@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/esm/PileupRenderer/colorBy.d.ts

@@ -0,0 +1,7 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+export declare function colorByInsertSize(feature: Feature): string;
+export declare function colorByMappingQuality(feature: Feature): string;
+export declare function colorByStrand(feature: Feature): "#EC8B8B" | "#8F8FD8";
+export declare function colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
+export declare function colorByStrandedRnaSeq(feature: Feature): string;

package/esm/PileupRenderer/colorBy.js

@@ -0,0 +1,61 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { fillColor } from '../shared/color';
+import { orientationTypes } from '../util';
+export function colorByInsertSize(feature) {
+    return feature.get('is_paired') &&
+        feature.get('refName') !== feature.get('next_ref')
+        ? '#555'
+        : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`;
+}
+export function colorByMappingQuality(feature) {
+    return `hsl(${feature.get('mq')},50%,50%)`;
+}
+function getOrientation(feature, config) {
+    const orientationType = readConfObject(config, 'orientationType');
+    const type = orientationTypes[orientationType];
+    const orientation = type[feature.get('pair_orientation')];
+    return {
+        LR: 'color_pair_lr',
+        RR: 'color_pair_rr',
+        RL: 'color_pair_rl',
+        LL: 'color_pair_ll',
+    }[orientation];
+}
+export function colorByStrand(feature) {
+    return feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B';
+}
+export function colorByOrientation(feature, config) {
+    return fillColor[getOrientation(feature, config) || 'color_nostrand'];
+}
+function getStranded(feature) {
+    const flags = feature.get('flags');
+    const strand = feature.get('strand');
+    // is paired
+    if (flags & 1) {
+        const revflag = flags & 64;
+        const flipper = revflag ? -1 : 1;
+        // proper pairing
+        if (flags & 2) {
+            return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand';
+        }
+        else if (feature.get('multi_segment_next_segment_unmapped')) {
+            return strand * flipper === 1
+                ? 'color_rev_missing_mate'
+                : 'color_fwd_missing_mate';
+        }
+        else if (feature.get('refName') === feature.get('next_refName')) {
+            return strand * flipper === 1
+                ? 'color_rev_strand_not_proper'
+                : 'color_fwd_strand_not_proper';
+        }
+        else {
+            // should only leave aberrant chr
+            return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
+        }
+    }
+    return strand === 1 ? 'color_fwd_strand' : 'color_rev_strand';
+}
+export function colorByStrandedRnaSeq(feature) {
+    return fillColor[getStranded(feature)];
+}
+//# sourceMappingURL=colorBy.js.map

package/esm/PileupRenderer/colorBy.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"colorBy.js","sourceRoot":"","sources":["../../src/PileupRenderer/colorBy.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AAEpC,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EAAE,gBAAgB,EAAE,MAAM,SAAS,CAAA;AAE1C,MAAM,UAAU,iBAAiB,CAAC,OAAgB;IAChD,OAAO,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;QAC7B,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,OAAO,CAAC,GAAG,CAAC,UAAU,CAAC;QAClD,CAAC,CAAC,MAAM;QACR,CAAC,CAAC,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,iBAAiB,CAAC,CAAC,GAAG,EAAE,WAAW,CAAA;AACrE,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,OAAO,OAAO,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;AAC5C,CAAC;AAED,SAAS,cAAc,CAAC,OAAgB,EAAE,MAA6B;IACrE,MAAM,eAAe,GAAG,cAAc,CAAC,MAAM,EAAE,iBAAiB,CAGxD,CAAA;IACR,MAAM,IAAI,GAAG,gBAAgB,CAAC,eAAe,CAAC,CAAA;IAC9C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAW,CAAC,CAAA;IACnE,OAAO;QACL,EAAE,EAAE,eAAwB;QAC5B,EAAE,EAAE,eAAwB;QAC5B,EAAE,EAAE,eAAwB;QAC5B,EAAE,EAAE,eAAwB;KAC7B,CAAC,WAAW,CAAC,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,OAAgB;IAC5C,OAAO,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;AAC7D,CAAC;AAED,MAAM,UAAU,kBAAkB,CAChC,OAAgB,EAChB,MAA6B;IAE7B,OAAO,SAAS,CAAC,cAAc,CAAC,OAAO,EAAE,MAAM,CAAC,IAAI,gBAAgB,CAAC,CAAA;AACvE,CAAC;AACD,SAAS,WAAW,CAAC,OAAgB;IACnC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;IACpC,YAAY;IACZ,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,MAAM,OAAO,GAAG,KAAK,GAAG,EAAE,CAAA;QAC1B,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEhC,iBAAiB;QACjB,IAAI,KAAK,GAAG,CAAC,EAAE;YACb,OAAO,MAAM,GAAG,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,kBAAkB,CAAA;SACxE;aAAM,IAAI,OAAO,CAAC,GAAG,CAAC,qCAAqC,CAAC,EAAE;YAC7D,OAAO,MAAM,GAAG,OAAO,KAAK,CAAC;gBAC3B,CAAC,CAAC,wBAAwB;gBAC1B,CAAC,CAAC,wBAAwB,CAAA;SAC7B;aAAM,IAAI,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE;YACjE,OAAO,MAAM,GAAG,OAAO,KAAK,CAAC;gBAC3B,CAAC,CAAC,6BAA6B;gBAC/B,CAAC,CAAC,6BAA6B,CAAA;SAClC;aAAM;YACL,iCAAiC;YACjC,OAAO,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,oBAAoB,CAAA;SAClE;KACF;IACD,OAAO,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,kBAAkB,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,OAAO,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;AACxC,CAAC"}

