClipStart = mismatch.start === 0 ? s - softClipLength : s + mismatch.start;
-                for (let k = 0; k < softClipLength; k += 1) {
-                    const base = seq.charAt(k + mismatch.start);
-                    // If softclip length+start is longer than sequence, no need to
-                    // continue showing base
-                    if (!base) {
-                        return;
-                    }
-                    const [softClipLeftPx, softClipRightPx] = (0, util_1.bpSpanPx)(softClipStart + k, softClipStart + k + 1, region, bpPerPx);
-                    const softClipWidthPx = Math.max(minFeatWidth, Math.abs(softClipLeftPx - softClipRightPx));
-                    // Black accounts for IUPAC ambiguity code bases such as N that
-                    // show in soft clipping
-                    const baseColor = colorForBase[base] || '#000000';
-                    ctx.fillStyle = baseColor;
-                    fillRect(ctx, softClipLeftPx, topPx, softClipWidthPx, heightPx, canvasWidth);
-                    if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {
-                        ctx.fillStyle = theme.palette.getContrastText(baseColor);
-                        ctx.fillText(base, softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1, topPx + heightPx);
-                    }
-                }
-            });
+        if (!(seq && mismatches)) {
+            return;
         }
+        mismatches
+            .filter(mismatch => mismatch.type === 'softclip')
+            .forEach(mismatch => {
+            const len = mismatch.cliplen || 0;
+            const s = feature.get('start');
+            const start = mismatch.start === 0 ? s - len : s + mismatch.start;
+            for (let k = 0; k < len; k += 1) {
+                const base = seq.charAt(k + mismatch.start);
+                // If softclip length+start is longer than sequence, no need to
+                // continue showing base
+                if (!base) {
+                    return;
+                }
+                const [leftPx, rightPx] = (0, util_1.bpSpanPx)(start + k, start + k + 1, region, bpPerPx);
+                const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
+                // Black accounts for IUPAC ambiguity code bases such as N that
+                // show in soft clipping
+                const baseColor = colorForBase[base] || '#000000';
+                ctx.fillStyle = baseColor;
+                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
+                if (widthPx >= charWidth && heightPx >= charHeight - 5) {
+                    ctx.fillStyle = theme.palette.getContrastText(baseColor);
+                    ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+                }
+            }
+        });
     }
     makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
         const { layout, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
@@ -717,7 +720,7 @@ class PileupRenderer extends BoxRendererType_1.default {
             throw new Error('invalid layout object');
         }
         ctx.font = 'bold 10px Courier New,monospace';
-        const { charWidth, charHeight } = this.getCharWidthHeight(ctx);
+        const { charWidth, charHeight } = this.getCharWidthHeight();
         const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
         const drawIndels = shouldDrawIndels(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
         for (let i = 0; i < layoutRecords.length; i++) {
@@ -804,12 +807,12 @@ class PileupRenderer extends BoxRendererType_1.default {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
         const { regions, bpPerPx } = renderProps;
+        const [region] = regions;
         const layoutRecords = this.layoutFeats({
             ...renderProps,
             features,
             layout,
         });
-        const [region] = regions;
         // only need reference sequence if there are features and only for some
         // cases
         const regionSequence = features.size && (0, util_2.shouldFetchReferenceSequence)((_a = renderProps.colorBy) === null || _a === void 0 ? void 0 : _a.type)

package/dist/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/configSchema.d.ts

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

package/dist/PileupRenderer/configSchema.js

@@ -2,20 +2,33 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
-    // default magenta here is used to detect the user has not customized this
+/**
+ * #config PileupRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const PileupRenderer = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
+    /**
+     * #slot
+     * default magenta here is used to detect the user has not customized this
+     */
     color: {
         type: 'color',
         description: 'the color of each feature in a pileup alignment',
         defaultValue: '#f0f',
         contextVariable: ['feature'],
     },
+    /**
+     * #slot
+     */
     orientationType: {
         type: 'stringEnum',
         model: mobx_state_tree_1.types.enumeration('orientationType', ['fr', 'rf', 'ff']),
         defaultValue: 'fr',
         description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
+    /**
+     * #slot
+     */
     displayMode: {
         type: 'stringEnum',
         model: mobx_state_tree_1.types.enumeration('displayMode', [
@@ -26,41 +39,63 @@ exports.default = (0, configuration_1.ConfigurationSchema)('PileupRenderer', {
         description: 'Alternative display modes',
         defaultValue: 'normal',
     },
+    /**
+     * #slot
+     */
     minSubfeatureWidth: {
         type: 'number',
         description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
         defaultValue: 0.7,
     },
+    /**
+     * #slot
+     */
     maxHeight: {
         type: 'integer',
         description: 'the maximum height to be used in a pileup rendering',
         defaultValue: 1200,
     },
+    /**
+     * #slot
+     */
     maxClippingSize: {
         type: 'integer',
         description: 'the max clip size to be used in a pileup rendering',
         defaultValue: 10000,
     },
+    /**
+     * #slot
+     */
     height: {
         type: 'number',
         description: 'the height of each feature in a pileup alignment',
         defaultValue: 7,
         contextVariable: ['feature'],
     },
+    /**
+     * #slot
+     */
     noSpacing: {
         type: 'boolean',
         description: 'remove spacing between features',
         defaultValue: false,
     },
+    /**
+     * #slot
+     */
     largeInsertionIndicatorScale: {
         type: 'number',
         description: 'scale at which to draw the large insertion indicators (bp/pixel)',
         defaultValue: 10,
     },
+    /**
+     * #slot
+     */
     mismatchAlpha: {
         type: 'boolean',
         defaultValue: false,
         description: 'Fade low quality mismatches',
     },
 }, { explicitlyTyped: true });
+exports.default = PileupRenderer;
 //# sourceMappingURL=configSchema.js.map

