@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/shared/minorAlleleFrequencyUtils.js

@@ -1,28 +1,263 @@
 import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
+const GENOTYPE_SPLIT_REGEX = /[/|]/;
+const SLASH = 47;
+const PIPE = 124;
+export function calculateAlleleCountsFast(feature) {
+    let count0 = 0;
+    let count1 = 0;
+    let count2 = 0;
+    let count3 = 0;
+    let countDot = 0;
+    const otherCounts = {};
+    feature.processGenotypes((str, start, end) => {
+        const len = end - start;
+        if (len === 3) {
+            const sep = str.charCodeAt(start + 1);
+            if (sep === SLASH || sep === PIPE) {
+                const c0 = str.charCodeAt(start);
+                const c1 = str.charCodeAt(start + 2);
+                if (c0 === 48) {
+                    count0++;
+                }
+                else if (c0 === 49) {
+                    count1++;
+                }
+                else if (c0 === 50) {
+                    count2++;
+                }
+                else if (c0 === 51) {
+                    count3++;
+                }
+                else if (c0 === 46) {
+                    countDot++;
+                }
+                else {
+                    const a0 = str[start];
+                    otherCounts[a0] = (otherCounts[a0] || 0) + 1;
+                }
+                if (c1 === 48) {
+                    count0++;
+                }
+                else if (c1 === 49) {
+                    count1++;
+                }
+                else if (c1 === 50) {
+                    count2++;
+                }
+                else if (c1 === 51) {
+                    count3++;
+                }
+                else if (c1 === 46) {
+                    countDot++;
+                }
+                else {
+                    const a1 = str[start + 2];
+                    otherCounts[a1] = (otherCounts[a1] || 0) + 1;
+                }
+                return;
+            }
+        }
+        if (len === 1) {
+            const c = str.charCodeAt(start);
+            if (c === 48) {
+                count0++;
+            }
+            else if (c === 49) {
+                count1++;
+            }
+            else if (c === 50) {
+                count2++;
+            }
+            else if (c === 51) {
+                count3++;
+            }
+            else if (c === 46) {
+                countDot++;
+            }
+            else {
+                const a = str[start];
+                otherCounts[a] = (otherCounts[a] || 0) + 1;
+            }
+            return;
+        }
+        const gt = str.slice(start, end);
+        const alleles = gt.split(GENOTYPE_SPLIT_REGEX);
+        for (const allele of alleles) {
+            if (allele === '0') {
+                count0++;
+            }
+            else if (allele === '1') {
+                count1++;
+            }
+            else if (allele === '2') {
+                count2++;
+            }
+            else if (allele === '3') {
+                count3++;
+            }
+            else if (allele === '.') {
+                countDot++;
+            }
+            else {
+                otherCounts[allele] = (otherCounts[allele] || 0) + 1;
+            }
+        }
+    });
+    const result = {};
+    if (count0 > 0) {
+        result['0'] = count0;
+    }
+    if (count1 > 0) {
+        result['1'] = count1;
+    }
+    if (count2 > 0) {
+        result['2'] = count2;
+    }
+    if (count3 > 0) {
+        result['3'] = count3;
+    }
+    if (countDot > 0) {
+        result['.'] = countDot;
+    }
+    for (const key in otherCounts) {
+        result[key] = otherCounts[key];
+    }
+    return result;
+}
 export function calculateAlleleCounts(genotypes, cacheSplit) {
-    const alleleCounts = {};
-    const vals = Object.values(genotypes);
-    for (const val of vals) {
-        const genotype = val;
-        const alleles = cacheSplit[genotype] ?? (cacheSplit[genotype] = genotype.split(/[/|]/));
+    let count0 = 0;
+    let count1 = 0;
+    let count2 = 0;
+    let count3 = 0;
+    let countDot = 0;
+    const otherCounts = {};
+    for (const key in genotypes) {
+        const genotype = genotypes[key];
+        const len = genotype.length;
+        if (len === 3) {
+            const sep = genotype[1];
+            if (sep === '/' || sep === '|') {
+                const a0 = genotype[0];
+                const a1 = genotype[2];
+                if (a0 === '0') {
+                    count0++;
+                }
+                else if (a0 === '1') {
+                    count1++;
+                }
+                else if (a0 === '2') {
+                    count2++;
+                }
+                else if (a0 === '3') {
+                    count3++;
+                }
+                else if (a0 === '.') {
+                    countDot++;
+                }
+                else {
+                    otherCounts[a0] = (otherCounts[a0] || 0) + 1;
+                }
+                if (a1 === '0') {
+                    count0++;
+                }
+                else if (a1 === '1') {
