@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,33 +1,33 @@
-/// <reference types="node" />
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { BamRecord } from '@gmod/bam';
-import BamAdapter from './BamAdapter';
-export default class BamSlightlyLazyFeature implements Feature {
-    private record;
-    private adapter;
-    private ref?;
-    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
-    _get_name(): any;
-    _get_type(): string;
-    _get_score(): number;
-    _get_flags(): string;
-    _get_strand(): number;
-    _get_pair_orientation(): string | null | undefined;
-    _get_next_seq_id(): number;
-    _get_seq_id(): number;
-    _get_next_refName(): string | undefined;
-    _get_next_segment_position(): string | undefined;
-    _get_seq(): string;
-    qualRaw(): Buffer | undefined;
-    set(): void;
-    tags(): string[];
-    id(): string;
-    get(field: string): any;
-    _get_refName(): string | undefined;
-    parent(): undefined;
-    children(): undefined;
-    pairedFeature(): boolean;
-    toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): import("./MismatchParser").Mismatch[];
-    _get_clipPos(): number;
-}
+/// <reference types="node" />
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { BamRecord } from '@gmod/bam';
+import BamAdapter from './BamAdapter';
+export default class BamSlightlyLazyFeature implements Feature {
+    private record;
+    private adapter;
+    private ref?;
+    constructor(record: BamRecord, adapter: BamAdapter, ref?: string | undefined);
+    _get_name(): any;
+    _get_type(): string;
+    _get_score(): number;
+    _get_flags(): string;
+    _get_strand(): number;
+    _get_pair_orientation(): string | null | undefined;
+    _get_next_seq_id(): number;
+    _get_seq_id(): number;
+    _get_next_refName(): string | undefined;
+    _get_next_segment_position(): string | undefined;
+    _get_seq(): string;
+    qualRaw(): Buffer | undefined;
+    set(): void;
+    tags(): string[];
+    id(): string;
+    get(field: string): any;
+    _get_refName(): string | undefined;
+    parent(): undefined;
+    children(): undefined;
+    pairedFeature(): boolean;
+    toJSON(): SimpleFeatureSerialized;
+    _get_mismatches(): import("./MismatchParser").Mismatch[];
+    _get_clipPos(): number;
+}

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
@@ -19,19 +19,19 @@ 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; }
+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);
+    (0, _classCallCheck2.default)(this, BamSlightlyLazyFeature);
     this.record = record;
     this.adapter = adapter;
     this.ref = ref;
   }
 
-  (0, _createClass2["default"])(BamSlightlyLazyFeature, [{
+  (0, _createClass2.default)(BamSlightlyLazyFeature, [{
     key: "_get_name",
     value: function _get_name() {
       return this.record.get('name');
@@ -101,7 +101,7 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
     key: "tags",
     value: function tags() {
       var properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
-      return (0, _toConsumableArray2["default"])(new Set(properties.filter(function (prop) {
+      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_', '');
@@ -173,4 +173,4 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
   return BamSlightlyLazyFeature;
 }();
 
-exports["default"] = BamSlightlyLazyFeature;
+exports.default = BamSlightlyLazyFeature;

package/dist/BamAdapter/MismatchParser.d.ts

@@ -1,28 +1,28 @@
-/// <reference types="node" />
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
-export declare function parseCigar(cigar: string): string[];
-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, 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;
-    positions: number[];
-} | {
-    type: string;
-    positions: never[];
-})[];
-export declare function getModificationTypes(mm: string): string[];
+/// <reference types="node" />
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export declare function parseCigar(cigar: string): string[];
+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, 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;
+    positions: number[];
+} | {
+    type: string;
+    positions: never[];
+})[];
+export declare function getModificationTypes(mm: string): string[];

package/dist/BamAdapter/MismatchParser.js

@@ -21,7 +21,7 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
 
 var _util = require("@jbrowse/core/util");
 
-var _marked = /*#__PURE__*/_regenerator["default"].mark(getNextRefPos);
+var _marked = /*#__PURE__*/_regenerator.default.mark(getNextRefPos);
 
 var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 
@@ -244,7 +244,7 @@ function getMismatches(cigar, md, seq, ref, qual) {
 
 function getNextRefPos(cigarOps, positions) {
   var cigarIdx, readPos, refPos, i, pos, len, op;
-  return _regenerator["default"].wrap(function getNextRefPos$(_context) {
+  return _regenerator.default.wrap(function getNextRefPos$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
@@ -297,7 +297,7 @@ function getModificationPositions(mm, fseq, fstrand) {
     return !!mod;
   }).map(function (mod) {
     var _mod$split = mod.split(','),
-        _mod$split2 = (0, _toArray2["default"])(_mod$split),
+        _mod$split2 = (0, _toArray2.default)(_mod$split),
         basemod = _mod$split2[0],
         skips = _mod$split2.slice(1); // regexes based on parse_mm.pl from hts-specs
 
@@ -308,7 +308,7 @@ function getModificationPositions(mm, fseq, fstrand) {
       throw new Error('bad format for MM tag');
     }
 
