@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/shared.d.ts

@@ -1,25 +1,25 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
+import { BlockSet } from '@jbrowse/core/util/blockTypes';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
+    adapterConfig: AnyConfigurationModel;
+}, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;
+export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
+    parentTrack: IAnyStateTreeNode & {
+        configuration: AnyConfigurationModel;
+    };
+}, adapterConfig: AnyConfigurationModel, colorScheme: {
+    type: string;
+    tag?: string;
+}, blocks: BlockSet, opts?: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters?: string[];
+}): Promise<string[]>;

package/dist/shared.js

@@ -0,0 +1,96 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.getUniqueModificationValues = getUniqueModificationValues;
+exports.getUniqueTagValues = getUniqueTagValues;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _util = require("@jbrowse/core/util");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+function getUniqueTagValues(_x, _x2, _x3, _x4) {
+  return _getUniqueTagValues.apply(this, arguments);
+}
+
+function _getUniqueTagValues() {
+  _getUniqueTagValues = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(self, colorScheme, blocks, opts) {
+    var _getSession, rpcManager, adapterConfig, sessionId, values;
+
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            _getSession = (0, _util.getSession)(self), rpcManager = _getSession.rpcManager;
+            adapterConfig = self.adapterConfig;
+            sessionId = (0, _tracks.getRpcSessionId)(self);
+            _context.next = 5;
+            return rpcManager.call((0, _tracks.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', _objectSpread({
+              adapterConfig: adapterConfig,
+              tag: colorScheme.tag,
+              sessionId: sessionId,
+              regions: blocks.contentBlocks
+            }, opts));
+
+          case 5:
+            values = _context.sent;
+            return _context.abrupt("return", values);
+
+          case 7:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _getUniqueTagValues.apply(this, arguments);
+}
+
+function getUniqueModificationValues(_x5, _x6, _x7, _x8, _x9) {
+  return _getUniqueModificationValues.apply(this, arguments);
+}
+
+function _getUniqueModificationValues() {
+  _getUniqueModificationValues = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(self, adapterConfig, colorScheme, blocks, opts) {
+    var _getSession2, rpcManager, sessionId, values;
+
+    return _regenerator["default"].wrap(function _callee2$(_context2) {
+      while (1) {
+        switch (_context2.prev = _context2.next) {
+          case 0:
+            _getSession2 = (0, _util.getSession)(self), rpcManager = _getSession2.rpcManager;
+            sessionId = (0, _tracks.getRpcSessionId)(self);
+            _context2.next = 4;
+            return rpcManager.call(sessionId, 'PileupGetVisibleModifications', _objectSpread({
+              adapterConfig: adapterConfig,
+              tag: colorScheme.tag,
+              sessionId: sessionId,
+              regions: blocks.contentBlocks
+            }, opts));
+
+          case 4:
+            values = _context2.sent;
+            return _context2.abrupt("return", values);
+
+          case 6:
+          case "end":
+            return _context2.stop();
+        }
+      }
+    }, _callee2);
+  }));
+  return _getUniqueModificationValues.apply(this, arguments);
+}

package/dist/util.d.ts

@@ -1,19 +1,19 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AugmentedRegion } from '@jbrowse/core/util';
-export declare function getTag(feature: Feature, tag: string): any;
-export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
-export declare const orientationTypes: {
-    fr: {
-        [key: string]: string;
-    };
-    rf: {
-        [key: string]: string;
-    };
-    ff: {
-        [key: string]: string;
-    };
-};
-export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
-export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-export declare function shouldFetchReferenceSequence(type?: string): boolean;
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { AugmentedRegion } from '@jbrowse/core/util';
+export declare function getTag(feature: Feature, tag: string): any;
+export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
+export declare const orientationTypes: {
+    fr: {
+        [key: string]: string;
+    };
+    rf: {
+        [key: string]: string;
+    };
+    ff: {
+        [key: string]: string;
+    };
+};
+export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
+export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
+export declare function shouldFetchReferenceSequence(type?: string): boolean;

