@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/shared/components/LDFilterDialog.js

@@ -0,0 +1,102 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
+import Dialog from '@jbrowse/core/ui/Dialog';
+import { Alert, Box, Button, DialogActions, DialogContent, FormControlLabel, Switch, TextField, Typography, } from '@mui/material';
+export default function LDFilterDialog({ model, handleClose, }) {
+    const { minorAlleleFrequencyFilter, hweFilterThreshold, callRateFilter, filterStats, } = model;
+    const [maf, setMaf] = useState(`${minorAlleleFrequencyFilter}`);
+    const [hweEnabled, setHweEnabled] = useState(hweFilterThreshold > 0);
+    const [hweThreshold, setHweThreshold] = useState(hweFilterThreshold > 0 ? `${hweFilterThreshold}` : '0.001');
+    const [callRateEnabled, setCallRateEnabled] = useState(callRateFilter > 0);
+    const [callRate, setCallRate] = useState(callRateFilter > 0 ? `${callRateFilter}` : '0.95');
+    const [mafError, setMafError] = useState();
+    const [hweError, setHweError] = useState();
+    const [callRateError, setCallRateError] = useState();
+    const validateMaf = (val) => {
+        const num = Number.parseFloat(val);
+        if (Number.isNaN(num)) {
+            setMafError('Please enter a valid number');
+            return false;
+        }
+        if (num < 0 || num > 0.5) {
+            setMafError('MAF must be between 0 and 0.5');
+            return false;
+        }
+        setMafError(undefined);
+        return true;
+    };
+    const validateHwe = (val) => {
+        const num = Number.parseFloat(val);
+        if (Number.isNaN(num)) {
+            setHweError('Please enter a valid number');
+            return false;
+        }
+        if (num <= 0 || num > 1) {
+            setHweError('P-value must be between 0 and 1');
+            return false;
+        }
+        setHweError(undefined);
+        return true;
+    };
+    const validateCallRate = (val) => {
+        const num = Number.parseFloat(val);
+        if (Number.isNaN(num)) {
+            setCallRateError('Please enter a valid number');
+            return false;
+        }
+        if (num < 0 || num > 1) {
+            setCallRateError('Call rate must be between 0 and 1');
+            return false;
+        }
+        setCallRateError(undefined);
+        return true;
+    };
+    const hasError = !!mafError ||
+        (hweEnabled && !!hweError) ||
+        (callRateEnabled && !!callRateError);
+    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "LD Filter Settings", children: [_jsxs(DialogContent, { style: { width: 500 }, children: [filterStats ? (_jsxs(Alert, { severity: "info", style: { marginBottom: 16 }, children: [_jsx(Typography, { variant: "subtitle2", gutterBottom: true, children: "Filter Statistics" }), _jsxs(Box, { component: "ul", sx: { margin: 0, paddingLeft: 2 }, children: [_jsxs("li", { children: ["Total variants in region: ", filterStats.totalVariants] }), _jsxs("li", { children: ["Passed all filters: ", filterStats.passedVariants] }), filterStats.filteredByMaf > 0 && (_jsxs("li", { children: ["Filtered by MAF: ", filterStats.filteredByMaf] })), filterStats.filteredByLength > 0 && (_jsxs("li", { children: ["Filtered by length: ", filterStats.filteredByLength] })), filterStats.filteredByMultiallelic > 0 && (_jsxs("li", { children: ["Filtered by multiallelic: ", filterStats.filteredByMultiallelic] })), filterStats.filteredByHwe > 0 && (_jsxs("li", { children: ["Filtered by HWE: ", filterStats.filteredByHwe] })), filterStats.filteredByCallRate > 0 && (_jsxs("li", { children: ["Filtered by call rate: ", filterStats.filteredByCallRate] }))] })] })) : null, _jsx(Typography, { variant: "subtitle1", gutterBottom: true, children: "Minor Allele Frequency (MAF) Filter" }), _jsx(Typography, { variant: "body2", color: "textSecondary", component: "p", children: "Exclude variants with minor allele frequency below this threshold." }), _jsx(TextField, { value: maf, fullWidth: true, size: "small", label: "MAF threshold (0-0.5)", error: !!mafError, helperText: mafError, onChange: event => {
