@jbrowse/plugin-variants 3.0.1 → 3.0.3

package/esm/shared/{multiVariantColor.js → drawAlleleCount.js}

@@ -1,14 +1,13 @@
-import { set1 } from '@jbrowse/core/ui/colors';
 import { colord } from '@jbrowse/core/util/colord';
-import { colorify } from '../util';
-export function getColorAlleleCount(alleles) {
+import { f2 } from './constants';
+function getColorAlleleCount(alleles, mostFrequentAlt) {
     const total = alleles.length;
     let alt = 0;
     let uncalled = 0;
     let alt2 = 0;
     let ref = 0;
     for (const allele of alleles) {
-        if (allele === '1') {
+        if (allele === mostFrequentAlt) {
             alt++;
         }
         else if (allele === '0') {
@@ -35,11 +34,7 @@ export function getColorAlleleCount(alleles) {
         return a1.toHex();
     }
 }
-export function getColorPhased(alleles, HP) {
-    const c = +alleles[HP];
-    return c ? set1[c - 1] || 'black' : '#ccc';
-}
-export function getColorPhasedWithPhaseSet(alleles, HP, PS) {
-    const c = +alleles[HP];
-    return c ? colorify(+PS) || 'black' : '#ccc';
+export function drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt) {
+    ctx.fillStyle = getColorAlleleCount(alleles, mostFrequentAlt);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
 }

package/esm/shared/drawPhased.d.ts

@@ -0,0 +1 @@
+export declare function drawPhased(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, HP: number, PS?: string): void;

package/esm/shared/drawPhased.js

@@ -0,0 +1,18 @@
+import { set1 } from '@jbrowse/core/ui/colors';
+import { f2 } from './constants';
+import { colorify } from './util';
+function getColorPhased(alleles, HP) {
+    const c = +alleles[HP];
+    return c ? set1[c - 1] || 'black' : '#ccc';
+}
+function getColorPhasedWithPhaseSet(alleles, HP, PS) {
+    const c = +alleles[HP];
+    return c ? colorify(+PS) || 'black' : '#ccc';
+}
+export function drawPhased(alleles, ctx, x, y, w, h, HP, PS) {
+    ctx.fillStyle =
+        PS !== undefined
+            ? getColorPhasedWithPhaseSet(alleles, HP, PS)
+            : getColorPhased(alleles, HP);
+    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+}

package/esm/shared/findSecondLargestNumber.js

@@ -0,0 +1 @@
+"use strict";

package/esm/shared/minorAlleleFrequencyUtils.d.ts

@@ -0,0 +1,11 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function findSecondLargestNumber(arr: Iterable<number>): number;
+export declare function calculateAlleleCounts(feat: Feature): {
+    alleleCounts: Map<any, any>;
+    mostFrequentAlt: any;
+};
+export declare function calculateMinorAlleleFrequency(alleleCounts: Map<string, number>): number;
+export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): {
+    feature: Feature;
+    mostFrequentAlt: string;
+}[];

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -0,0 +1,56 @@
+import { sum } from '@jbrowse/core/util';
+export function findSecondLargestNumber(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 calculateAlleleCounts(feat) {
+    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);
+        }
+    }
+    let mostFrequentAlt;
+    let max = 0;
+    for (const [alt, altCount] of alleleCounts.entries()) {
+        if (alt !== '.' && alt !== '0') {
+            if (altCount > max) {
+                mostFrequentAlt = alt;
+                max = altCount;
+            }
+        }
+    }
+    return { alleleCounts, mostFrequentAlt };
+}
+export function calculateMinorAlleleFrequency(alleleCounts) {
+    return (findSecondLargestNumber(alleleCounts.values()) /
+        (sum(alleleCounts.values()) || 1));
+}
+export function getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter) {
+    const results = [];
+    for (const feature of feats) {
+        if (feature.get('end') - feature.get('start') <= 10) {
+            const { mostFrequentAlt, alleleCounts } = calculateAlleleCounts(feature);
+            if (calculateMinorAlleleFrequency(alleleCounts) >=
+                minorAlleleFrequencyFilter) {
+                results.push({
+                    feature,
+                    mostFrequentAlt,
+                });
+            }
+        }
+    }
+    return results;
+}