package/dist/util.js

@@ -0,0 +1,135 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.fetchSequence = fetchSequence;
+exports.getColorWGBS = getColorWGBS;
+exports.getTag = getTag;
+exports.getTagAlt = getTagAlt;
+exports.orientationTypes = void 0;
+exports.shouldFetchReferenceSequence = shouldFetchReferenceSequence;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
+// BAM does not
+function getTag(feature, tag) {
+  var tags = feature.get('tags');
+  return tags ? tags[tag] : feature.get(tag);
+} // use fallback alt tag, used in situations where upper case/lower case tags
+// exist e.g. Mm/MM for base modifications
+
+
+function getTagAlt(feature, tag, alt) {
+  return getTag(feature, tag) || getTag(feature, alt);
+} // orientation definitions from igv.js, see also
+// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
+
+
+var orientationTypes = {
+  fr: {
+    F1R2: 'LR',
+    F2R1: 'LR',
+    F1F2: 'LL',
+    F2F1: 'LL',
+    R1R2: 'RR',
+    R2R1: 'RR',
+    R1F2: 'RL',
+    R2F1: 'RL'
+  },
+  rf: {
+    R1F2: 'LR',
+    R2F1: 'LR',
+    R1R2: 'LL',
+    R2R1: 'LL',
+    F1F2: 'RR',
+    F2F1: 'RR',
+    F1R2: 'RL',
+    F2R1: 'RL'
+  },
+  ff: {
+    F2F1: 'LR',
+    R1R2: 'LR',
+    F2R1: 'LL',
+    R1F2: 'LL',
+    R2F1: 'RR',
+    F1R2: 'RR',
+    R2R1: 'RL',
+    F1F2: 'RL'
+  }
+};
+exports.orientationTypes = orientationTypes;
+
+function getColorWGBS(strand, base) {
+  if (strand === 1) {
+    if (base === 'C') {
+      return '#f00';
+    }
+
+    if (base === 'T') {
+      return '#00f';
+    }
+  } else if (strand === -1) {
+    if (base === 'G') {
+      return '#f00';
+    }
+
+    if (base === 'A') {
+      return '#00f';
+    }
+  }
+
+  return '#888';
+}
+
+function fetchSequence(_x, _x2) {
+  return _fetchSequence.apply(this, arguments);
+} // has to check underlying C-G (aka CpG) on the reference sequence
+
+
+function _fetchSequence() {
+  _fetchSequence = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(region, adapter) {
+    var _feats$;
+
+    var end, originalRefName, refName, feats;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            end = region.end, originalRefName = region.originalRefName, refName = region.refName;
+            _context.next = 3;
+            return adapter.getFeatures(_objectSpread(_objectSpread({}, region), {}, {
+              refName: originalRefName || refName,
+              end: end + 1
+            })).pipe((0, _operators.toArray)()).toPromise();
+
+          case 3:
+            feats = _context.sent;
+            return _context.abrupt("return", (_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq'));
+
+          case 5:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  }));
+  return _fetchSequence.apply(this, arguments);
+}
+
+function shouldFetchReferenceSequence(type) {
+  return type === 'methylation';
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.6.9",
+  "version": "1.7.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,13 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-alignments.esm.js",
-  "module": "dist/plugin-alignments.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "postbuild": "tsc --build tsconfig.build.json",
     "test": "cd ../..; jest plugins/alignments",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -43,8 +41,7 @@
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
     "generic-filehandle": "^2.2.2",
-    "json-stable-stringify": "^1.0.1",
-    "react-d3-axis-mod": "^0.1.3"
+    "json-stable-stringify": "^1.0.1"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -61,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
 }

package/src/BamAdapter/BamAdapter.ts

@@ -4,11 +4,7 @@ import {
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { Region } from '@jbrowse/core/util/types'
-import {
-  checkAbortSignal,
-  bytesForRegions,
-  updateStatus,
-} from '@jbrowse/core/util'
+import { bytesForRegions, updateStatus } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
@@ -170,17 +166,29 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
 
   getFeatures(
     region: Region & { originalRefName?: string },
-    opts?: BaseOptions,
+    opts?: BaseOptions & {
+      filterBy: {
+        flagInclude: number
+        flagExclude: number
+        tagFilter: { tag: string; value: unknown }
+        name: string
+      }
+    },
   ) {
     const { refName, start, end, originalRefName } = region
-    const { signal, statusCallback = () => {} } = opts || {}
+    const { signal, filterBy, statusCallback = () => {} } = opts || {}
     return ObservableCreate<Feature>(async observer => {
       const { bam } = await this.configure()
       await this.setup(opts)
       statusCallback('Downloading alignments')
       const records = await bam.getRecordsForRange(refName, start, end, opts)
 