package/esm/PileupRenderer/components/PileupRendering.d.ts

@@ -17,7 +17,12 @@ declare function PileupRendering(props: {
         type: string;
         tag?: string;
     };
-    onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void;
-}): JSX.Element;
+    filterBy?: {
+        tagFilter?: {
+            tag: string;
+        };
+    };
+    onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
+}): React.JSX.Element;
 declare const _default: typeof PileupRendering;
 export default _default;

package/esm/PileupRenderer/components/PileupRendering.js

@@ -6,7 +6,8 @@ import { observer } from 'mobx-react';
 // (issue #1248)
 const canvasPadding = 100;
 function PileupRendering(props) {
-    const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, } = props;
+    var _a;
+    const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, filterBy, } = props;
     const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } = displayModel;
     const [region] = regions;
     const highlightOverlayCanvas = useRef(null);
@@ -92,25 +93,18 @@ function PileupRendering(props) {
         callMouseHandler('ContextMenu', event);
     }
     function mouseMove(event) {
+        if (!highlightOverlayCanvas.current) {
+            return;
+        }
         if (mouseIsDown) {
             setMovedDuringLastMouseDown(true);
         }
-        let offsetX = 0;
-        let offsetY = 0;
-        const canvas = highlightOverlayCanvas.current;
-        if (canvas) {
-            const { left, top } = canvas.getBoundingClientRect();
-            offsetX = left;
-            offsetY = top;
-        }
-        offsetX = event.clientX - offsetX;
-        offsetY = event.clientY - offsetY;
+        const rect = highlightOverlayCanvas.current.getBoundingClientRect();
+        const offsetX = event.clientX - rect.left;
+        const offsetY = event.clientY - rect.top;
         const px = region.reversed ? width - offsetX : offsetX;
         const clientBp = region.start + bpPerPx * px;
-        const featIdUnderMouse = displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY);
-        if (onMouseMove) {
-            onMouseMove(event, featIdUnderMouse);
-        }
+        onMouseMove === null || onMouseMove === void 0 ? void 0 : onMouseMove(event, displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY));
     }
     function callMouseHandler(handlerName, event) {
         // @ts-expect-error
@@ -128,9 +122,14 @@ function PileupRendering(props) {
     }
     const canvasWidth = Math.ceil(width);
     // need to call this in render so we get the right observer behavior
-    return (React.createElement("div", { className: "PileupRendering", "data-testid": `pileup-${sortedBy || colorBy
-            ? `${(sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) || ''}`
-            : 'normal'}`, style: { position: 'relative', width: canvasWidth, height } },
+    return (React.createElement("div", { "data-testid": `pileup-${[
+            sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type,
+            colorBy === null || colorBy === void 0 ? void 0 : colorBy.type,
+            colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag,
+            (_a = filterBy === null || filterBy === void 0 ? void 0 : filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag,
+        ]
+            .filter(f => !!f)
+            .join('-')}`, style: { position: 'relative', width: canvasWidth, height } },
         React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }),
         React.createElement("canvas", { "data-testid": "pileup_overlay_canvas", width: canvasWidth, height: height + canvasPadding, style: { position: 'absolute', left: 0, top: 0 }, className: "highlightOverlayCanvas", ref: highlightOverlayCanvas, onMouseDown: event => onMouseDown(event), onMouseEnter: event => onMouseEnter(event), onMouseOut: event => onMouseOut(event), onMouseOver: event => onMouseOver(event), onMouseUp: event => onMouseUp(event), onMouseLeave: event => onMouseLeave(event), onMouseMove: event => mouseMove(event), onClick: event => onClick(event), onContextMenu: event => onContextMenu(event), onFocus: () => { }, onBlur: () => { } })));
 }

