Bugfix to JBrowse

Author: bbimber

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts

@@ -1,32 +1,14 @@
 import { VcfFeature } from '@jbrowse/plugin-variants'
-import VcfParser from '@gmod/vcf'
+import VcfParser, { Variant } from '@gmod/vcf';
 
 export default class ExtendedVcfFeature extends VcfFeature {
-    private readonly vcfParser: VcfParser
-
-    constructor(args: { variant: any; parser: VcfParser; id: string }) {
+    constructor(args: { variant: Variant; parser: VcfParser; id: string }) {
         args.variant = ExtendedVcfFeature.extractImpact(args.variant)
-        //args.variant = ExtendedVcfFeature.calculateVariableSamples(args.variant)
 
         super(args)
-
-        this.vcfParser = args.parser
-    }
-
-    public getInfoFieldMeta(propKey: string): VcfParser {
-        const map = this.vcfParser.getMetadata("INFO")
-
-        return map ? map[propKey] :  null
     }
 
-    static extractImpact(variant:  {
-        REF: string
-        POS: number
-        ALT: string[]
-        CHROM: string
-        INFO: any
-        ID: string[]
-    }) {
+    static extractImpact(variant: Variant) {
         // Only append if not present:
         if (variant.INFO["IMPACT"]) {
             return(variant);

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/ExtendedVariantRendering.tsx

@@ -1,10 +1,10 @@
-import jexl from 'jexl';
 import { SvgFeatureRendererReactComponent } from '@jbrowse/plugin-svg';
 import { observer } from 'mobx-react';
 import React from 'react';
 import { deserializeFilters } from '../../InfoFilterWidget/filterUtil';
 import Diamond from './Diamond';
 import { passesInfoFilters, passesSampleFilters } from '../../../../../utils';
+import { VcfFeature } from '@jbrowse/plugin-variants';
 
 export function ExtendedVariantRendering(props) {
     const { features, rendererConfig } = props
@@ -17,11 +17,11 @@ export function ExtendedVariantRendering(props) {
 
     const sampleFilters = activeSamples.value ? activeSamples.value.split(',') : null
 
-    function diamondValidator(feature) {
+    function diamondValidator(feature: VcfFeature) {
         return feature.get('type') === "SNV";
     }
 
-    function isFeatureDisplayed(feature) {
+    function isFeatureDisplayed(feature: VcfFeature) {
         return passesInfoFilters(feature, expandedFilters) && passesSampleFilters(feature, sampleFilters)
     }
 

jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx

@@ -101,10 +101,11 @@ const VariantTableWidget = observer(props => {
 
     // Maintain a cached list of all non-WT samples at this position:
     filteredFeatures.forEach(variant => {
-      if (!variant.get('INFO')['variableSamples'] && variant.get('SAMPLES')) {
+      if (!variant.get('INFO')['variableSamples']) {
         variant.get('INFO')['variableSamples'] = []
-        Object.keys(variant.get('SAMPLES')).forEach(function(sampleId) {
-          const gt = variant.get('SAMPLES')[sampleId]["GT"] ? variant.get('SAMPLES')[sampleId]["GT"][0] : null
+        const genotypes = variant.get('GENOTYPES')()
+        Object.keys(genotypes).forEach(function(sampleId) {
+          const gt = genotypes[sampleId] ? genotypes[sampleId] : null
           if (isVariant(gt)) {
             variant.get('INFO')['variableSamples'].push(sampleId)
           }

jbrowse/src/client/JBrowse/utils.ts

@@ -4,14 +4,14 @@ import { createViewState, loadPlugins } from '@jbrowse/react-linear-genome-view2
 import { ActionURL, Ajax } from '@labkey/api';
 import {
     getGridNumericOperators,
-    GridCellParams,
     GridColDef,
     GridColType,
     GridComparatorFn,
     GridFilterItem,
     GridFilterOperator
 } from '@mui/x-data-grid';
 import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
+import { VcfFeature } from '@jbrowse/plugin-variants';
 
 export function arrayMax(array) {
     return Array.isArray(array) ? Math.max(...array) : array
@@ -43,31 +43,30 @@ export function passesInfoFilters(feature, filters) {
     return true
 }
 
-export function passesSampleFilters(feature, sampleIDs){
+export function passesSampleFilters(variant : VcfFeature, sampleIDs){
     if (!sampleIDs || sampleIDs.length === 0) {
         return true
     }
 
-    const featureVariant = feature.variant ?? feature.data
-    const samples = featureVariant.SAMPLES || featureVariant.samples
-    if (!samples || isEmptyObject(samples)) {
-        return false
-    }
-
     // Preferentially use pre-computed values:
-    if (featureVariant.INFO._variableSamples) {
+    if (variant.get('INFO')['_variableSamples']) {
         for (const sampleId of sampleIDs) {
-            if (featureVariant.INFO._variableSamples.indexOf(sampleId) > -1) {
+            if (variant.get('INFO')._variableSamples.indexOf(sampleId) > -1) {
                 return true
             }
         }
 
         return false
     }
 
+    const genotypes = variant.get('GENOTYPES')()
+    if (!genotypes || isEmptyObject(genotypes)) {
+        return false
+    }
+
     for (const sampleId of sampleIDs) {
-        if (samples[sampleId]) {
-            const gt = samples[sampleId]["GT"][0]
+        if (genotypes[sampleId]) {
+            const gt = genotypes[sampleId]
 
             // If any sample in the whitelist is non-WT, show this site. Otherwise filter.
             if (isVariant(gt)) {