@jbrowse/plugin-variants 4.0.3 → 4.1.1

package/esm/MultiLinearVariantMatrixDisplay/model.js

@@ -14,6 +14,12 @@ export default function stateModelFactory(configSchema) {
         get prefersOffset() {
             return true;
         },
+        get featureWidgetType() {
+            return {
+                type: 'VariantFeatureWidget',
+                id: 'variantFeature',
+            };
+        },
     }))
         .views(self => ({
         renderProps() {

package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts

@@ -1,6 +1,6 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import VariantRendererType from '../shared/VariantRendererType.ts';
 import type { RenderArgsDeserialized } from './types.ts';
-export default class LinearVariantMatrixRenderer extends FeatureRendererType {
+export default class LinearVariantMatrixRenderer extends VariantRendererType {
     supportsSVG: boolean;
     render(renderProps: RenderArgsDeserialized): Promise<import("librpc-web-mod").RpcResult>;
 }

package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js

@@ -1,14 +1,15 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import { renderToAbstractCanvas } from '@jbrowse/core/util';
 import { rpcResult } from '@jbrowse/core/util/librpc';
 import { collectTransferables } from '@jbrowse/core/util/offscreenCanvasPonyfill';
-export default class LinearVariantMatrixRenderer extends FeatureRendererType {
+import VariantRendererType from "../shared/VariantRendererType.js";
+export default class LinearVariantMatrixRenderer extends VariantRendererType {
     supportsSVG = true;
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
-        const { height, regions, bpPerPx, scrollTop, rowHeight } = renderProps;
+        const { height, regions, bpPerPx, scrollTop, rowHeight, sessionId, trackInstanceId, } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
+        this.cacheFeatures({ sessionId, trackInstanceId }, region.refName, features);
         const { makeImageData } = await import("./makeImageData.js");
         const { mafs, ...rest } = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
             ctx,
@@ -16,14 +17,15 @@ export default class LinearVariantMatrixRenderer extends FeatureRendererType {
             canvasHeight: height,
             renderArgs: { ...renderProps, features },
         }));
+        const simplifiedFeatures = mafs.map(({ feature }) => ({
+            uniqueId: feature.id(),
+            start: feature.get('start'),
+            end: feature.get('end'),
+            refName: feature.get('refName'),
+        }));
         const serialized = {
             ...rest,
-            simplifiedFeatures: mafs.map(({ feature }) => ({
-                uniqueId: feature.id(),
-                start: feature.get('start'),
-                end: feature.get('end'),
-                refName: feature.get('refName'),
-            })),
+            simplifiedFeatures,
             height,
             width,
             origScrollTop: scrollTop,

package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts

@@ -6,6 +6,12 @@ interface FeatureData {
     description: string;
     length: number;
 }
+interface SimplifiedFeature {
+    uniqueId: string;
+}
+interface RenderingProps {
+    onFeatureClick?: (event: React.MouseEvent, featureId: string) => void;
+}
 declare const MultiLinearVariantMatrixRendering: (props: {
     width: number;
     height: number;
@@ -15,5 +21,7 @@ declare const MultiLinearVariantMatrixRendering: (props: {
     rowHeight: number;
     origScrollTop: number;
     totalHeight: number;
+    simplifiedFeatures?: SimplifiedFeature[];
+    renderingProps?: RenderingProps;
 }) => import("react/jsx-runtime").JSX.Element;
 export default MultiLinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js

@@ -5,7 +5,7 @@ import { getBpDisplayStr } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { makeSimpleAltString } from "../../VcfFeature/util.js";
 const MultiLinearVariantMatrixRendering = observer(function MultiLinearVariantMatrixRendering(props) {
-    const { arr, width, displayModel, featureData, totalHeight, origScrollTop, rowHeight, } = props;
+    const { arr, width, displayModel, featureData, totalHeight, origScrollTop, rowHeight, simplifiedFeatures, renderingProps, } = props;
     const ref = useRef(null);
     const lastHoveredRef = useRef(undefined);
     const getFeatureUnderMouse = useCallback((eventClientX, eventClientY) => {
@@ -52,7 +52,19 @@ const MultiLinearVariantMatrixRendering = observer(function MultiLinearVariantMa
             displayModel.setHoveredGenotype(undefined);
         }
     }, [displayModel]);
-    return (_jsx("div", { ref: ref, onMouseMove: handleMouseMove, onMouseLeave: handleMouseLeave, onMouseOut: handleMouseLeave, style: {
+    const handleClick = useCallback((e) => {
+        if (!ref.current || !simplifiedFeatures) {
+            return;
+        }
+        const r = ref.current.getBoundingClientRect();
+        const offsetX = e.clientX - r.left;
+        const featureIdx = Math.floor((offsetX / width) * arr.length);
+        const feature = simplifiedFeatures[featureIdx];
+        if (feature) {
+            renderingProps?.onFeatureClick?.(e, feature.uniqueId);
+        }
+    }, [arr.length, width, simplifiedFeatures, renderingProps]);
+    return (_jsx("div", { ref: ref, onMouseMove: handleMouseMove, onMouseLeave: handleMouseLeave, onMouseOut: handleMouseLeave, onClick: handleClick, style: {
             overflow: 'visible',
             position: 'relative',
             height: totalHeight,