-      checkAbortSignal(signal)
+      const {
+        flagInclude = 0,
+        flagExclude = 0,
+        tagFilter,
+        name,
+      } = filterBy || {}
 
       for (const record of records) {
         let ref: string | undefined
@@ -191,6 +199,25 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             record.get('end'),
           )
         }
+
+        const flags = record.flags
+        if (
+          !((flags & flagInclude) === flagInclude && !(flags & flagExclude))
+        ) {
+          continue
+        }
+
+        if (tagFilter) {
+          const val = record.get(tagFilter.tag)
+          if (!(val === '*' ? val !== undefined : val === tagFilter.value)) {
+            continue
+          }
+        }
+
+        if (name && record.get('name') !== name) {
+          continue
+        }
+
         observer.next(new BamSlightlyLazyFeature(record, this, ref))
       }
       statusCallback('')

package/src/CramAdapter/CramAdapter.ts

@@ -3,12 +3,9 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
-import { checkAbortSignal } from '@jbrowse/core/util'
+import { checkAbortSignal, Region, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { toArray } from 'rxjs/operators'
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature'
 
@@ -39,8 +36,8 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   private seqIdToOriginalRefName: string[] = []
 
   public async configure() {
-    const cramLocation = readConfObject(this.config, 'cramLocation')
-    const craiLocation = readConfObject(this.config, 'craiLocation')
+    const cramLocation = this.getConf('cramLocation')
+    const craiLocation = this.getConf('craiLocation')
     if (!cramLocation) {
       throw new Error('missing cramLocation argument')
     }
@@ -59,16 +56,13 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       fetchSizeLimit: 200_000_000, // just make this a large size to avoid hitting it
     })
     // instantiate the sequence adapter
-    const sequenceAdapterType = readConfObject(this.config, [
-      'sequenceAdapter',
-      'type',
-    ])
+    const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type'])
 
     if (!this.getSubAdapter) {
       throw new Error('Error getting subadapter')
     }
 
-    const seqConf = readConfObject(this.config, 'sequenceAdapter')
+    const seqConf = this.getConf('sequenceAdapter')
     const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf)
 
     if (!(sequenceAdapter instanceof BaseFeatureDataAdapter)) {
@@ -211,9 +205,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   getFeatures(
     region: Region & { originalRefName?: string },
-    opts?: BaseOptions,
+    opts?: BaseOptions & {
+      filterBy: {
+        flagInclude: number
+        flagExclude: number
+        tagFilter: { tag: string; value: unknown }
+        name: string
+      }
+    },
   ) {
-    const { signal, statusCallback = () => {} } = opts || {}
+    const { signal, filterBy, statusCallback = () => {} } = opts || {}
     const { refName, start, end, originalRefName } = region
 
     return ObservableCreate<Feature>(async observer => {
@@ -229,8 +230,34 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         }
         const records = await cram.getRecordsForRange(refId, start, end, opts)
         checkAbortSignal(signal)
+        const {
+          flagInclude = 0,
+          flagExclude = 0,
+          tagFilter,
+          name,
+        } = filterBy || {}
+
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        let filtered = records.filter((record: any) => {
+          const flags = record.flags
+          return (flags & flagInclude) === flagInclude && !(flags & flagExclude)
+        })
+
+        if (tagFilter) {
+          // eslint-disable-next-line @typescript-eslint/no-explicit-any
+          filtered = filtered.filter((record: any) => {
+            const val = record[tagFilter.tag]
+            return val === '*' ? val !== undefined : val === tagFilter.value
+          })
+        }
+
+        if (name) {
+          // eslint-disable-next-line @typescript-eslint/no-explicit-any
+          filtered = filtered.filter((record: any) => record.name === name)
+        }
+
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        records.forEach((record: any) => {
+        filtered.forEach((record: any) => {
           observer.next(this.cramRecordToFeature(record))
         })
       } else {
@@ -250,7 +277,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   // we return the configured fetchSizeLimit, and the bytes for the region
   async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
     const bytes = await this.bytesForRegions(regions, opts)
-    const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')
+    const fetchSizeLimit = this.getConf('fetchSizeLimit')
     return {
       bytes,
       fetchSizeLimit,

package/src/LinearPileupDisplay/components/SetMaxHeight.tsx

@@ -55,7 +55,7 @@ function SetMaxHeightDlg(props: {
       <DialogContent className={classes.root}>
         <Typography>
           Set max height for the track. For example, you can increase this if
-          the layout says "Max height reached"
+          the layout says &quot;Max height reached&quot;
         </Typography>
         <TextField
           value={max}

package/src/LinearPileupDisplay/model.ts

@@ -27,7 +27,6 @@ import FilterListIcon from '@material-ui/icons/ClearAll'
 
 import { autorun, observable } from 'mobx'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
 import { LinearPileupDisplayConfigModel } from './configSchema'
 import LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb'
 
