@jbrowse/plugin-alignments 1.6.7 → 1.7.0

package/dist/BamAdapter/BamAdapter.test.js

@@ -0,0 +1,177 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+var _BamAdapter = _interopRequireDefault(require("./BamAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, features, featuresArray, featuresJsonArray, adapterCSI, featuresCSI, featuresArrayCSI, featuresJsonArrayCSI;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+            bamLocation: {
+              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          features = adapter.getFeatures({
+            assemblyName: 'volvox',
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context.sent;
+          expect(featuresArray[0].get('refName')).toBe('ctgA');
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.length).toEqual(3809);
+          expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot();
+          expect(adapter.refIdToName(0)).toBe('ctgA');
+          expect(adapter.refIdToName(1)).toBe(undefined);
+          _context.t0 = expect;
+          _context.next = 14;
+          return adapter.hasDataForRefName('ctgA');
+
+        case 14:
+          _context.t1 = _context.sent;
+          (0, _context.t0)(_context.t1).toBe(true);
+          adapterCSI = new _BamAdapter["default"](_configSchema["default"].create({
+            bamLocation: {
+              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              indexType: 'CSI',
+              location: {
+                localPath: require.resolve('../../test_data/volvox-sorted.bam.csi'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          featuresCSI = adapterCSI.getFeatures({
+            assemblyName: 'volvox',
+            refName: 'ctgA',
+            start: 0,
+            end: 20000
+          });
+          _context.next = 20;
+          return featuresCSI.pipe((0, _operators.toArray)()).toPromise();
+
+        case 20:
+          featuresArrayCSI = _context.sent;
+          featuresJsonArrayCSI = featuresArrayCSI.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArrayCSI).toEqual(featuresJsonArray);
+
+        case 23:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var adapter, features, featuresArray, f;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+            bamLocation: {
+              localPath: require.resolve('../../test_data/volvox-sorted.bam'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
+                locationType: 'LocalPathLocation'
+              },
+              indexType: 'BAI'
+            }
+          }));
+          features = adapter.getFeatures({
+            assemblyName: 'volvox',
+            refName: 'ctgA',
+            start: 0,
+            end: 100
+          });
+          _context2.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context2.sent;
+          f = featuresArray[0].toJSON();
+          expect(f.refName).toBe('ctgA');
+          expect(f.start).toBe(2);
+          expect(f.end).toBe(102);
+          expect(f.mismatches).not.toBeTruthy();
+
+        case 10:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));
+test('test usage of BamSlightlyLazyFeature for extended CIGAR', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+  var adapter, features, featuresArray, f;
+  return _regenerator["default"].wrap(function _callee3$(_context3) {
+    while (1) {
+      switch (_context3.prev = _context3.next) {
+        case 0:
+          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+            bamLocation: {
+              localPath: require.resolve('../../test_data/extended_cigar.bam'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('../../test_data/extended_cigar.bam.bai'),
+                locationType: 'LocalPathLocation'
+              },
+              indexType: 'BAI'
+            }
+          }));
+          features = adapter.getFeatures({
+            assemblyName: 'hg19',
+            refName: '1',
+            start: 13260,
+            end: 13340
+          });
+          _context3.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context3.sent;
+          f = featuresArray[0];
+          expect(f.get('mismatches')).toMatchSnapshot();
+
+        case 7:
+        case "end":
+          return _context3.stop();
+      }
+    }
+  }, _callee3);
+})));

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,13 +1,11 @@
 /// <reference types="node" />
 import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { BamRecord } from '@gmod/bam';
-import { Mismatch } from './MismatchParser';
 import BamAdapter from './BamAdapter';
 export default class BamSlightlyLazyFeature implements Feature {
     private record;
     private adapter;
     private ref?;
-    private cachedMD;
     constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
     _get_name(): any;
     _get_type(): string;
@@ -20,7 +18,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_next_refName(): string | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;
-    _get_MD(): any;
     qualRaw(): Buffer | undefined;
     set(): void;
     tags(): string[];
@@ -31,12 +28,6 @@ export default class BamSlightlyLazyFeature implements Feature {
     children(): undefined;
     pairedFeature(): boolean;
     toJSON(): SimpleFeatureSerialized;
-    _get_skips_and_dels(opts?: {
-        cigarAttributeName: string;
-    }): Mismatch[];
-    _get_mismatches({ cigarAttributeName, mdAttributeName, }?: {
-        cigarAttributeName?: string;
-        mdAttributeName?: string;
-    }): Mismatch[];
+    _get_mismatches(): import("./MismatchParser").Mismatch[];
     _get_clipPos(): number;
 }