package/dist/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/index.js

@@ -7,12 +7,14 @@ const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function register(pluginManager) {
-    pluginManager.addRendererType(() => new PileupRenderer_1.default({
-        name: 'PileupRenderer',
-        ReactComponent: PileupRendering_1.default,
-        configSchema: configSchema_1.default,
-        pluginManager,
-    }));
+    pluginManager.addRendererType(() => {
+        return new PileupRenderer_1.default({
+            name: 'PileupRenderer',
+            ReactComponent: PileupRendering_1.default,
+            configSchema: configSchema_1.default,
+            pluginManager,
+        });
+    });
 }
 exports.default = register;
 //# sourceMappingURL=index.js.map

package/dist/PileupRenderer/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,wBAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc,EAAd,yBAAc;QACd,YAAY,EAAZ,sBAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,wBAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,cAAc,EAAd,yBAAc;YACd,YAAY,EAAZ,sBAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AATD,2BASC"}

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,3 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/SNPCoverageAdapter/configSchema.js

@@ -1,8 +1,19 @@
 "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) => mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
-    subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
-}, { explicitlyTyped: true }));
+/**
+ * #config SNPCoverageAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true });
+exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,qDAAuC;AAEvC,kBAAe,CAAC,aAA4B,EAAE,EAAE,CAC9C,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CACd,IAAA,mCAAmB,EACjB,oBAAoB,EACpB;IACE,UAAU,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;CAC/D,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,oBAAoB,EACpB;IACE;;;OAGG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,YAAY,CAAA"}

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function (pluginManager: PluginManager): void;

package/dist/SNPCoverageAdapter/index.js

@@ -29,18 +29,21 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const SNPCoverageAdapter_1 = require("./SNPCoverageAdapter");
-exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'SNPCoverageAdapter',
-        adapterMetadata: {
-            category: null,
-            displayName: null,
-            hiddenFromGUI: true,
-            description: null,
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
-        configSchema: (0, configSchema_1.default)(pluginManager),
-        adapterCapabilities: SNPCoverageAdapter_1.capabilities,
-    }));
-};
+function default_1(pluginManager) {
+    pluginManager.addAdapterType(() => {
+        return new AdapterType_1.default({
+            name: 'SNPCoverageAdapter',
+            adapterMetadata: {
+                category: null,
+                displayName: null,
+                hiddenFromGUI: true,
+                description: null,
+            },
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SNPCoverageAdapter'))).then(r => r.default),
+            configSchema: configSchema_1.default,
+            adapterCapabilities: SNPCoverageAdapter_1.capabilities,
+        });
+    });
+}
+exports.default = default_1;
 //# sourceMappingURL=index.js.map

package/dist/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
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+{"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"}

package/dist/SNPCoverageRenderer/configSchema.d.ts

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

package/dist/SNPCoverageRenderer/configSchema.js

@@ -1,31 +1,51 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {
+/**
+ * #config SNPCoverageRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const SNPCoverageRenderer = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {
+    /**
+     * #slot
+     */
     clipColor: {
         type: 'color',
         description: 'the color of the clipping marker',
         defaultValue: 'red',
     },
+    /**
+     * #slot
+     */
     indicatorThreshold: {
         type: 'number',
         description: 'the proportion of reads containing a insertion/clip indicator',
         defaultValue: 0.4,
     },
+    /**
+     * #slot
+     */
     drawArcs: {
         type: 'boolean',
         description: 'Draw sashimi-style arcs for intron features',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     drawInterbaseCounts: {
         type: 'boolean',
         description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     drawIndicators: {
         type: 'boolean',
         description: 'draw a triangular indicator where an event has been detected',
         defaultValue: true,
     },
 }, { explicitlyTyped: true });
+exports.default = SNPCoverageRenderer;
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,+DAA+D;QACjE,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,6CAA6C;QAC1D,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EACT,iJAAiJ;QACnJ,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,SAAS;QACf,WAAW,EACT,8DAA8D;QAChE,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}

package/dist/SNPCoverageRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export default function register(pluginManager: PluginManager): void;

package/dist/SNPCoverageRenderer/index.js

@@ -3,17 +3,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema_1 = __importDefault(require("./configSchema"));
 const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {}, { baseConfiguration: configSchema_1.default, explicitlyTyped: true });
 function register(pluginManager) {
     pluginManager.addRendererType(() => new SNPCoverageRenderer_1.default({
         name: 'SNPCoverageRenderer',
         ReactComponent: plugin_wiggle_1.WiggleRendering,
-        configSchema: exports.configSchema,
+        configSchema: configSchema_1.default,
         pluginManager,
     }));
 }

package/dist/SNPCoverageRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAEzC,gFAAuD;AAEvD,0DAAwD;AAExD,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,6BAAmB,CAAC;QACtB,IAAI,EAAE,qBAAqB;QAC3B,cAAc,EAAE,+BAAe;QAC/B,YAAY,EAAZ,sBAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}

package/dist/index.d.ts

@@ -2,9 +2,10 @@ import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
 import * as MismatchParser from './BamAdapter/MismatchParser';
 import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-export { MismatchParser };
-export type { LinearPileupDisplayModel };
+import { linearPileupDisplayStateModelFactory, linearPileupDisplayConfigSchemaFactory } from './LinearPileupDisplay';
 export default class AlignmentsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
+export { linearPileupDisplayConfigSchemaFactory, linearPileupDisplayStateModelFactory, MismatchParser, };
+export type { LinearPileupDisplayModel };