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -17,8 +17,10 @@ function drawPhasedMode(drawCtx, mafs) {
             const samp = feature.get('samples');
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name, HP } = sources[j];
-                const s = samp[name];
+                const source = sources[j];
+                const { name, HP, baseName } = source;
+                const sampleName = baseName ?? name;
+                const s = samp[sampleName];
                 if (s) {
                     const genotype = s.GT?.[0];
                     if (genotype) {
@@ -47,8 +49,10 @@ function drawPhasedMode(drawCtx, mafs) {
             }
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name, HP } = sources[j];
-                const genotype = samp[name];
+                const source = sources[j];
+                const { name, HP, baseName } = source;
+                const sampleName = baseName ?? name;
+                const genotype = samp[sampleName];
                 if (genotype) {
                     arr2.push(genotype);
                     const isPhased = genotype.includes('|');
@@ -82,8 +86,9 @@ function drawAlleleCountMode(drawCtx, mafs) {
             const samp = feature.get('samples');
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name } = sources[j];
-                const s = samp[name];
+                const source = sources[j];
+                const sampleName = source.baseName ?? source.name;
+                const s = samp[sampleName];
                 if (s) {
                     const genotype = s.GT?.[0];
                     if (genotype) {
@@ -105,8 +110,9 @@ function drawAlleleCountMode(drawCtx, mafs) {
             }
             for (let j = startRow; j < endRow; j++) {
                 const y = j * h - scrollTop;
-                const { name } = sources[j];
-                const genotype = samp[name];
+                const source = sources[j];
+                const sampleName = source.baseName ?? source.name;
+                const genotype = samp[sampleName];
                 if (genotype) {
                     arr2.push(genotype);
                     const c = getAlleleColor(genotype, mostFrequentAlt, colorCache, splitCache, true);

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -1,6 +1,6 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import VariantRendererType from '../shared/VariantRendererType.ts';
 import type { MultiRenderArgsDeserialized } from './types.ts';
-export default class MultiVariantRenderer extends FeatureRendererType {
+export default class MultiVariantRenderer extends VariantRendererType {
     supportsSVG: boolean;
     render(renderProps: MultiRenderArgsDeserialized): Promise<import("librpc-web-mod").RpcResult>;
 }

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -1,14 +1,15 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import { renderToAbstractCanvas } from '@jbrowse/core/util';
 import { rpcResult } from '@jbrowse/core/util/librpc';
 import { collectTransferables } from '@jbrowse/core/util/offscreenCanvasPonyfill';
-export default class MultiVariantRenderer extends FeatureRendererType {
+import VariantRendererType from "../shared/VariantRendererType.js";
+export default class MultiVariantRenderer extends VariantRendererType {
     supportsSVG = true;
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
-        const { height, referenceDrawingMode, regions, bpPerPx, scrollTop } = renderProps;
+        const { height, referenceDrawingMode, regions, bpPerPx, scrollTop, sessionId, trackInstanceId, } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
+        this.cacheFeatures({ sessionId, trackInstanceId }, region.refName, features);
         const { makeImageData } = await import("./makeImageData.js");
         const ret = await renderToAbstractCanvas(width, height, renderProps, ctx => {
             if (referenceDrawingMode === 'skip') {

