@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/esm/util.js

@@ -0,0 +1,77 @@
+import { sum } from '@jbrowse/core/util';
+export function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+export function getCol(gt) {
+    if (gt === '0|0' || gt === '0/0') {
+        return '#ccc';
+    }
+    else if (gt === '1|0' || gt === '0|1' || gt === '0/1' || gt === '1/0') {
+        return 'teal';
+    }
+    else if (gt === '1|1' || gt === '1/1') {
+        return 'blue';
+    }
+    else {
+        return '#CBC3E3';
+    }
+}
+export function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
+    }
+    return `hsl(${colorify(sum * 10)}, 50%, 50%)`;
+}
+export function colorify(n) {
+    return `hsl(${n % 255}, 50%, 50%)`;
+}
+export function findSecondLargest(arr) {
+    let firstMax = 0;
+    let secondMax = 0;
+    for (const num of arr) {
+        if (num > firstMax) {
+            secondMax = firstMax;
+            firstMax = num;
+        }
+        else if (num > secondMax && num !== firstMax) {
+            secondMax = num;
+        }
+    }
+    return secondMax;
+}
+export function calculateMinorAlleleFrequency(feat) {
+    if (feat.get('end') - feat.get('start') <= 10) {
+        const samp = feat.get('genotypes');
+        const alleleCounts = new Map();
+        for (const val of Object.values(samp)) {
+            const alleles = val.split(/[/|]/);
+            for (const allele of alleles) {
+                alleleCounts.set(allele, (alleleCounts.get(allele) || 0) + 1);
+            }
+        }
+        return (findSecondLargest(alleleCounts.values()) /
+            (sum(alleleCounts.values()) || 1));
+    }
+    return -1;
+}
+export function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+    const mafs = [];
+    for (const feat of feats) {
+        if (calculateMinorAlleleFrequency(feat) >= minorAlleleFrequencyFilter) {
+            mafs.push(feat);
+        }
+    }
+    return mafs;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,13 +37,12 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/tabix": "^1.5.6",
-    "@gmod/vcf": "^5.0.9",
-    "@jbrowse/sv-core": "^2.17.0",
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/tabix": "^2.0.0",
+    "@gmod/vcf": "^6.0.0",
+    "@jbrowse/sv-core": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
-    "@mui/x-data-grid": "^7.0.0",
-    "generic-filehandle": "^3.0.0"
+    "@mui/x-data-grid": "^7.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -63,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }

package/dist/VariantFeatureWidget/AnnotGrid.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
-export default function VariantAnnotPanel({ rows, columns, }: {
-    rows: GridValidRowModel[];
-    columns: GridColDef[];
-}): React.JSX.Element | null;

package/dist/VariantFeatureWidget/AnnotGrid.js

@@ -1,39 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantAnnotPanel;
-const react_1 = __importStar(require("react"));
-const x_data_grid_1 = require("@mui/x-data-grid");
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
-function VariantAnnotPanel({ rows, columns, }) {
-    const [checked, setChecked] = (0, react_1.useState)(false);
-    const widths = columns.map(e => (0, util_1.measureGridWidth)(rows.map(r => r[e.field])));
-    return rows.length ? (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => {
-                    setChecked(event.target.checked);
-                } }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
-        react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? x_data_grid_1.GridToolbar : null } }))) : null;
-}

package/dist/VariantFeatureWidget/VariantAnnotationTable.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-export default function VariantAnnotationTable({ data, fields, title, }: {
-    data: string[];
-    fields: string[];
-    title: string;
-}): React.JSX.Element | null;

package/dist/VariantFeatureWidget/VariantAnnotationTable.js

@@ -1,16 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantAnnotationTable;
-const react_1 = __importDefault(require("react"));
-const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
-const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-function VariantAnnotationTable({ data, fields, title, }) {
-    return data.length ? (react_1.default.createElement(BaseCard_1.default, { title: title },
-        react_1.default.createElement(AnnotGrid_1.default, { rows: data.map((elt, id) => ({
-                id,
-                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
-            })), columns: fields.map(c => ({ field: c })) }))) : null;
-}

package/esm/VariantFeatureWidget/AnnotGrid.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { GridColDef, GridValidRowModel } from '@mui/x-data-grid';
-export default function VariantAnnotPanel({ rows, columns, }: {
-    rows: GridValidRowModel[];
-    columns: GridColDef[];
-}): React.JSX.Element | null;

package/esm/VariantFeatureWidget/AnnotGrid.js

@@ -1,13 +0,0 @@
-import React, { useState } from 'react';
-import { DataGrid, GridToolbar, } from '@mui/x-data-grid';
-import { Checkbox, FormControlLabel, Typography } from '@mui/material';
-import { measureGridWidth } from '@jbrowse/core/util';
-export default function VariantAnnotPanel({ rows, columns, }) {
-    const [checked, setChecked] = useState(false);
-    const widths = columns.map(e => measureGridWidth(rows.map(r => r[e.field])));
-    return rows.length ? (React.createElement("div", null,
-        React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => {
-                    setChecked(event.target.checked);
-                } }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
-        React.createElement(DataGrid, { rowHeight: 25, rows: rows, columns: columns.map((c, i) => ({ ...c, width: widths[i] })), slots: { toolbar: checked ? GridToolbar : null } }))) : null;
-}

package/esm/VariantFeatureWidget/VariantAnnotationTable.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-export default function VariantAnnotationTable({ data, fields, title, }: {
-    data: string[];
-    fields: string[];
-    title: string;
-}): React.JSX.Element | null;

package/esm/VariantFeatureWidget/VariantAnnotationTable.js

@@ -1,10 +0,0 @@
-import React from 'react';
-import AnnotGrid from './AnnotGrid';
-import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-export default function VariantAnnotationTable({ data, fields, title, }) {
-    return data.length ? (React.createElement(BaseCard, { title: title },
-        React.createElement(AnnotGrid, { rows: data.map((elt, id) => ({
-                id,
-                ...Object.fromEntries(elt.split('|').map((e, i) => [fields[i], e])),
-            })), columns: fields.map(c => ({ field: c })) }))) : null;
-}