@@ -377,26 +376,6 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
           return LinearPileupDisplayBlurb
         },
 
-        get filters() {
-          let filters: string[] = []
-          const { flagInclude, flagExclude, tagFilter, readName } =
-            self.filterBy
-
-          filters = [
-            `jexl:((get(feature,'flags')&${flagInclude})==${flagInclude}) && !(get(feature,'flags')&${flagExclude})`,
-          ]
-          if (tagFilter) {
-            const { tag, value } = tagFilter
-            filters.push(
-              `jexl:"${value}" =='*' ? getTag(feature,"${tag}") != undefined : getTag(feature,"${tag}") == "${value}"`,
-            )
-          }
-          if (readName) {
-            filters.push(`jexl:get(feature,'name') == "${readName}"`)
-          }
-          return new SerializableFilterChain({ filters })
-        },
-
         renderProps() {
           const view = getContainingView(self) as LGV
           const {
@@ -404,6 +383,7 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
             modificationTagMap,
             sortedBy,
             colorBy,
+            filterBy,
             rpcDriverName,
           } = self
 
@@ -419,9 +399,9 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
             displayModel: self,
             sortedBy,
             colorBy,
+            filterBy,
             colorTagMap: JSON.parse(JSON.stringify(colorTagMap)),
             modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),
-            filters: this.filters,
             showSoftClip: self.showSoftClipping,
             config: self.rendererConfig,
           }

package/src/LinearSNPCoverageDisplay/models/model.ts

@@ -1,13 +1,14 @@
 import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree'
 import { observable, autorun } from 'mobx'
-import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
 import {
+  getConf,
+  readConfObject,
   AnyConfigurationSchemaType,
   AnyConfigurationModel,
-} from '@jbrowse/core/configuration/configurationSchema'
+} from '@jbrowse/core/configuration'
+import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
+
 import PluginManager from '@jbrowse/core/PluginManager'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
 import { getContainingView } from '@jbrowse/core/util'
 import Tooltip from '../components/Tooltip'
 import { getUniqueModificationValues } from '../../shared'
@@ -135,7 +136,6 @@ const stateModelFactory = (
           return {
             ...superProps,
             notReady: superProps.notReady || !this.modificationsReady,
-            filters: self.filters,
             modificationTagMap: JSON.parse(
               JSON.stringify(self.modificationTagMap),
             ),
@@ -143,6 +143,7 @@ const stateModelFactory = (
             // must use getSnapshot because otherwise changes to e.g. just the
             // colorBy.type are not read
             colorBy: self.colorBy ? getSnapshot(self.colorBy) : undefined,
+            filterBy: self.filterBy,
           }
         },
       }
@@ -241,37 +242,6 @@ const stateModelFactory = (
             },
           ]
         },
-        // The SNPCoverage filters are called twice because the BAM/CRAM
-        // features pass filters and then the SNPCoverage score features pass
-        // through here, and are already have 'snpinfo' are passed through
-        get filters() {
-          let filters: string[] = []
-          if (self.filterBy) {
-            const { flagInclude, flagExclude, tagFilter, readName } =
-              self.filterBy
-            filters = [
-              `jexl:get(feature,'snpinfo') != undefined ? true : ` +
-                `((get(feature,'flags')&${flagInclude})==${flagInclude}) && ` +
-                `!((get(feature,'flags')&${flagExclude}))`,
-            ]
-
-            if (tagFilter) {
-              const { tag, value } = tagFilter
-              filters.push(
-                `jexl:get(feature,'snpinfo') != undefined ? true : ` +
-                  `"${value}" =='*' ? getTag(feature,"${tag}") != undefined : ` +
-                  `getTag(feature,"${tag}") == "${value}"`,
-              )
-            }
-            if (readName) {
-              filters.push(
-                `jexl:get(feature,'snpinfo') != undefined ? true : ` +
-                  `get(feature,'name') == "${readName}"`,
-              )
-            }
-          }
-          return new SerializableFilterChain({ filters })
-        },
       }
     })