@jbrowse/plugin-alignments 1.6.7 → 1.7.0

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

@@ -1,4 +1,6 @@
+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: {
@@ -13,3 +15,5 @@ export declare const orientationTypes: {
     };
 };
 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": "1.6.7",
+  "version": "1.7.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "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",
     "test": "cd ../..; jest plugins/alignments",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -35,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bam": "^1.1.14",
+    "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.1",
     "@material-ui/icons": "^4.9.1",
     "abortable-promise-cache": "^1.5.0",
@@ -43,8 +40,7 @@
     "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 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }

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'
@@ -38,7 +34,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
       const bamLocation = readConfObject(this.config, 'bamLocation')
       const location = readConfObject(this.config, ['index', 'location'])
       const indexType = readConfObject(this.config, ['index', 'indexType'])
-      const chunkSizeLimit = readConfObject(this.config, 'chunkSizeLimit')
       const bam = new BamFile({
         bamFilehandle: openLocation(bamLocation, this.pluginManager),
         csiFilehandle:
@@ -49,8 +44,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           indexType !== 'CSI'
             ? openLocation(location, this.pluginManager)
             : undefined,
-        chunkSizeLimit,
-        fetchSizeLimit: 100_000_000,
+
+        // chunkSizeLimit and fetchSizeLimit are more troublesome than
+        // helpful, and have given overly large values on the ultra long
+        // nanopore reads even with 500MB limits, so disabled with infinity
+        chunkSizeLimit: Infinity,
+        fetchSizeLimit: Infinity,
+        yieldThreadTime: Infinity,
       })
 
       const adapterConfig = readConfObject(this.config, 'sequenceAdapter')
@@ -139,7 +139,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
 
     const seqChunks = await features.pipe(toArray()).toPromise()
 
-    const trimmed: string[] = []
+    let sequence = ''
     seqChunks
       .sort((a, b) => a.get('start') - b.get('start'))
       .forEach(chunk => {
@@ -149,10 +149,9 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)
         const trimLength = trimEnd - trimStart
         const chunkSeq = chunk.get('seq') || chunk.get('residues')
-        trimmed.push(chunkSeq.substr(trimStart, trimLength))
+        sequence += chunkSeq.substr(trimStart, trimLength)
       })
 
-    const sequence = trimmed.join('')
     if (sequence.length !== end - start) {
       throw new Error(
         `sequence fetch failed: fetching ${refName}:${(
@@ -167,27 +166,58 @@ 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
-        if (!record.get('md')) {
+        if (!record.get('MD')) {
           ref = await this.seqFetch(
             originalRefName || refName,
             record.get('start'),
             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/BamAdapter/BamSlightlyLazyFeature.ts

@@ -4,18 +4,13 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { BamRecord } from '@gmod/bam'
-import {
-  parseCigar,
-  generateMD,
-  cigarToMismatches,
-  mdToMismatches,
-  Mismatch,
-} from './MismatchParser'
+import { getMismatches } from './MismatchParser'
 
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {
-  private cachedMD = ''
+  // uses parameter properties to automatically create fields on the class
+  // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
   constructor(
     private record: BamRecord,
     private adapter: BamAdapter,
@@ -70,18 +65,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     return this.record.getReadBases()
   }
 
-  _get_MD() {
-    const md = this.record.get('MD') || this.cachedMD
-    if (!md) {
-      const seq = this.get('seq')
-      if (seq && this.ref) {
-        this.cachedMD = generateMD(this.ref, this.get('seq'), this.get('CIGAR'))
-        return this.cachedMD
-      }
-    }
-    return md
-  }
-
   qualRaw() {
     return this.record.qualRaw()
   }
@@ -100,8 +83,6 @@ export default class BamSlightlyLazyFeature implements Feature {
             prop =>
               prop.startsWith('_get_') &&
               prop !== '_get_mismatches' &&
-              prop !== '_get_skips_and_dels' &&
-              prop !== '_get_cram_read_features' &&
               prop !== '_get_tags' &&
               prop !== '_get_next_seq_id' &&
               prop !== '_get_seq_id',
@@ -154,63 +135,14 @@ export default class BamSlightlyLazyFeature implements Feature {
     }
   }
 
-  _get_skips_and_dels(
-    opts: {
-      cigarAttributeName: string
-    } = {
-      cigarAttributeName: 'CIGAR',
-    },
-  ) {
-    const { cigarAttributeName } = opts
-    let mismatches: Mismatch[] = []
-    let cigarOps: string[] = []
-
-    // parse the CIGAR tag if it has one
-    const cigarString = this.get(cigarAttributeName)
-    if (cigarString) {
-      cigarOps = parseCigar(cigarString)
-      mismatches = mismatches.concat(
-        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),
-      )
-    }
-    return mismatches
-  }
-
-  _get_mismatches({
-    cigarAttributeName = 'CIGAR',
-    mdAttributeName = 'MD',
-  }: {
-    cigarAttributeName?: string
-    mdAttributeName?: string
-  } = {}) {
-    let mismatches: Mismatch[] = []
-    let cigarOps: string[] = []
-
-    // parse the CIGAR tag if it has one
-    const cigarString = this.get(cigarAttributeName)
-    const seq = this.get('seq')
-    const qual = this.qualRaw()
-    if (cigarString) {
-      cigarOps = parseCigar(cigarString)
-      mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))
-    }
-
-    // now let's look for CRAM or MD mismatches
-    const mdString = this.get(mdAttributeName)
-    if (mdString) {
-      mismatches = mismatches.concat(
-        mdToMismatches(mdString, cigarOps, mismatches, seq, qual),
-      )
-    }
-
-    // uniqify the mismatches
-    const seen: { [index: string]: boolean } = {}
-    return mismatches.filter(m => {
-      const key = `${m.type},${m.start},${m.length}`
-      const s = seen[key]
-      seen[key] = true
-      return !s
-    })
+  _get_mismatches() {
+    return getMismatches(
+      this.get('CIGAR'),
+      this.get('MD'),
+      this.get('seq'),
+      this.ref,
+      this.qualRaw(),
+    )
   }
 
   _get_clipPos() {