jbrowse-plugin-mafviewer 1.3.2 → 1.4.1

package/README.md

@@ -92,36 +92,6 @@ can use nhLocation or samples array on adapter
 }
 ```
 
-### Example BgzipTaffyAdapter config
-
-Note: TAF files are actually significantly slower and has known bugs...will
-update once fixed
-
-This notice will be removed it it is improved
-
-As with other adapters, you can use nhLocation or samples array on adapter
-
-```json
-{
-  "type": "MafTrack",
-  "trackId": "bigMaf",
-  "name": "taffy",
-  "adapter": {
-    "type": "BgzipTaffyAdapter",
-    "nhLocation": {
-      "uri": "hg38.30way.nh"
-    },
-    "tafGzLocation": {
-      "uri": "30way.taf.gz"
-    },
-    "taiGzLocation": {
-      "uri": "30way.taf.gz.tai"
-    }
-  },
-  "assemblyNames": ["hg38"]
-}
-```
-
 ### Example with customized sample names and colors
 
 ```json
@@ -191,9 +161,6 @@ the case
 2. MAF tabix based format, based on a custom BED created via conversion tools in
    this repo (see maf2bed)
 
-3. TAF format (new!). Currently only supports bgzip'd TAF. This is pioneered by
-   https://github.com/ComparativeGenomicsToolkit/taffy
-
 _Note: All these formats generally start with a MAF as input. Note that your MAF
 file should contain the species name and chromosome name e.g. hg38.chr1 in the
 sequence identifiers._
@@ -229,17 +196,3 @@ separated by `:`.
 
 Note: If you can't use the `cargo install maf2bed` binary, there is a
 `bin/maf2bed.pl` perl version of it in this repo
-
-### Option 3. Preparing TAF
-
-Follow steps from https://github.com/ComparativeGenomicsToolkit/taffy
-
-```
-taffy view -i chr22.maf -o chr22.taf
-bgzip chr22.taf
-taffy index -i chr22.taf.gz
-```
-
-The above workflow requires that taffy is built with "htslib support"
-
-Note that the TAF support is beta, let me know if you run into any issues

package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -27,7 +27,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
@@ -36,7 +38,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         imageData: any;
         reactElement?: React.ReactElement;
         html?: string;
@@ -45,7 +49,9 @@ export default class LinearMafRenderer extends FeatureRendererType {
         width: number;
         height: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        samples: import("./rendering").Sample[];
+        flatbush: ArrayBufferLike;
+        items: import("./rendering").RenderedBase[];
         reactElement: React.ReactElement;
         html?: string;
     }>;

package/dist/LinearMafRenderer/components/LinearMafRendering.d.ts

@@ -0,0 +1,13 @@
+import React from 'react';
+import { RenderedBase } from '../rendering';
+import { Sample } from '../../LinearMafDisplay/types';
+type SerializedRBush = any;
+declare const LinearMafRendering: (props: {
+    width: number;
+    height: number;
+    displayModel: any;
+    flatbush: SerializedRBush;
+    items: RenderedBase[];
+    samples: Sample[];
+}) => React.JSX.Element;
+export default LinearMafRendering;

package/dist/LinearMafRenderer/components/LinearMafRendering.js

@@ -0,0 +1,47 @@
+import React, { useMemo, useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import Flatbush from 'flatbush';
+import { observer } from 'mobx-react';
+const LinearMafRendering = observer(function (props) {
+    const { items, displayModel, height, samples, flatbush } = props;
+    const ref = useRef(null);
+    const rbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        let offsetX = 0;
+        let offsetY = 0;
+        if (ref.current) {
+            const r = ref.current.getBoundingClientRect();
+            offsetX = eventClientX - r.left;
+            offsetY = eventClientY - r.top;
+        }
+        const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
+        if (x.length) {
+            const elt = x.find(idx => items[idx]?.isInsertion);
+            const r = elt !== undefined ? items[elt] : items[x[0]];
+            console.log({ x, r });
+            const s = samples[r.sampleId];
+            return {
+                ...r,
+                sampleId: s?.label || s?.id || 'unknown',
+            };
+        }
+        else {
+            return undefined;
+        }
+    }
+    return (React.createElement("div", { ref: ref, onMouseMove: e => displayModel.setHoveredInfo?.(getFeatureUnderMouse(e.clientX, e.clientY)), onMouseLeave: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, onMouseOut: () => {
+            displayModel.setHoveredInfo?.(undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        } },
+        React.createElement(PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+            } })));
+});
+export default LinearMafRendering;
+//# sourceMappingURL=LinearMafRendering.js.map

package/dist/LinearMafRenderer/components/LinearMafRendering.js.map

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

@@ -1,5 +1,5 @@
 import LinearMafRenderer from './LinearMafRenderer';
-import ReactComponent from './components/ReactComponent';
+import ReactComponent from './components/LinearMafRendering';
 import configSchema from './configSchema';
 export default function LinearMafRendererF(pluginManager) {
     pluginManager.addRendererType(() => new LinearMafRenderer({

package/dist/LinearMafRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/index.ts"],"names":[],"mappings":"AAEA,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,cAAc,MAAM,iCAAiC,CAAA;AAC5D,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,mBAAmB;QACzB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/LinearMafRenderer/makeImageData.d.ts