package/esm/PileupRenderer/components/PileupRendering.js.map

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

@@ -1,2 +1,88 @@
-declare const PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * default magenta here is used to detect the user has not customized this
+     */
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    orientationType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    displayMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    minSubfeatureWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxHeight: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxClippingSize: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        description: string;
+        defaultValue: number;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    noSpacing: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    largeInsertionIndicatorScale: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    mismatchAlpha: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PileupRenderer;

package/esm/PileupRenderer/getAlignmentShapeColor.d.ts

@@ -0,0 +1,10 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+export declare function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }: {
+    colorType: string;
+    tag: string;
+    feature: Feature;
+    defaultColor: boolean;
+    config: AnyConfigurationModel;
+    colorTagMap: Record<string, string>;
+}): any;

package/esm/PileupRenderer/getAlignmentShapeColor.js

@@ -0,0 +1,56 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { fillColor } from '../shared/color';
+import { colorByInsertSize, colorByMappingQuality, colorByOrientation, colorByStrand, colorByStrandedRnaSeq, } from './colorBy';
+export function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }) {
+    // first pass for simple color changes that change the color of the
+    // alignment
+    switch (colorType) {
+        case 'insertSize':
+            return colorByInsertSize(feature);
+        case 'strand':
+            return colorByStrand(feature);
+        case 'mappingQuality':
+            return colorByMappingQuality(feature);
+        case 'pairOrientation':
+            return colorByOrientation(feature, config);
+        case 'stranded':
+            return colorByStrandedRnaSeq(feature);
+        case 'xs':
+        case 'tag': {
+            const tags = feature.get('tags');
+            const val = tags ? tags[tag] : feature.get(tag);
+            if (tag === 'XS' || tag === 'TS') {
+                return fillColor[{
+                    '-': 'color_rev_strand',
+                    '+': 'color_fwd_strand',
+                }[val] || 'color_nostrand'];
+            }
+            else if (tag === 'ts') {
+                return fillColor[{
+                    '-': feature.get('strand') === -1
+                        ? 'color_fwd_strand'
+                        : 'color_rev_strand',
+                    '+': feature.get('strand') === -1
+                        ? 'color_rev_strand'
+                        : 'color_fwd_strand',
+                }[val] || 'color_nostrand'];
+            }
+            else {
+                return colorTagMap[val] || fillColor['color_nostrand'];
+            }
+        }
+        case 'insertSizeAndPairOrientation':
+            break;
+        case 'modifications':
+        case 'methylation':
+            // this coloring is similar to igv.js, and is helpful to color negative
+            // strand reads differently because their c-g will be flipped (e.g. g-c
+            // read right to left)
+            return feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
+        default:
+            return defaultColor
+                ? 'lightgrey'
+                : readConfObject(config, 'color', { feature });
+    }
+}
+//# sourceMappingURL=getAlignmentShapeColor.js.map

package/esm/PileupRenderer/getAlignmentShapeColor.js.map

@@ -0,0 +1 @@
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package/esm/PileupRenderer/index.js

@@ -1,6 +1,6 @@
 import PileupRenderer from './PileupRenderer';
-import ReactComponent from './components/PileupRendering';
 import configSchema from './configSchema';
+import ReactComponent from './components/PileupRendering';
 export default function register(pluginManager) {
     pluginManager.addRendererType(() => {
         return new PileupRenderer({

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,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,8BAA8B,CAAA;AAEzD,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,cAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,iBAAiB;YAC9B,cAAc;YACd,YAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/PileupRenderer/layoutFeature.d.ts

@@ -0,0 +1,18 @@
+import { Feature, Region } from '@jbrowse/core/util';
+import { BaseLayout } from '@jbrowse/core/util/layouts';
+export interface LayoutRecord {
+    feature: Feature;
+    leftPx: number;
+    rightPx: number;
+    topPx: number;
+    heightPx: number;
+}
+export declare function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+    feature: Feature;
+    layout: BaseLayout<Feature>;
+    bpPerPx: number;
+    region: Region;
+    showSoftClip?: boolean;
+    heightPx: number;
+    displayMode: string;
+}): LayoutRecord | null;

package/esm/PileupRenderer/layoutFeature.js

@@ -0,0 +1,37 @@
+import { bpSpanPx } from '@jbrowse/core/util';
+export function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }) {
+    let expansionBefore = 0;
+    let expansionAfter = 0;
+    // Expand the start and end of feature when softclipping enabled
+    if (showSoftClip) {
+        const mismatches = feature.get('mismatches');
+        const seq = feature.get('seq');
+        if (seq) {
+            for (let i = 0; i < mismatches.length; i += 1) {
+                const { type, start, cliplen = 0 } = mismatches[i];
+                if (type === 'softclip') {
+                    start === 0 ? (expansionBefore = cliplen) : (expansionAfter = cliplen);
+                }
+            }
+        }
+    }
+    const [leftPx, rightPx] = bpSpanPx(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx);
+    if (displayMode === 'compact') {
+        heightPx /= 3;
+    }
+    if (feature.get('refName') !== region.refName) {
+        throw new Error(`feature ${feature.id()} is not on the current region's reference sequence ${region.refName}`);
+    }
+    const topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
+    if (topPx === null) {
+        return null;
+    }
+    return {
+        feature,
+        leftPx,
+        rightPx,
+        topPx: displayMode === 'collapse' ? 0 : topPx,
+        heightPx,
+    };
+}
+//# sourceMappingURL=layoutFeature.js.map

package/esm/PileupRenderer/layoutFeature.js.map

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package/esm/PileupRenderer/layoutFeatures.d.ts

