@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/esm/PileupRenderer/PileupRenderer.js

@@ -67,7 +67,7 @@ export default class PileupRenderer extends BoxRendererType {
     }
     // get width and height of chars the height is an approximation: width
     // letter M is approximately the height
-    getCharWidthHeight(ctx) {
+    getCharWidthHeight() {
         const charWidth = measureText('A');
         const charHeight = measureText('M') - 2;
         return { charWidth, charHeight };
@@ -79,7 +79,7 @@ export default class PileupRenderer extends BoxRendererType {
         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') {
@@ -116,8 +116,7 @@ export default class PileupRenderer extends BoxRendererType {
         const { config, showSoftClip } = renderArgs;
         const maxClippingSize = 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,
@@ -516,6 +515,9 @@ export default class PileupRenderer extends BoxRendererType {
         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) {
@@ -634,7 +636,7 @@ export default class PileupRenderer extends BoxRendererType {
         const minFeatWidth = 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,
@@ -644,34 +646,35 @@ export default class PileupRenderer extends BoxRendererType {
             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] = 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] = 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;
@@ -689,7 +692,7 @@ export default class PileupRenderer extends BoxRendererType {
             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++) {
@@ -776,12 +779,12 @@ export default class PileupRenderer extends BoxRendererType {
         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 && shouldFetchReferenceSequence((_a = renderProps.colorBy) === null || _a === void 0 ? void 0 : _a.type)

package/esm/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/esm/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/esm/PileupRenderer/configSchema.js

@@ -1,19 +1,32 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-export default 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 = 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: 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: types.enumeration('displayMode', [
@@ -24,41 +37,63 @@ export default 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 });
+export default PileupRenderer;
 //# sourceMappingURL=configSchema.js.map

package/esm/PileupRenderer/configSchema.js.map

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package/esm/PileupRenderer/index.js

@@ -2,11 +2,13 @@ import PileupRenderer from './PileupRenderer';
 import ReactComponent from './components/PileupRendering';
 import configSchema from './configSchema';
 export default function register(pluginManager) {
-    pluginManager.addRendererType(() => new PileupRenderer({
-        name: 'PileupRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-    }));
+    pluginManager.addRendererType(() => {
+        return new PileupRenderer({
+            name: 'PileupRenderer',
+            ReactComponent,
+            configSchema,
+            pluginManager,
+        });
+    });
 }
 //# sourceMappingURL=index.js.map

package/esm/PileupRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,cAAc,MAAM,8BAA8B,CAAA;AACzD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,cAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,cAAc;YACd,YAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/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/esm/SNPCoverageAdapter/configSchema.js

@@ -1,6 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-export default (pluginManager) => types.late(() => ConfigurationSchema('SNPCoverageAdapter', {
-    subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
-}, { explicitlyTyped: true }));
+/**
+ * #config SNPCoverageAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('SNPCoverageAdapter', {
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true });
+export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageAdapter/configSchema.js.map

@@ -1 +1 @@
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package/esm/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/esm/SNPCoverageAdapter/index.js

@@ -1,18 +1,20 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchemaFactory from './configSchema';
+import configSchema from './configSchema';
 import { capabilities } from './SNPCoverageAdapter';
-export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'SNPCoverageAdapter',
-        adapterMetadata: {
-            category: null,
-            displayName: null,
-            hiddenFromGUI: true,
-            description: null,
-        },
-        getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
-        configSchema: configSchemaFactory(pluginManager),
-        adapterCapabilities: capabilities,
-    }));
-};
+export default function (pluginManager) {
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'SNPCoverageAdapter',
+            adapterMetadata: {
+                category: null,
+                displayName: null,
+                hiddenFromGUI: true,
+                description: null,
+            },
+            getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
+            configSchema,
+            adapterCapabilities: capabilities,
+        });
+    });
+}
 //# sourceMappingURL=index.js.map

package/esm/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
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package/esm/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/esm/SNPCoverageRenderer/configSchema.js

@@ -1,29 +1,49 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('SNPCoverageRenderer', {
+/**
+ * #config SNPCoverageRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const SNPCoverageRenderer = 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 });
+export default SNPCoverageRenderer;
 //# sourceMappingURL=configSchema.js.map

package/esm/SNPCoverageRenderer/configSchema.js.map

@@ -1 +1 @@
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package/esm/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/esm/SNPCoverageRenderer/index.js

@@ -1,8 +1,6 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import ConfigSchema from './configSchema';
+import configSchema from './configSchema';
 import SNPCoverageRenderer from './SNPCoverageRenderer';
 import { WiggleRendering } from '@jbrowse/plugin-wiggle';
-export const configSchema = ConfigurationSchema('SNPCoverageRenderer', {}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
 export default function register(pluginManager) {
     pluginManager.addRendererType(() => new SNPCoverageRenderer({
         name: 'SNPCoverageRenderer',

package/esm/SNPCoverageRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAEvD,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAA;AAExD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,mBAAmB,CAAC;QACtB,IAAI,EAAE,qBAAqB;QAC3B,cAAc,EAAE,eAAe;QAC/B,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/esm/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 };