+                            const val = event.target.value;
+                            setMaf(val);
+                            validateMaf(val);
+                        }, style: { marginBottom: 24 } }), _jsx(Typography, { variant: "subtitle1", gutterBottom: true, children: "Hardy-Weinberg Equilibrium (HWE) Filter" }), _jsx(Typography, { variant: "body2", color: "textSecondary", component: "p", children: "Exclude variants that deviate significantly from HWE, which may indicate genotyping errors or population stratification. This follows Haploview's approach." }), _jsx(FormControlLabel, { control: _jsx(Switch, { checked: hweEnabled, onChange: e => {
+                                setHweEnabled(e.target.checked);
+                            } }), label: "Enable HWE filter" }), hweEnabled ? (_jsx(TextField, { value: hweThreshold, fullWidth: true, size: "small", label: "P-value threshold", error: !!hweError, helperText: hweError ||
+                            'Variants with HWE p-value below this threshold are excluded (default: 0.001)', onChange: event => {
+                            const val = event.target.value;
+                            setHweThreshold(val);
+                            validateHwe(val);
+                        }, style: { marginTop: 8, marginBottom: 24 } })) : (_jsx("div", { style: { marginBottom: 24 } })), _jsx(Typography, { variant: "subtitle1", gutterBottom: true, children: "Call Rate Filter" }), _jsx(Typography, { variant: "body2", color: "textSecondary", component: "p", children: "Exclude variants with too many missing genotypes. Call rate is the proportion of samples with non-missing genotype calls." }), _jsx(FormControlLabel, { control: _jsx(Switch, { checked: callRateEnabled, onChange: e => {
+                                setCallRateEnabled(e.target.checked);
+                            } }), label: "Enable call rate filter" }), callRateEnabled ? (_jsx(TextField, { value: callRate, fullWidth: true, size: "small", label: "Minimum call rate (0-1)", error: !!callRateError, helperText: callRateError ||
+                            'Variants with call rate below this threshold are excluded (default: 0.95 = 95%)', onChange: event => {
+                            const val = event.target.value;
+                            setCallRate(val);
+                            validateCallRate(val);
+                        }, style: { marginTop: 8 } })) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: handleClose, color: "primary", children: "Cancel" }), _jsx(Button, { onClick: () => {
+                            const mafVal = Number.parseFloat(maf);
+                            if (!Number.isNaN(mafVal) && mafVal >= 0 && mafVal <= 0.5) {
+                                model.setMafFilter(mafVal);
+                            }
+                            if (hweEnabled) {
+                                const hweVal = Number.parseFloat(hweThreshold);
+                                if (!Number.isNaN(hweVal) && hweVal > 0 && hweVal <= 1) {
+                                    model.setHweFilter(hweVal);
+                                }
+                            }
+                            else {
+                                model.setHweFilter(0);
+                            }
+                            if (callRateEnabled) {
+                                const callRateVal = Number.parseFloat(callRate);
+                                if (!Number.isNaN(callRateVal) &&
+                                    callRateVal >= 0 &&
+                                    callRateVal <= 1) {
+                                    model.setCallRateFilter(callRateVal);
+                                }
+                            }
+                            else {
+                                model.setCallRateFilter(0);
+                            }
+                            handleClose();
+                        }, color: "primary", variant: "contained", disabled: hasError, children: "Apply" })] })] }));
+}