@@ -15,6 +15,8 @@ export declare function makeImageData({ ctx, renderArgs, }: {
     ctx: CanvasRenderingContext2D;
     renderArgs: RenderArgs;
 }): {
-    rbush: any;
+    flatbush: ArrayBufferLike;
+    items: import("./rendering").RenderedBase[];
+    samples: Sample[];
 };
 export {};

package/dist/LinearMafRenderer/makeImageData.js

@@ -1,5 +1,5 @@
 import { createJBrowseTheme } from '@jbrowse/core/ui';
-import RBush from 'rbush';
+import Flatbush from 'flatbush';
 import { FONT_CONFIG, processFeatureAlignment, processFeatureInsertions, } from './rendering';
 import { getColorBaseMap, getContrastBaseMap } from './util';
 export function makeImageData({ ctx, renderArgs, }) {
@@ -28,7 +28,8 @@ export function makeImageData({ ctx, renderArgs, }) {
         showAllLetters,
         mismatchRendering,
         showAsUpperCase,
-        spatialIndex: new RBush(),
+        spatialIndex: [],
+        spatialIndexCoords: [],
         lastInsertedX: -Infinity, // Start with -Infinity so first item is always inserted
     };
     // First pass: render alignments (gaps, matches, mismatches, text)
@@ -39,9 +40,15 @@ export function makeImageData({ ctx, renderArgs, }) {
     for (const feature of features.values()) {
         processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext);
     }
-    // Return serialized RBush spatial index
+    const flatbush = new Flatbush(renderingContext.spatialIndex.length);
+    for (let i = 0, l = renderingContext.spatialIndexCoords.length; i < l; i += 4) {
+        flatbush.add(renderingContext.spatialIndexCoords[i], renderingContext.spatialIndexCoords[i + 1], renderingContext.spatialIndexCoords[i + 2], renderingContext.spatialIndexCoords[i + 3]);
+    }
+    flatbush.finish();
     return {
-        rbush: renderingContext.spatialIndex.toJSON(),
+        flatbush: flatbush.data,
+        items: renderingContext.spatialIndex,
+        samples,
     };
 }
 //# sourceMappingURL=makeImageData.js.map

package/dist/LinearMafRenderer/makeImageData.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/features.d.ts

@@ -1,21 +1,4 @@
 import { Feature } from '@jbrowse/core/util';
 import type { GenomicRegion, RenderingContext } from './types';
-/**
- * Processes alignment data for a single feature, rendering gaps, matches, mismatches, and text
- * @param feature - JBrowse feature containing alignment data
- * @param region - Genomic region being rendered
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param sampleToRowMap - Maps sample IDs to row indices
- * @param renderingContext - Shared rendering parameters
- */
 export declare function processFeatureAlignment(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;
-/**
- * Processes insertion data for a single feature in a separate pass
- * Insertions are rendered on top to ensure visibility
- * @param feature - JBrowse feature containing alignment data
- * @param region - Genomic region being rendered
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param sampleToRowMap - Maps sample IDs to row indices
- * @param renderingContext - Shared rendering parameters
- */
 export declare function processFeatureInsertions(feature: Feature, region: GenomicRegion, bpPerPx: number, sampleToRowMap: Map<string, number>, renderingContext: RenderingContext): void;