package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.d.ts

@@ -17,6 +17,9 @@ interface MinimizedVariantRecord {
 interface MultiVariantDisplayModel {
     setHoveredGenotype?: (genotype?: Record<string, unknown>) => void;
 }
+interface RenderingProps {
+    onFeatureClick?: (event: React.MouseEvent, featureId: string) => void;
+}
 declare const MultiVariantRendering: (props: {
     regions: Region[];
     features: Map<string, Feature>;
@@ -30,5 +33,6 @@ declare const MultiVariantRendering: (props: {
     flatbush: any;
     items: Item[];
     displayModel: MultiVariantDisplayModel;
+    renderingProps?: RenderingProps;
 }) => import("react/jsx-runtime").JSX.Element;
 export default MultiVariantRendering;

package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.js

@@ -7,7 +7,7 @@ import { observer } from 'mobx-react';
 import { minElt } from "./util.js";
 import { makeSimpleAltString } from "../../VcfFeature/util.js";
 const MultiVariantRendering = observer(function MultiVariantRendering(props) {
-    const { flatbush, items, displayModel, featureGenotypeMap, totalHeight, origScrollTop, } = props;
+    const { flatbush, items, displayModel, featureGenotypeMap, totalHeight, origScrollTop, renderingProps, } = props;
     const ref = useRef(null);
     const lastHoveredRef = useRef(undefined);
     const flatbush2 = useMemo(() => Flatbush.from(flatbush), [flatbush]);
@@ -53,7 +53,28 @@ const MultiVariantRendering = observer(function MultiVariantRendering(props) {
             displayModel.setHoveredGenotype?.(undefined);
         }
     }, [displayModel]);
-    return (_jsx("div", { ref: ref, onMouseMove: handleMouseMove, onMouseLeave: handleMouseLeave, onMouseOut: handleMouseLeave, style: {
+    const getFeatureIdUnderMouse = useCallback((eventClientX, eventClientY) => {
+        if (!ref.current) {
+            return undefined;
+        }
+        const rect = ref.current.getBoundingClientRect();
+        const offsetX = eventClientX - rect.left;
+        const offsetY = eventClientY - rect.top;
+        const canvasOffsetY = offsetY - origScrollTop;
+        const x = flatbush2.search(offsetX, canvasOffsetY, offsetX + 1, canvasOffsetY + 1);
+        if (x.length) {
+            const res = minElt(x, idx => items[idx]?.bpLen ?? 0);
+            return items[res]?.featureId;
+        }
+        return undefined;
+    }, [flatbush2, items, origScrollTop]);
+    const handleClick = useCallback((e) => {
+        const featureId = getFeatureIdUnderMouse(e.clientX, e.clientY);
+        if (featureId) {
+            renderingProps?.onFeatureClick?.(e, featureId);
+        }
+    }, [getFeatureIdUnderMouse, renderingProps]);
+    return (_jsx("div", { ref: ref, onMouseMove: handleMouseMove, onMouseLeave: handleMouseLeave, onMouseOut: handleMouseLeave, onClick: handleClick, style: {
             overflow: 'visible',
             position: 'relative',
             height: totalHeight,

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -20,15 +20,20 @@ function drawPhasedMode(drawCtx, itemData, mafs) {
             samp = feature.get('genotypes');
             genotypesCache.set(featureId, samp);
         }
+        const featureType = feature.get('type');
+        const featureStrand = feature.get('strand');
+        const alpha = bpLen > 5 ? 0.75 : 1;
         for (let j = startRow; j < endRow; j++) {
             const y = j * h - scrollTop;
-            const { name, HP } = sources[j];
-            const genotype = samp[name];
+            const source = sources[j];
+            const { name, HP, baseName } = source;
+            const sampleName = baseName ?? name;
+            const genotype = samp[sampleName];
             if (genotype) {
                 const isPhased = genotype.includes('|');
                 if (isPhased) {
                     const alleles = splitCache[genotype] ?? (splitCache[genotype] = genotype.split('|'));
-                    if (drawPhased(alleles, ctx, x, y, w, drawH, HP, undefined, drawRef)) {
+                    if (drawPhased(alleles, ctx, x, y, w, drawH, HP, undefined, drawRef, alpha, featureType, featureStrand)) {
                         items.push({ name, genotype, featureId, bpLen });
                         coords.push(x, y, x + w, y + drawH);
                     }