package/esm/shared/components/MAFFilterDialog.js

@@ -1,22 +1,29 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { Button, Dialog, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
-const useStyles = makeStyles()({
-    root: {
-        width: 500,
-    },
-});
+import Dialog from '@jbrowse/core/ui/Dialog';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 export default function MAFFilterDialog({ model, handleClose, }) {
-    const { minorAlleleFrequencyFilter = '' } = model;
-    const { classes } = useStyles();
+    const { minorAlleleFrequencyFilter = 0 } = model;
     const [maf, setMaf] = useState(`${minorAlleleFrequencyFilter}`);
-    return (_jsx(Dialog, { open: true, onClose: handleClose, title: "Set minor allele frequency (MAF)", children: _jsxs(DialogContent, { className: classes.root, children: [_jsx(Typography, { children: "Set minor allele frequency cutoff track. This will filter out rare variants that might not contribute to meaningful large scale patterns" }), _jsx(TextField, { value: maf, autoFocus: true, placeholder: "Enter MAF", onChange: event => {
-                        setMaf(event.target.value);
-                    } }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                                if (!Number.isNaN(+maf)) {
-                                    model.setMafFilter(+maf);
-                                }
+    const [error, setError] = useState();
+    return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Set minor allele frequency (MAF) filter", children: [_jsxs(DialogContent, { style: { width: 400 }, children: [_jsx(Typography, { children: "Filter out variants with minor allele frequency below this threshold. Valid range: 0 to 0.5" }), _jsx(TextField, { value: maf, autoFocus: true, fullWidth: true, margin: "normal", label: "MAF threshold", placeholder: "Enter MAF (0-0.5)", error: !!error, helperText: error, onChange: event => {
+                            const val = event.target.value;
+                            setMaf(val);
+                            const num = Number.parseFloat(val);
+                            if (Number.isNaN(num)) {
+                                setError('Please enter a valid number');
+                            }
+                            else if (num < 0 || num > 0.5) {
+                                setError('MAF must be between 0 and 0.5');
+                            }
+                            else {
+                                setError(undefined);
+                            }
+                        } })] }), _jsxs(DialogActions, { children: [_jsx(Button, { onClick: handleClose, color: "primary", children: "Cancel" }), _jsx(Button, { onClick: () => {
+                            const val = Number.parseFloat(maf);
+                            if (!Number.isNaN(val) && val >= 0 && val <= 0.5) {
+                                model.setMafFilter(val);
                                 handleClose();
-                            }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }) }));
+                            }
+                        }, color: "primary", variant: "contained", disabled: !!error, children: "Submit" })] })] }));
 }

package/esm/shared/components/RecombinationTrack.d.ts

@@ -0,0 +1,21 @@
+interface RecombinationTrackModel {
+    recombination?: {
+        values: number[];
+        positions: number[];
+    };
+    recombinationZoneHeight: number;
+}
+declare const RecombinationTrack: ({ model, recombination: recombinationProp, width, height, exportSVG, useGenomicPositions, regionStart, bpPerPx, }: {
+    model?: RecombinationTrackModel;
+    recombination?: {
+        values: number[];
+        positions: number[];
+    };
+    width: number;
+    height?: number;
+    exportSVG?: boolean;
+    useGenomicPositions?: boolean;
+    regionStart?: number;
+    bpPerPx?: number;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default RecombinationTrack;