package/dist/LinearMafRenderer/rendering/features.js

@@ -4,19 +4,10 @@ import { renderInsertions } from './insertions';
 import { renderMatches } from './matches';
 import { renderMismatches } from './mismatches';
 import { renderText } from './text';
-/**
- * Processes alignment data for a single feature, rendering gaps, matches, mismatches, and text
- * @param feature - JBrowse feature containing alignment data
- * @param region - Genomic region being rendered
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param sampleToRowMap - Maps sample IDs to row indices
- * @param renderingContext - Shared rendering parameters
- */
 export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap, renderingContext) {
     const [leftPx] = featureSpanPx(feature, region, bpPerPx);
     const alignments = feature.get('alignments');
     const referenceSeq = feature.get('seq').toLowerCase();
-    const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
     for (const [sampleId, alignmentData] of Object.entries(alignments)) {
         const row = sampleToRowMap.get(sampleId);
         if (row === undefined) {
@@ -25,26 +16,16 @@ export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap
         const originalAlignment = alignmentData.seq;
         const alignment = originalAlignment.toLowerCase();
         const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
-        renderGaps(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
-        renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
-        renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, sampleId, featureId, alignmentData.start, alignmentData.chr);
-        renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop, sampleId, featureId);
+        renderGaps(renderingContext, alignment, referenceSeq, leftPx, rowTop);
+        renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
+        renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
+        renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop);
     }
 }
-/**
- * Processes insertion data for a single feature in a separate pass
- * Insertions are rendered on top to ensure visibility
- * @param feature - JBrowse feature containing alignment data
- * @param region - Genomic region being rendered
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param sampleToRowMap - Maps sample IDs to row indices
- * @param renderingContext - Shared rendering parameters
- */
 export function processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext) {
     const [leftPx] = featureSpanPx(feature, region, bpPerPx);
     const alignments = feature.get('alignments');
     const referenceSeq = feature.get('seq').toLowerCase();
-    const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
     for (const [sampleId, alignmentData] of Object.entries(alignments)) {
         const row = sampleToRowMap.get(sampleId);
         if (row === undefined) {
@@ -52,7 +33,7 @@ export function processFeatureInsertions(feature, region, bpPerPx, sampleToRowMa
         }
         const alignment = alignmentData.seq.toLowerCase();
         const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
-        renderInsertions(renderingContext, alignment, referenceSeq, leftPx, rowTop, bpPerPx, sampleId, featureId, alignmentData.start, alignmentData.chr);
+        renderInsertions(renderingContext, alignment, referenceSeq, leftPx, rowTop, bpPerPx, row, alignmentData.start, alignmentData.chr);
     }
 }
 //# sourceMappingURL=features.js.map

package/dist/LinearMafRenderer/rendering/features.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/gaps.d.ts

@@ -1,12 +1,2 @@
 import type { RenderingContext } from './types';
-/**
- * Renders gap indicators (horizontal lines) where the alignment has deletions relative to reference
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export declare function renderGaps(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;
+export declare function renderGaps(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number): void;

package/dist/LinearMafRenderer/rendering/gaps.js

@@ -1,16 +1,5 @@
-import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
 import { GAP_STROKE_OFFSET } from './types';
-/**
- * Renders gap indicators (horizontal lines) where the alignment has deletions relative to reference
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export function renderGaps(context, alignment, seq, leftPx, rowTop, sampleId, featureId, alignmentStart, chr) {
+export function renderGaps(context, alignment, seq, leftPx, rowTop) {
     const { ctx, scale } = context;
     const h2 = context.rowHeight / 2;
     ctx.beginPath();
@@ -21,11 +10,6 @@ export function renderGaps(context, alignment, seq, leftPx, rowTop, sampleId, fe
                 const xPos = leftPx + scale * genomicOffset;
                 ctx.moveTo(xPos, rowTop + h2);
                 ctx.lineTo(xPos + scale + GAP_STROKE_OFFSET, rowTop + h2);
-                // Add to spatial index if distance filter allows
-                if (shouldAddToSpatialIndex(xPos, context)) {
-                    const renderedBase = createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, '-', false, false, true, false, featureId);
-                    addToSpatialIndex(context, renderedBase);
-                }
             }
             genomicOffset++;
         }

package/dist/LinearMafRenderer/rendering/gaps.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/insertions.d.ts

@@ -1,14 +1,2 @@
 import type { RenderingContext } from './types';
-/**
- * Renders insertion markers where the alignment has bases not present in reference
- * Large insertions show count, small ones show as colored bars with optional borders
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;
+export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/insertions.js

@@ -1,20 +1,8 @@
 import { measureText } from '@jbrowse/core/util';
 import { fillRect, getCharWidthHeight } from '../util';
-import { addToSpatialIndex, createRenderedInsertion, shouldAddToSpatialIndex, } from './spatialIndex';
+import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { CHAR_SIZE_WIDTH, HIGH_BP_PER_PX_THRESHOLD, HIGH_ZOOM_THRESHOLD, INSERTION_BORDER_HEIGHT, INSERTION_BORDER_WIDTH, INSERTION_LINE_WIDTH, INSERTION_PADDING, LARGE_INSERTION_THRESHOLD, MIN_ROW_HEIGHT_FOR_BORDERS, } from './types';
-/**
- * Renders insertion markers where the alignment has bases not present in reference
- * Large insertions show count, small ones show as colored bars with optional borders
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param bpPerPx - Base pairs per pixel (zoom level)
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, featureId, alignmentStart, chr) {
+export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, rowHeight } = context;
     const { charHeight } = getCharWidthHeight();
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
@@ -75,7 +63,13 @@ export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerP
             // Add insertion to spatial index with actual rendered dimensions
             // Insertions always bypass distance filter
             if (shouldAddToSpatialIndex(actualXPos, context, true)) {
-                addToSpatialIndex(context, createRenderedInsertion(actualXPos, rowTop, actualWidth, context, genomicOffset + alignmentStart, chr, sampleId, insertionSequence, featureId));
+                addToSpatialIndex(context, actualXPos, rowTop, actualXPos + actualWidth, rowTop + context.h, {
+                    pos: genomicOffset + alignmentStart,
+                    chr,
+                    base: insertionSequence,
+                    sampleId,
+                    isInsertion: true,
+                });
             }
         }
         genomicOffset++;