package/esm/PlinkLDAdapter/PlinkLDAdapter.d.ts

@@ -0,0 +1,25 @@
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { PlinkLDHeader, PlinkLDRecord } from './types.ts';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+export default class PlinkLDAdapter extends BaseAdapter {
+    private configured?;
+    private configurePre;
+    private parseHeader;
+    protected configurePre2(opts?: BaseOptions): Promise<{
+        records: PlinkLDRecord[];
+        header: PlinkLDHeader;
+        refNames: string[];
+    }>;
+    configure(opts?: BaseOptions): Promise<{
+        records: PlinkLDRecord[];
+        header: PlinkLDHeader;
+        refNames: string[];
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<PlinkLDHeader>;
+    getLDRecords(query: NoAssemblyRegion, opts?: BaseOptions): Promise<PlinkLDRecord[]>;
+    getLDRecordsInRegion(query: NoAssemblyRegion, opts?: BaseOptions): Promise<PlinkLDRecord[]>;
+    private parseLine;
+    freeResources(): void;
+}

package/esm/PlinkLDAdapter/PlinkLDAdapter.js

@@ -0,0 +1,147 @@
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzipText, updateStatus } from '@jbrowse/core/util';
+export default class PlinkLDAdapter extends BaseAdapter {
+    configured;
+    async configurePre(opts) {
+        const ldLocation = this.getConf('ldLocation');
+        const text = await fetchAndMaybeUnzipText(ldLocation, opts);
+        const lines = text.split('\n').filter(line => line.trim());
+        if (lines.length === 0) {
+            throw new Error('Empty LD file');
+        }
+        const header = this.parseHeader(lines[0]);
+        const records = [];
+        const refNamesSet = new Set();
+        for (let i = 1; i < lines.length; i++) {
+            const record = this.parseLine(lines[i], header);
+            if (record) {
+                records.push(record);
+                refNamesSet.add(record.chrA);
+                refNamesSet.add(record.chrB);
+            }
+        }
+        const refNames = [...refNamesSet].sort();
+        return { records, header, refNames };
+    }
+    parseHeader(headerLine) {
+        const columns = headerLine.trim().split(/\s+/);
+        const findIdx = (names) => {
+            for (const name of names) {
+                const idx = columns.indexOf(name);
+                if (idx !== -1) {
+                    return idx;
+                }
+            }
+            return -1;
+        };
+        const chrAIdx = findIdx(['CHR_A', 'CHR1']);
+        const bpAIdx = findIdx(['BP_A', 'BP1', 'POS_A', 'POS1']);
+        const snpAIdx = findIdx(['SNP_A', 'SNP1', 'ID_A', 'ID1']);
+        const chrBIdx = findIdx(['CHR_B', 'CHR2']);
+        const bpBIdx = findIdx(['BP_B', 'BP2', 'POS_B', 'POS2']);
+        const snpBIdx = findIdx(['SNP_B', 'SNP2', 'ID_B', 'ID2']);
+        const r2Idx = findIdx(['R2', 'R^2', 'RSQ']);
+        const dprimeIdx = findIdx(['DP', 'DPRIME', "D'"]);
+        const mafAIdx = findIdx(['MAF_A', 'MAF1']);
+        const mafBIdx = findIdx(['MAF_B', 'MAF2']);
+        if (chrAIdx === -1 || bpAIdx === -1 || chrBIdx === -1 || bpBIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected columns CHR_A, BP_A, CHR_B, BP_B. Got: ${columns.join(', ')}`);
+        }