package/esm/shared/sourcesGridUtils.d.ts

@@ -0,0 +1,10 @@
+export declare function moveUp(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];
+export declare function moveDown(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];

package/esm/shared/sourcesGridUtils.js

@@ -0,0 +1,28 @@
+export function moveUp(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => a - b);
+    let lastIdx = 0;
+    for (const old of idxs) {
+        const idx = Math.max(lastIdx, old - by);
+        if (idx >= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx + 1;
+    }
+    return arr;
+}
+export function moveDown(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => b - a);
+    let lastIdx = arr.length - 1;
+    for (const old of idxs) {
+        const idx = Math.min(lastIdx, old + by);
+        if (idx <= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx - 1;
+    }
+    return arr;
+}

package/esm/shared/util.d.ts

@@ -1,10 +1,3 @@
-export declare function moveUp(arr: {
-    name: string;
-}[], sel: string[], by?: number): {
-    name: string;
-}[];
-export declare function moveDown(arr: {
-    name: string;
-}[], sel: string[], by?: number): {
-    name: string;
-}[];
+export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;
+export declare function randomColor(str: string): string;
+export declare function colorify(n: number): string;

package/esm/shared/util.js

@@ -1,28 +1,24 @@
-export function moveUp(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => a - b);
-    let lastIdx = 0;
-    for (const old of idxs) {
-        const idx = Math.max(lastIdx, old - by);
-        if (idx >= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx + 1;
+export function fillRectCtx(x, y, width, height, ctx, color) {
+    if (width < 0) {
+        x += width;
+        width = -width;
     }
-    return arr;
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (color) {
+        ctx.fillStyle = color;
+    }
+    ctx.fillRect(x, y, width, height);
 }
-export function moveDown(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => b - a);
-    let lastIdx = arr.length - 1;
-    for (const old of idxs) {
-        const idx = Math.min(lastIdx, old + by);
-        if (idx <= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx - 1;
+export function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
     }
-    return arr;
+    return colorify(sum * 10);
+}
+export function colorify(n) {
+    return `hsl(${n % 255}, 50%, 50%)`;
 }

package/esm/util.d.ts

@@ -1,8 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, color?: string): void;
-export declare function getCol(gt: string): "blue" | "teal" | "#ccc" | "#CBC3E3";
-export declare function randomColor(str: string): string;
-export declare function colorify(n: number): string;
-export declare function findSecondLargest(arr: Iterable<number>): number;
-export declare function calculateMinorAlleleFrequency(feat: Feature): number;
-export declare function getFeaturesThatPassMinorAlleleFrequencyFilter(feats: Iterable<Feature>, minorAlleleFrequencyFilter: number): Feature[];

package/esm/util.js

@@ -1,77 +1 @@
-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;
-}
+"use strict";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.0.1",
+  "version": "3.0.3",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -39,11 +39,11 @@
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/tabix": "^2.0.0",
-    "@gmod/vcf": "^6.0.0",
-    "@jbrowse/core": "^3.0.1",
-    "@jbrowse/plugin-circular-view": "^3.0.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
-    "@jbrowse/sv-core": "^3.0.1",
+    "@gmod/vcf": "^6.0.8",
+    "@jbrowse/core": "^3.0.3",
+    "@jbrowse/plugin-circular-view": "^3.0.3",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.3",
+    "@jbrowse/sv-core": "^3.0.3",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
+  "gitHead": "f516540428282351d26e46743e69a724651bfb2c"
 }

package/dist/shared/multiVariantColor.d.ts

@@ -1,3 +0,0 @@
-export declare function getColorAlleleCount(alleles: string[]): string;
-export declare function getColorPhased(alleles: string[], HP: number): string;
-export declare function getColorPhasedWithPhaseSet(alleles: string[], HP: number, PS: string): string;

package/esm/shared/multiVariantColor.d.ts

@@ -1,3 +0,0 @@
-export declare function getColorAlleleCount(alleles: string[]): string;
-export declare function getColorPhased(alleles: string[], HP: number): string;
-export declare function getColorPhasedWithPhaseSet(alleles: string[], HP: number, PS: string): string;