package/dist/LinearMafRenderer/rendering/insertions.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/matches.d.ts

@@ -1,13 +1,2 @@
 import type { RenderingContext } from './types';
-/**
- * Renders background rectangles for positions where alignment matches reference
- * Only renders when showAllLetters is false
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;
+export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/matches.js

@@ -1,18 +1,7 @@
 import { fillRect } from '../util';
-import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
+import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { GAP_STROKE_OFFSET } from './types';
-/**
- * Renders background rectangles for positions where alignment matches reference
- * Only renders when showAllLetters is false
- * @param context - Rendering context with canvas and styling info
- * @param alignment - The aligned sequence for this sample
- * @param seq - The reference sequence
- * @param leftPx - Left pixel position of the feature
- * @param rowTop - Top pixel position of the row
- * @param alignmentStart - Start position of the alignment
- * @param chr - Chromosome/sequence name
- */
-export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId, featureId, alignmentStart, chr) {
+export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
     if (context.showAllLetters) {
         return;
     }
@@ -30,8 +19,12 @@ export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId,
                 fillRect(ctx, xPos, rowTop, scale + GAP_STROKE_OFFSET, h, canvasWidth);
                 // Add to spatial index if distance filter allows
                 if (shouldAddToSpatialIndex(xPos, context)) {
-                    const renderedBase = createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar || '', true, false, false, false, featureId);
-                    addToSpatialIndex(context, renderedBase);
+                    addToSpatialIndex(context, xPos, rowTop, xPos + context.scale + GAP_STROKE_OFFSET, rowTop + context.h, {
+                        pos: genomicOffset + alignmentStart,
+                        chr,
+                        base: currentChar || '',
+                        sampleId,
+                    });
                 }
             }
             genomicOffset++;

package/dist/LinearMafRenderer/rendering/matches.js.map

@@ -1 +1 @@
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package/dist/LinearMafRenderer/rendering/mismatches.d.ts

@@ -10,4 +10,4 @@ import type { RenderingContext } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: string, featureId: string, alignmentStart: number, chr: string): void;
+export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/mismatches.js

@@ -1,5 +1,5 @@
 import { fillRect } from '../util';
-import { addToSpatialIndex, createRenderedBase, shouldAddToSpatialIndex, } from './spatialIndex';
+import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
 import { GAP_STROKE_OFFSET } from './types';
 /**
  * Renders colored rectangles for mismatches and matches (when showAllLetters is true)
@@ -12,7 +12,7 @@ import { GAP_STROKE_OFFSET } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, featureId, alignmentStart, chr) {
+export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, showAllLetters, mismatchRendering, colorForBase, } = context;
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
         const currentChar = alignment[i];
@@ -26,7 +26,12 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                         : 'orange');
                     // Add to spatial index if distance filter allows
                     if (shouldAddToSpatialIndex(xPos, context)) {
-                        addToSpatialIndex(context, createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar, false, true, false, false, featureId));
+                        addToSpatialIndex(context, xPos, rowTop, xPos + context.scale + GAP_STROKE_OFFSET, rowTop + context.h, {
+                            pos: genomicOffset + alignmentStart,
+                            chr,
+                            base: currentChar,
+                            sampleId,
+                        });
                     }
                 }
                 else if (showAllLetters) {
@@ -36,7 +41,12 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                         : 'lightblue');
                     // Add to spatial index if distance filter allows
                     if (shouldAddToSpatialIndex(xPos, context)) {
-                        addToSpatialIndex(context, createRenderedBase(xPos, rowTop, context, genomicOffset + alignmentStart, chr, sampleId, currentChar, true, false, false, false, featureId));
+                        addToSpatialIndex(context, xPos, rowTop, xPos + context.scale + GAP_STROKE_OFFSET, rowTop + context.h, {
+                            pos: genomicOffset + alignmentStart,
+                            chr,
+                            base: currentChar,
+                            sampleId,
+                        });
                     }
                 }
             }

package/dist/LinearMafRenderer/rendering/mismatches.js.map

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