+        if (r2Idx === -1 && dprimeIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected at least R2 or DP column. Got: ${columns.join(', ')}`);
+        }
+        return {
+            columns,
+            hasR2: r2Idx !== -1,
+            hasDprime: dprimeIdx !== -1,
+            hasMafA: mafAIdx !== -1,
+            hasMafB: mafBIdx !== -1,
+            chrAIdx,
+            bpAIdx,
+            snpAIdx,
+            chrBIdx,
+            bpBIdx,
+            snpBIdx,
+            r2Idx,
+            dprimeIdx,
+            mafAIdx,
+            mafBIdx,
+        };
+    }
+    async configurePre2(opts) {
+        if (!this.configured) {
+            this.configured = this.configurePre(opts).catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async configure(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Loading LD data', statusCallback, () => this.configurePre2(opts));
+    }
+    async getRefNames(opts = {}) {
+        const { refNames } = await this.configure(opts);
+        return refNames;
+    }
+    async getHeader(opts) {
+        const { header } = await this.configure(opts);
+        return header;
+    }
+    async getLDRecords(query, opts = {}) {
+        const { refName, start, end } = query;
+        const { records } = await this.configure(opts);
+        const filtered = records.filter(r => r.chrA === refName && r.bpA >= start && r.bpA <= end);
+        return filtered;
+    }
+    async getLDRecordsInRegion(query, opts = {}) {
+        const { refName, start, end } = query;
+        const records = await this.getLDRecords(query, opts);
+        const filtered = records.filter(r => r.chrB === refName &&
+            r.bpB >= start &&
+            r.bpB <= end &&
+            r.chrA === refName &&
+            r.bpA >= start &&
+            r.bpA <= end);
+        return filtered;
+    }
+    parseLine(line, header) {
+        const fields = line.trim().split(/\s+/);
+        const chrA = fields[header.chrAIdx];
+        const bpA = Number.parseInt(fields[header.bpAIdx] ?? '', 10);
+        const snpA = header.snpAIdx >= 0 ? fields[header.snpAIdx] : `${chrA}:${bpA}`;
+        const chrB = fields[header.chrBIdx];
+        const bpB = Number.parseInt(fields[header.bpBIdx] ?? '', 10);
+        const snpB = header.snpBIdx >= 0 ? fields[header.snpBIdx] : `${chrB}:${bpB}`;
+        if (!chrA || !chrB || Number.isNaN(bpA) || Number.isNaN(bpB)) {
+            return null;
+        }
+        const r2 = header.r2Idx >= 0
+            ? Number.parseFloat(fields[header.r2Idx] ?? '')
+            : undefined;
+        const dprime = header.dprimeIdx >= 0
+            ? Number.parseFloat(fields[header.dprimeIdx] ?? '')
+            : undefined;
+        const mafA = header.mafAIdx >= 0
+            ? Number.parseFloat(fields[header.mafAIdx] ?? '')
+            : undefined;
+        const mafB = header.mafBIdx >= 0
+            ? Number.parseFloat(fields[header.mafBIdx] ?? '')
+            : undefined;
+        return {
+            chrA,
+            bpA,
+            snpA: snpA ?? `${chrA}:${bpA}`,
+            chrB,
+            bpB,
+            snpB: snpB ?? `${chrB}:${bpB}`,
+            r2: r2 ?? 0,
+            dprime,
+            mafA,
+            mafB,
+        };
+    }
+    freeResources() {
+    }
+}