package/esm/shared/components/RecombinationTrack.js

@@ -0,0 +1,54 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { getFillProps, getStrokeProps } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const YSCALEBAR_LABEL_OFFSET = 5;
+const FILL_COLOR = 'rgba(59, 130, 246, 0.2)';
+const STROKE_COLOR = 'rgb(59, 130, 246)';
+const RecombinationTrack = observer(function RecombinationTrack({ model, recombination: recombinationProp, width, height, exportSVG, useGenomicPositions, regionStart, bpPerPx, }) {
+    const recombination = recombinationProp ?? model?.recombination;
+    const trackHeight = height ?? model?.recombinationZoneHeight ?? 50;
+    if (!recombination || recombination.values.length === 0) {
+        return null;
+    }
+    const topPadding = YSCALEBAR_LABEL_OFFSET;
+    const bottomPadding = YSCALEBAR_LABEL_OFFSET;
+    const plotHeight = trackHeight - topPadding - bottomPadding;
+    const maxValue = Math.max(...recombination.values, 0.1);
+    const points = [];
+    let firstX;
+    let lastX;
+    const numSnps = recombination.values.length + 1;
+    for (let i = 0; i < recombination.values.length; i++) {
+        const value = recombination.values[i];
+        let x;
+        if (useGenomicPositions && regionStart !== undefined && bpPerPx) {
+            x = (recombination.positions[i] - regionStart) / bpPerPx;
+        }
+        else {
+            x = ((i + 1) * width) / numSnps;
+        }
+        const y = topPadding + plotHeight * (1 - value / maxValue);
+        if (firstX === undefined) {
+            firstX = x;
+        }
+        lastX = x;
+        points.push(`${points.length === 0 ? 'M' : 'L'} ${x.toFixed(1)} ${y.toFixed(1)}`);
+    }
+    if (points.length < 2 || firstX === undefined || lastX === undefined) {
+        return null;
+    }
+    const baseY = topPadding + plotHeight;
+    const areaPath = `${points.join(' ')} L ${lastX.toFixed(1)} ${baseY.toFixed(1)} L ${firstX.toFixed(1)} ${baseY.toFixed(1)} Z`;
+    if (exportSVG) {
+        return (_jsxs("g", { children: [_jsx("path", { d: areaPath, ...getFillProps(FILL_COLOR) }), _jsx("path", { d: points.join(' '), fill: "none", ...getStrokeProps(STROKE_COLOR), strokeWidth: 1.5 })] }));
+    }
+    return (_jsxs("svg", { style: {
+            position: 'absolute',
+            left: 0,
+            top: 0,
+            width,
+            height: trackHeight,
+            pointerEvents: 'none',
+        }, children: [_jsx("path", { d: areaPath, fill: FILL_COLOR }), _jsx("path", { d: points.join(' '), fill: "none", stroke: STROKE_COLOR, strokeWidth: 1.5 })] }));
+});
+export default RecombinationTrack;

package/esm/shared/components/RecombinationYScaleBar.d.ts

@@ -0,0 +1,7 @@
+declare const Y_AXIS_WIDTH = 40;
+export default function RecombinationYScaleBar({ height, maxValue, exportSVG, }: {
+    height: number;
+    maxValue: number;
+    exportSVG?: boolean;
+}): import("react/jsx-runtime").JSX.Element;
+export { Y_AXIS_WIDTH };

package/esm/shared/components/RecombinationYScaleBar.js

@@ -0,0 +1,34 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useTheme } from '@mui/material';
+const Y_AXIS_WIDTH = 40;
+const YSCALEBAR_LABEL_OFFSET = 5;
+export default function RecombinationYScaleBar({ height, maxValue, exportSVG, }) {
+    const theme = useTheme();
+    const topPadding = YSCALEBAR_LABEL_OFFSET;
+    const bottomPadding = YSCALEBAR_LABEL_OFFSET;
+    const plotHeight = height - topPadding - bottomPadding;
+    const fg = exportSVG ? '#333' : theme.palette.text.primary;
+    const bg = exportSVG ? '#fafafa' : theme.palette.background.default;
+    const numTicks = 4;
+    const ticks = [];
+    for (let i = 0; i <= numTicks; i++) {
+        const value = (maxValue * i) / numTicks;
+        const y = topPadding + plotHeight * (1 - i / numTicks);
+        ticks.push({ value, y });
+    }
+    const range0 = topPadding + 0.5;
+    const range1 = topPadding + plotHeight + 0.5;
+    const content = (_jsxs(_Fragment, { children: [_jsx("rect", { x: 0, y: 0, width: Y_AXIS_WIDTH, height: height, fill: bg }), _jsxs("g", { fill: "none", fontSize: 9, fontFamily: "sans-serif", textAnchor: "end", strokeWidth: 1, children: [_jsx("path", { stroke: fg, d: `M${Y_AXIS_WIDTH - 6},${range0}H${Y_AXIS_WIDTH - 0.5}V${range1}H${Y_AXIS_WIDTH - 6}` }), ticks.map((tick, idx) => (_jsxs("g", { transform: `translate(0,${tick.y})`, children: [_jsx("line", { stroke: fg, x1: Y_AXIS_WIDTH - 6, x2: Y_AXIS_WIDTH, y1: 0.5, y2: 0.5 }), _jsx("text", { stroke: bg, strokeWidth: 2, paintOrder: "stroke", fill: fg, dy: "0.32em", x: Y_AXIS_WIDTH - 9, y: 0.5, children: tick.value.toFixed(2) })] }, idx)))] }), _jsx("text", { x: 10, y: height / 2, fontSize: 10, fill: fg, fontFamily: "sans-serif", textAnchor: "middle", transform: `rotate(-90, 10, ${height / 2})`, children: "1 - r\u00B2" })] }));
+    if (exportSVG) {
+        return _jsx("g", { children: content });
+    }
+    return (_jsx("svg", { style: {
+            position: 'absolute',
+            left: 0,
+            top: 0,
+            width: Y_AXIS_WIDTH,
+            height,
+            zIndex: 1,
+        }, width: Y_AXIS_WIDTH, height: height, children: content }));
+}
+export { Y_AXIS_WIDTH };