+                    count1++;
+                }
+                else if (a1 === '2') {
+                    count2++;
+                }
+                else if (a1 === '3') {
+                    count3++;
+                }
+                else if (a1 === '.') {
+                    countDot++;
+                }
+                else {
+                    otherCounts[a1] = (otherCounts[a1] || 0) + 1;
+                }
+                continue;
+            }
+        }
+        if (len === 1) {
+            if (genotype === '0') {
+                count0++;
+            }
+            else if (genotype === '1') {
+                count1++;
+            }
+            else if (genotype === '2') {
+                count2++;
+            }
+            else if (genotype === '3') {
+                count3++;
+            }
+            else if (genotype === '.') {
+                countDot++;
+            }
+            else {
+                otherCounts[genotype] = (otherCounts[genotype] || 0) + 1;
+            }
+            continue;
+        }
+        let alleles = cacheSplit[genotype];
+        if (!alleles) {
+            alleles = genotype.split(GENOTYPE_SPLIT_REGEX);
+            cacheSplit[genotype] = alleles;
+        }
         for (const allele of alleles) {
-            const a = allele;
-            alleleCounts[a] = (alleleCounts[a] || 0) + 1;
+            if (allele === '0') {
+                count0++;
+            }
+            else if (allele === '1') {
+                count1++;
+            }
+            else if (allele === '2') {
+                count2++;
+            }
+            else if (allele === '3') {
+                count3++;
+            }
+            else if (allele === '.') {
+                countDot++;
+            }
+            else {
+                otherCounts[allele] = (otherCounts[allele] || 0) + 1;
+            }
         }
     }
-    return alleleCounts;
+    const result = {};
+    if (count0 > 0) {
+        result['0'] = count0;
+    }
+    if (count1 > 0) {
+        result['1'] = count1;
+    }
+    if (count2 > 0) {
+        result['2'] = count2;
+    }
+    if (count3 > 0) {
+        result['3'] = count3;
+    }
+    if (countDot > 0) {
+        result['.'] = countDot;
+    }
+    for (const key in otherCounts) {
+        result[key] = otherCounts[key];
+    }
+    return result;
 }
 export function calculateMinorAlleleFrequency(alleleCounts) {
     let firstMax = 0;
     let secondMax = 0;
     let total = 0;
-    for (const count of Object.values(alleleCounts)) {
+    for (const key in alleleCounts) {
+        const count = alleleCounts[key];
         total += count;
         if (count > firstMax) {
             secondMax = firstMax;
             firstMax = count;
         }
-        else if (count > secondMax && count !== firstMax) {
+        else if (count > secondMax) {
             secondMax = count;
         }
     }
@@ -31,7 +266,8 @@ export function calculateMinorAlleleFrequency(alleleCounts) {
 function getMostFrequentAlt(alleleCounts) {
     let mostFrequentAlt;
     let max = 0;
-    for (const [alt, altCount] of Object.entries(alleleCounts)) {
+    for (const alt in alleleCounts) {
+        const altCount = alleleCounts[alt];
         if (alt !== '.' && alt !== '0' && altCount > max) {
             mostFrequentAlt = alt;
             max = altCount;
@@ -39,17 +275,23 @@ function getMostFrequentAlt(alleleCounts) {
     }
     return mostFrequentAlt;
 }
-export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, lastCheck, genotypesCache, splitCache = {}, }) {
+export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorAlleleFrequencyFilter, lengthCutoffFilter, stopTokenCheck, genotypesCache, splitCache = {}, }) {
     const results = [];
     for (const feature of features) {
         if (feature.get('end') - feature.get('start') <= lengthCutoffFilter) {
-            const featureId = feature.id();
-            let genotypes = genotypesCache?.get(featureId);
-            if (!genotypes) {
-                genotypes = feature.get('genotypes');
-                genotypesCache?.set(featureId, genotypes);
+            let alleleCounts;
+            if ('processGenotypes' in feature) {
+                alleleCounts = calculateAlleleCountsFast(feature);
+            }
+            else {
+                const featureId = feature.id();
+                let genotypes = genotypesCache?.get(featureId);
+                if (!genotypes) {
+                    genotypes = feature.get('genotypes');
+                    genotypesCache?.set(featureId, genotypes);
+                }
+                alleleCounts = calculateAlleleCounts(genotypes, splitCache);
             }
-            const alleleCounts = calculateAlleleCounts(genotypes, splitCache);
             if (calculateMinorAlleleFrequency(alleleCounts) >=
                 minorAlleleFrequencyFilter) {
                 results.push({
@@ -59,7 +301,7 @@ export function getFeaturesThatPassMinorAlleleFrequencyFilter({ features, minorA
                 });
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return results;
 }