@@ -0,0 +1,2 @@
+import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer';
+export declare function layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (import("./layoutFeature").LayoutRecord | null)[];

package/esm/PileupRenderer/layoutFeatures.js

@@ -0,0 +1,31 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { iterMap } from '@jbrowse/core/util';
+// locals
+import { layoutFeature } from './layoutFeature';
+import { sortFeature } from './sortUtil';
+// layout determines the height of the canvas that we use to render
+export function layoutFeats(props) {
+    const { layout, features, sortedBy, config, bpPerPx, showSoftClip, regions } = props;
+    const [region] = regions;
+    if (!layout) {
+        throw new Error(`layout required`);
+    }
+    if (!layout.addRect) {
+        throw new Error('invalid layout object');
+    }
+    const featureMap = (sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) && region.start === sortedBy.pos
+        ? sortFeature(features, sortedBy)
+        : features;
+    const heightPx = readConfObject(config, 'height');
+    const displayMode = readConfObject(config, 'displayMode');
+    return iterMap(featureMap.values(), feature => layoutFeature({
+        feature,
+        layout,
+        bpPerPx,
+        region,
+        showSoftClip,
+        heightPx,
+        displayMode,
+    }), featureMap.size);
+}
+//# sourceMappingURL=layoutFeatures.js.map

package/esm/PileupRenderer/layoutFeatures.js.map

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package/esm/PileupRenderer/makeImageData.d.ts

@@ -0,0 +1,17 @@
+import { Feature } from '@jbrowse/core/util';
+import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer';
+export interface RenderArgsWithColor extends RenderArgsDeserializedWithFeaturesAndLayout {
+    Color: Awaited<typeof import('color')>;
+}
+interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export declare function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }: {
+    ctx: CanvasRenderingContext2D;
+    canvasWidth: number;
+    layoutRecords: LayoutFeature[];
+    renderArgs: RenderArgsWithColor;
+}): void;
+export {};

package/esm/PileupRenderer/makeImageData.js

@@ -0,0 +1,60 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { createJBrowseTheme } from '@jbrowse/core/ui';
+import { getCharWidthHeight, getColorBaseMap, getContrastBaseMap, shouldDrawIndels, shouldDrawSNPsMuted, } from './util';
+import { renderAlignment } from './renderAlignment';
+import { renderMismatches } from './renderMismatches';
+import { renderSoftClipping } from './renderSoftClipping';
+export function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
+    const { config, showSoftClip, colorBy, theme: configTheme } = renderArgs;
+    const mismatchAlpha = readConfObject(config, 'mismatchAlpha');
+    const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth');
+    const largeInsertionIndicatorScale = readConfObject(config, 'largeInsertionIndicatorScale');
+    const defaultColor = readConfObject(config, 'color') === '#f0f';
+    const theme = createJBrowseTheme(configTheme);
+    const colorForBase = getColorBaseMap(theme);
+    const contrastForBase = getContrastBaseMap(theme);
+    ctx.font = 'bold 10px Courier New,monospace';
+    const { charWidth, charHeight } = getCharWidthHeight();
+    const drawSNPsMuted = shouldDrawSNPsMuted(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
+    const drawIndels = shouldDrawIndels();
+    for (const feat of layoutRecords) {
+        renderAlignment({
+            ctx,
+            feat,
+            renderArgs,
+            defaultColor,
+            colorForBase,
+            contrastForBase,
+            charWidth,
+            charHeight,
+            canvasWidth,
+        });
+        renderMismatches({
+            ctx,
+            feat,
+            renderArgs,
+            mismatchAlpha,
+            drawSNPsMuted,
+            drawIndels,
+            largeInsertionIndicatorScale,
+            minSubfeatureWidth,
+            charWidth,
+            charHeight,
+            colorForBase,
+            contrastForBase,
+            canvasWidth,
+        });
+        if (showSoftClip) {
+            renderSoftClipping({
+                ctx,
+                feat,
+                renderArgs,
+                colorForBase,
+                config,
+                theme,
+                canvasWidth,
+            });
+        }
+    }
+}
+//# sourceMappingURL=makeImageData.js.map