package/esm/PlinkLDAdapter/PlinkLDTabixAdapter.d.ts

@@ -0,0 +1,24 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { PlinkLDHeader, PlinkLDRecord } from './types.ts';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+export default class PlinkLDTabixAdapter extends BaseAdapter {
+    private configured?;
+    private configurePre;
+    private parseHeader;
+    protected configurePre2(): Promise<{
+        ld: TabixIndexedFile;
+        header: PlinkLDHeader;
+    }>;
+    configure(opts?: BaseOptions): Promise<{
+        ld: TabixIndexedFile;
+        header: PlinkLDHeader;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<PlinkLDHeader>;
+    getLDRecords(query: NoAssemblyRegion, opts?: BaseOptions): Promise<PlinkLDRecord[]>;
+    getLDRecordsInRegion(query: NoAssemblyRegion, opts?: BaseOptions): Promise<PlinkLDRecord[]>;
+    private parseLine;
+    freeResources(): void;
+}

package/esm/PlinkLDAdapter/PlinkLDTabixAdapter.js

@@ -0,0 +1,156 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { updateStatus } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+export default class PlinkLDTabixAdapter extends BaseAdapter {
+    configured;
+    async configurePre(_opts) {
+        const ldLocation = this.getConf('ldLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = openLocation(ldLocation, this.pluginManager);
+        const isCSI = indexType === 'CSI';
+        const ld = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        const headerLine = await ld.getHeader();
+        const header = this.parseHeader(headerLine);
+        return { ld, header };
+    }
+    parseHeader(headerLine) {
+        const columns = headerLine.trim().split(/\s+/);
+        const findIdx = (names) => {
+            for (const name of names) {
+                const idx = columns.indexOf(name);
+                if (idx !== -1) {
+                    return idx;
+                }
+            }
+            return -1;
+        };
+        const chrAIdx = findIdx(['CHR_A', 'CHR1']);
+        const bpAIdx = findIdx(['BP_A', 'BP1', 'POS_A', 'POS1']);
+        const snpAIdx = findIdx(['SNP_A', 'SNP1', 'ID_A', 'ID1']);
+        const chrBIdx = findIdx(['CHR_B', 'CHR2']);
+        const bpBIdx = findIdx(['BP_B', 'BP2', 'POS_B', 'POS2']);
+        const snpBIdx = findIdx(['SNP_B', 'SNP2', 'ID_B', 'ID2']);
+        const r2Idx = findIdx(['R2', 'R^2', 'RSQ']);
+        const dprimeIdx = findIdx(['DP', 'DPRIME', "D'"]);
+        const mafAIdx = findIdx(['MAF_A', 'MAF1']);
+        const mafBIdx = findIdx(['MAF_B', 'MAF2']);
+        if (chrAIdx === -1 || bpAIdx === -1 || chrBIdx === -1 || bpBIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected columns CHR_A, BP_A, CHR_B, BP_B. Got: ${columns.join(', ')}`);
+        }
+        if (r2Idx === -1 && dprimeIdx === -1) {
+            throw new Error(`Invalid PLINK LD header. Expected at least R2 or DP column. Got: ${columns.join(', ')}`);
+        }
+        return {
+            columns,
+            hasR2: r2Idx !== -1,
+            hasDprime: dprimeIdx !== -1,
+            hasMafA: mafAIdx !== -1,
+            hasMafB: mafBIdx !== -1,
+            chrAIdx,
+            bpAIdx,
+            snpAIdx,
+            chrBIdx,
+            bpBIdx,
+            snpBIdx,
+            r2Idx,
+            dprimeIdx,
+            mafAIdx,
+            mafBIdx,
+        };
+    }
+    async configurePre2() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async configure(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.configurePre2());
+    }
+    async getRefNames(opts = {}) {
+        const { ld } = await this.configure(opts);
+        return ld.getReferenceSequenceNames(opts);
+    }
+    async getHeader(opts) {
+        const { header } = await this.configure(opts);
+        return header;
+    }
+    async getLDRecords(query, opts = {}) {
+        const { refName, start, end } = query;
+        const { ld, header } = await this.configure(opts);
+        const records = [];
+        await ld.getLines(refName, start, end, {
+            lineCallback: (line) => {
+                const record = this.parseLine(line, header);
+                if (record) {
+                    records.push(record);
+                }
+            },
+            ...opts,
+        });
+        return records;
+    }
+    async getLDRecordsInRegion(query, opts = {}) {
+        const { refName, start, end } = query;
+        const records = await this.getLDRecords(query, opts);
+        return records.filter(r => r.chrB === refName &&
+            r.bpB >= start &&
+            r.bpB <= end &&
+            r.chrA === refName &&
+            r.bpA >= start &&
+            r.bpA <= end);
+    }
+    parseLine(line, header) {
+        const fields = line.trim().split(/\s+/);
+        const chrA = fields[header.chrAIdx];
+        const bpA = Number.parseInt(fields[header.bpAIdx] ?? '', 10);
+        const snpA = header.snpAIdx >= 0 ? fields[header.snpAIdx] : `${chrA}:${bpA}`;
+        const chrB = fields[header.chrBIdx];
+        const bpB = Number.parseInt(fields[header.bpBIdx] ?? '', 10);
+        const snpB = header.snpBIdx >= 0 ? fields[header.snpBIdx] : `${chrB}:${bpB}`;
+        if (!chrA || !chrB || Number.isNaN(bpA) || Number.isNaN(bpB)) {
+            return null;
+        }
+        const r2 = header.r2Idx >= 0
+            ? Number.parseFloat(fields[header.r2Idx] ?? '')
+            : undefined;
+        const dprime = header.dprimeIdx >= 0
+            ? Number.parseFloat(fields[header.dprimeIdx] ?? '')
+            : undefined;
+        const mafA = header.mafAIdx >= 0
+            ? Number.parseFloat(fields[header.mafAIdx] ?? '')
+            : undefined;
+        const mafB = header.mafBIdx >= 0
+            ? Number.parseFloat(fields[header.mafBIdx] ?? '')
+            : undefined;
+        return {
+            chrA,
+            bpA,
+            snpA: snpA ?? `${chrA}:${bpA}`,
+            chrB,
+            bpB,
+            snpB: snpB ?? `${chrB}:${bpB}`,
+            r2: r2 ?? 0,
+            dprime,
+            mafA,
+            mafB,
+        };
+    }
+    freeResources() {
+    }
+}

package/esm/PlinkLDAdapter/configSchema.d.ts

@@ -0,0 +1,10 @@
+declare const PlinkLDAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    ldLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default PlinkLDAdapter;