package/esm/shared/setupMultiVariantAutoruns.js

@@ -1,3 +1,4 @@
+import { setupColorByAutorun } from "./colorByAutorun.js";
 import { getMultiVariantFeaturesAutorun } from "./getMultiVariantFeaturesAutorun.js";
 import { getMultiVariantSourcesAutorun } from "./getMultiVariantSourcesAutorun.js";
 import { setupTreeDrawingAutorun } from "./treeDrawingAutorun.js";
@@ -5,4 +6,5 @@ export function setupMultiVariantAutoruns(self) {
     getMultiVariantSourcesAutorun(self);
     getMultiVariantFeaturesAutorun(self);
     setupTreeDrawingAutorun(self);
+    setupColorByAutorun(self);
 }

package/package.json

@@ -1,6 +1,7 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "4.0.4",
+  "version": "4.1.3",
+  "type": "module",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -23,12 +24,12 @@
     "@flatten-js/interval-tree": "^2.0.3",
     "@gmod/hclust": "^1.0.7",
     "@gmod/tabix": "^3.2.2",
-    "@gmod/vcf": "^6.1.0",
+    "@gmod/vcf": "^7.0.0",
     "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/icons-material": "^7.3.6",
-    "@mui/material": "^7.3.6",
-    "@mui/x-charts-vendor": "^8.25.0",
-    "@mui/x-data-grid": "^8.25.0",
+    "@mui/icons-material": "^7.3.7",
+    "@mui/material": "^7.3.7",
+    "@mui/x-charts-vendor": "^8.26.0",
+    "@mui/x-data-grid": "^8.26.0",
     "@types/file-saver-es": "^2.0.3",
     "copy-to-clipboard": "^3.3.3",
     "escape-html": "^1.0.3",
@@ -37,10 +38,10 @@
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/plugin-circular-view": "^4.0.4",
-    "@jbrowse/plugin-linear-genome-view": "^4.0.4",
-    "@jbrowse/sv-core": "^4.0.4",
-    "@jbrowse/core": "^4.0.4"
+    "@jbrowse/plugin-linear-genome-view": "^4.1.3",
+    "@jbrowse/core": "^4.1.3",
+    "@jbrowse/plugin-circular-view": "^4.1.3",
+    "@jbrowse/sv-core": "^4.1.3"
   },
   "peerDependencies": {
     "react": ">=18.0.0"