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -0,0 +1,176 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _MismatchParser = require("./MismatchParser");
+
+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; }
+
+var BamSlightlyLazyFeature = /*#__PURE__*/function () {
+  // uses parameter properties to automatically create fields on the class
+  // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
+  function BamSlightlyLazyFeature(record, adapter, ref) {
+    (0, _classCallCheck2["default"])(this, BamSlightlyLazyFeature);
+    this.record = record;
+    this.adapter = adapter;
+    this.ref = ref;
+  }
+
+  (0, _createClass2["default"])(BamSlightlyLazyFeature, [{
+    key: "_get_name",
+    value: function _get_name() {
+      return this.record.get('name');
+    }
+  }, {
+    key: "_get_type",
+    value: function _get_type() {
+      return 'match';
+    }
+  }, {
+    key: "_get_score",
+    value: function _get_score() {
+      return this.record.get('mq');
+    }
+  }, {
+    key: "_get_flags",
+    value: function _get_flags() {
+      return this.record.flags;
+    }
+  }, {
+    key: "_get_strand",
+    value: function _get_strand() {
+      return this.record.isReverseComplemented() ? -1 : 1;
+    }
+  }, {
+    key: "_get_pair_orientation",
+    value: function _get_pair_orientation() {
+      return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
+    }
+  }, {
+    key: "_get_next_seq_id",
+    value: function _get_next_seq_id() {
+      return this.record._next_refid();
+    }
+  }, {
+    key: "_get_seq_id",
+    value: function _get_seq_id() {
+      // @ts-ignore
+      return this.record._refID;
+    }
+  }, {
+    key: "_get_next_refName",
+    value: function _get_next_refName() {
+      return this.adapter.refIdToName(this.record._next_refid());
+    }
+  }, {
+    key: "_get_next_segment_position",
+    value: function _get_next_segment_position() {
+      var record = this.record,
+          adapter = this.adapter;
+      return record.isPaired() ? "".concat(adapter.refIdToName(record._next_refid()), ":").concat(record._next_pos() + 1) : undefined;
+    }
+  }, {
+    key: "_get_seq",
+    value: function _get_seq() {
+      return this.record.getReadBases();
+    }
+  }, {
+    key: "qualRaw",
+    value: function qualRaw() {
+      return this.record.qualRaw();
+    }
+  }, {
+    key: "set",
+    value: function set() {}
+  }, {
+    key: "tags",
+    value: function tags() {
+      var properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
+      return (0, _toConsumableArray2["default"])(new Set(properties.filter(function (prop) {
+        return prop.startsWith('_get_') && prop !== '_get_mismatches' && prop !== '_get_tags' && prop !== '_get_next_seq_id' && prop !== '_get_seq_id';
+      }).map(function (methodName) {
+        return methodName.replace('_get_', '');
+      }).concat(this.record._tags())));
+    }
+  }, {
+    key: "id",
+    value: function id() {
+      return "".concat(this.adapter.id, "-").concat(this.record.id());
+    } // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  }, {
+    key: "get",
+    value: function get(field) {
+      var methodName = "_get_".concat(field); // @ts-ignore
+
+      if (this[methodName]) {
+        // @ts-ignore
+        return this[methodName]();
+      }
+
+      return this.record.get(field);
+    }
+  }, {
+    key: "_get_refName",
+    value: function _get_refName() {
+      return this.adapter.refIdToName(this.record.seq_id());
+    }
+  }, {
+    key: "parent",
+    value: function parent() {
+      return undefined;
+    }
+  }, {
+    key: "children",
+    value: function children() {
+      return undefined;
+    }
+  }, {
+    key: "pairedFeature",
+    value: function pairedFeature() {
+      return false;
+    }
+  }, {
+    key: "toJSON",
+    value: function toJSON() {
+      var _this = this;
+
+      return _objectSpread(_objectSpread({}, Object.fromEntries(this.tags().map(function (t) {
+        return [t, _this.get(t)];
+      }).filter(function (elt) {
+        return elt[1] !== undefined;
+      }))), {}, {
+        uniqueId: this.id()
+      });
+    }
+  }, {
+    key: "_get_mismatches",
+    value: function _get_mismatches() {
+      return (0, _MismatchParser.getMismatches)(this.get('CIGAR'), this.get('MD'), this.get('seq'), this.ref, this.qualRaw());
+    }
+  }, {
+    key: "_get_clipPos",
+    value: function _get_clipPos() {
+      var cigar = this.get('CIGAR') || '';
+      return this.get('strand') === -1 ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0 : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0;
+    }
+  }]);
+  return BamSlightlyLazyFeature;
+}();
+
+exports["default"] = BamSlightlyLazyFeature;

package/dist/BamAdapter/MismatchParser.d.ts

@@ -10,15 +10,13 @@ export interface Mismatch {
     cliplen?: number;
 }
 export declare function parseCigar(cigar: string): string[];
-export declare function cigarToMismatches(ops: string[], seq: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference
  * @returns array of mismatches and their positions
  */
-export declare function mdToMismatches(mdstring: string, cigarOps: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
-export declare function getTemplateCoord(refCoord: number, cigarOps: string[]): number;
-export declare function getMismatches(cigarString: string, mdString: string, seq: string, qual?: Buffer): Mismatch[];
-export declare function generateMD(target: string, query: string, cigar: string): string;
+export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar: string, md: string, seq: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): ({
     type: string;