package/esm/shared/components/SetColorDialogRowPalettizer.d.ts

@@ -1,10 +1,5 @@
+import type { Source } from '../types.ts';
 export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }: {
-    currLayout: {
-        name: string;
-        [key: string]: unknown;
-    }[];
-    setCurrLayout: (arg: {
-        name: string;
-        [key: string]: unknown;
-    }[]) => void;
+    currLayout: Source[];
+    setCurrLayout: (arg: Source[]) => void;
 }): import("react/jsx-runtime").JSX.Element | null;

package/esm/shared/components/SetColorDialogRowPalettizer.js

@@ -1,7 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { set1 } from '@jbrowse/core/ui/colors';
-import { randomColor } from '@jbrowse/core/util/color';
 import { Button } from '@mui/material';
+import { applyColorPalette } from "../applyColorPalette.js";
 const excludedFields = new Set(['name', 'color', 'label', 'id', 'HP']);
 export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout, }) {
     const firstRow = currLayout[0];
@@ -10,18 +9,7 @@ export default function SetColorDialogRowPalettizer({ setCurrLayout, currLayout,
     }
     const fields = Object.keys(firstRow).filter(f => !excludedFields.has(f));
     return (_jsxs("div", { children: ["Create color palette based on...", fields.map(field => (_jsx(Button, { variant: "contained", color: "inherit", onClick: () => {
-                    const counts = new Map();
-                    for (const row of currLayout) {
-                        const key = row[field];
-                        counts.set(key, (counts.get(key) || 0) + 1);
-                    }
-                    const colorMap = Object.fromEntries([...counts.entries()]
-                        .sort((a, b) => a[1] - b[1])
-                        .map(([key], idx) => [key, set1[idx] || randomColor(key)]));
-                    setCurrLayout(currLayout.map(row => ({
-                        ...row,
-                        color: colorMap[row[field]],
-                    })));
+                    setCurrLayout(applyColorPalette(currLayout, field));
                 }, children: field }, field))), _jsx(Button, { onClick: () => {
                     setCurrLayout(currLayout.map(row => ({ ...row, color: undefined })));
                 }, children: "Clear colors" })] }));

package/esm/shared/drawAlleleCount.js

@@ -74,6 +74,15 @@ export function drawColorAlleleCount(c, ctx, x, y, w, h, featureType = '', featu
             ctx.fill();
         }
     }
+    else if (featureType === 'insertion') {
+        const widthExtension = 3;
+        ctx.beginPath();
+        ctx.moveTo(x - f2 - widthExtension, y - f2);
+        ctx.lineTo(x + w + f2 + widthExtension, y - f2);
+        ctx.lineTo(x + w / 2, y + h + f2);
+        ctx.closePath();
+        ctx.fill();
+    }
     else {
         ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
     }

package/esm/shared/drawPhased.d.ts

@@ -1 +1 @@
-export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string, drawReference?: boolean, alpha?: number): string | undefined;
+export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string, drawReference?: boolean, alpha?: number, featureType?: string, featureStrand?: number): string | undefined;

package/esm/shared/drawPhased.js

@@ -4,7 +4,7 @@ import { REFERENCE_COLOR, UNPHASED_COLOR, f2 } from "./constants.js";
 function colorify(n) {
     return `hsl(${n % 255}, 50%, 50%)`;
 }
-export function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = true, alpha = 1) {
+export function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = true, alpha = 1, featureType = '', featureStrand) {
     const allele = +alleles[HP];
     const c = allele
         ? PS !== undefined
@@ -15,7 +15,36 @@ export function drawPhased(alleles, ctx, x, y, w, h, HP, PS, drawReference = tru
             : undefined;
     if (c) {
         ctx.fillStyle = alpha !== 1 ? colord(c).alpha(alpha).toHex() : c;
-        ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+        if (featureType === 'inversion') {
+            if (featureStrand === 1) {
+                ctx.beginPath();
+                ctx.moveTo(x - f2, y - f2);
+                ctx.lineTo(x - f2, y + h + f2);
+                ctx.lineTo(x + w + f2, y + h / 2);
+                ctx.closePath();
+                ctx.fill();
+            }
+            else {
+                ctx.beginPath();
+                ctx.moveTo(x + w + f2, y - f2);
+                ctx.lineTo(x + w + f2, y + h + f2);
+                ctx.lineTo(x - f2, y + h / 2);
+                ctx.closePath();
+                ctx.fill();
+            }
+        }
+        else if (featureType === 'insertion') {
+            const widthExtension = 3;
+            ctx.beginPath();
+            ctx.moveTo(x - f2 - widthExtension, y - f2);
+            ctx.lineTo(x + w + f2 + widthExtension, y - f2);
+            ctx.lineTo(x + w / 2, y + h + f2);
+            ctx.closePath();
+            ctx.fill();
+        }
+        else {
+            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+        }
     }
     return c;
 }

package/esm/shared/mafFilterUtils.d.ts

@@ -0,0 +1,5 @@
+import type { MenuItem } from '@jbrowse/core/ui';
+export declare function createMAFFilterMenuItem(model: {
+    minorAlleleFrequencyFilter?: number;
+    setMafFilter: (arg: number) => void;
+}): MenuItem;

package/esm/shared/mafFilterUtils.js

@@ -0,0 +1,17 @@
+import { lazy } from 'react';
+import { getSession } from '@jbrowse/core/util';
+const MAFFilterDialog = lazy(() => import("./components/MAFFilterDialog.js"));
+export function createMAFFilterMenuItem(model) {
+    return {
+        label: 'Minor allele frequency',
+        onClick: () => {
+            getSession(model).queueDialog(handleClose => [
+                MAFFilterDialog,
+                {
+                    model,
+                    handleClose,
+                },
+            ]);
+        },
+    };
+}

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -1,11 +1,13 @@
+import type VcfFeature from '../VcfFeature/index.ts';
 import type { Feature, LastStopTokenCheck } from '@jbrowse/core/util';
+export declare function calculateAlleleCountsFast(feature: VcfFeature): Record<string, number>;
 export declare function calculateAlleleCounts(genotypes: Record<string, string>, cacheSplit: Record<string, string[]>): Record<string, number>;
 export declare function calculateMinorAlleleFrequency(alleleCounts: Record<string, number>): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache, }: {
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopTokenCheck, genotypesCache, splitCache, }: {
     features: Iterable<Feature>;
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
-    lastCheck?: LastStopTokenCheck;
+    stopTokenCheck?: LastStopTokenCheck;
     genotypesCache?: Map<string, Record<string, string>>;
     splitCache?: Record<string, string[]>;
 }): {