-    var _matches = (0, _slicedToArray2["default"])(matches, 4),
+    var _matches = (0, _slicedToArray2.default)(matches, 4),
         base = _matches[1],
         strand = _matches[2],
         typestr = _matches[3]; // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
@@ -363,7 +363,7 @@ function getModificationTypes(mm) {
     return !!mod;
   }).map(function (mod) {
     var _mod$split3 = mod.split(','),
-        _mod$split4 = (0, _slicedToArray2["default"])(_mod$split3, 1),
+        _mod$split4 = (0, _slicedToArray2.default)(_mod$split3, 1),
         basemod = _mod$split4[0];
 
     var matches = basemod.match(/([A-Z])([-+])([^,]+)/);
@@ -372,7 +372,7 @@ function getModificationTypes(mm) {
       throw new Error('bad format for MM tag');
     }
 
-    var _matches2 = (0, _slicedToArray2["default"])(matches, 4),
+    var _matches2 = (0, _slicedToArray2.default)(matches, 4),
         typestr = _matches2[3]; // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
     // split, and they can also be chemical codes (ChEBI) e.g. C+16061
 

package/dist/BamAdapter/MismatchParser.test.js

@@ -220,7 +220,7 @@ test('getNextRefPos basic', function () {
   var cigar = (0, _MismatchParser.parseCigar)('10S10M1I4M1D15M');
   var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15, 20, 25, 30, 35]);
 
-  var _iter = (0, _toArray2["default"])(iter),
+  var _iter = (0, _toArray2.default)(iter),
       vals = _iter.slice(0);
 
   expect(vals).toEqual([-5, 0, 5, 10, 14, 20, 25]);
@@ -229,7 +229,7 @@ test('getNextRefPos with many indels', function () {
   var cigar = (0, _MismatchParser.parseCigar)('10S4M1D1IM10');
   var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15]);
 
-  var _iter2 = (0, _toArray2["default"])(iter),
+  var _iter2 = (0, _toArray2.default)(iter),
       vals = _iter2.slice(0);
 
   expect(vals).toEqual([-5, 0, 5]);

package/dist/BamAdapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/BamAdapter/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -45,4 +45,4 @@ var _default = _mobxStateTree.types.late(function () {
   });
 });
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/BamAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/BamAdapter/index.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
@@ -15,22 +15,22 @@ var _configSchema = _interopRequireDefault(require("./configSchema"));
 
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2.default)(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 var _default = function _default(pluginManager) {
   pluginManager.addAdapterType(function () {
-    return new _AdapterType["default"]({
+    return new _AdapterType.default({
       name: 'BamAdapter',
-      configSchema: _configSchema["default"],
+      configSchema: _configSchema.default,
       getAdapterClass: function getAdapterClass() {
         return Promise.resolve().then(function () {
           return _interopRequireWildcard(require('./BamAdapter'));
         }).then(function (r) {
-          return r["default"];
+          return r.default;
         });
       }
     });
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,43 +1,52 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
-interface Header {
-    idToName?: string[];
-    nameToId?: Record<string, number>;
-    readGroups?: number[];
-}
-export default class CramAdapter extends BaseFeatureDataAdapter {
-    samHeader: Header;
-    private setupP?;
-    private seqIdToRefName;
-    private seqIdToOriginalRefName;
-    configure(): Promise<{
-        cram: any;
-        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
-    }>;
-    getHeader(opts?: BaseOptions): Promise<any>;
-    private seqFetch;
-    private setupPre;
-    private setup;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    refNameToId(refName: string): number | undefined;
-    refIdToName(refId: number): string | undefined;
-    refIdToOriginalName(refId: number): string;
-    getFeatures(region: Region & {
-        originalRefName?: string;
-    }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
-        bytes: any;
-        fetchSizeLimit: any;
-    }>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
-    private bytesForRegions;
-}
-export {};
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
+interface Header {
+    idToName?: string[];
+    nameToId?: Record<string, number>;
+    readGroups?: number[];
+}
+export default class CramAdapter extends BaseFeatureDataAdapter {
+    samHeader: Header;
+    private setupP?;
+    private seqIdToRefName;
+    private seqIdToOriginalRefName;
+    configure(): Promise<{
+        cram: any;
+        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
+    }>;
+    getHeader(opts?: BaseOptions): Promise<any>;
+    private seqFetch;
+    private setupPre;
+    private setup;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    refNameToId(refName: string): number | undefined;
+    refIdToName(refId: number): string | undefined;
+    refIdToOriginalName(refId: number): string;
+    getFeatures(region: Region & {
+        originalRefName?: string;
+    }, opts?: BaseOptions & {
+        filterBy: {
+            flagInclude: number;
+            flagExclude: number;
+            tagFilter: {
+                tag: string;
+                value: unknown;
+            };
+            name: string;
+        };
+    }): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+        bytes: any;
+        fetchSizeLimit: any;
+    }>;
+    /**
+     * get the approximate number of bytes queried from the file for the given
+     * query regions
+     * @param regions - list of query regions
+     */
+    private bytesForRegions;
+}
+export {};

package/dist/CramAdapter/CramAdapter.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -41,41 +41,41 @@ var _CramSlightlyLazyFeature = _interopRequireDefault(require("./CramSlightlyLaz
 
 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 _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 _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
 var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(CramAdapter, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(CramAdapter, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(CramAdapter);
 
   function CramAdapter() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, CramAdapter);
+    (0, _classCallCheck2.default)(this, CramAdapter);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "samHeader", {});
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "setupP", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "seqIdToRefName", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "seqIdToOriginalRefName", []);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "samHeader", {});
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "setupP", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "seqIdToRefName", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "seqIdToOriginalRefName", []);
     return _this;
   }
 
-  (0, _createClass2["default"])(CramAdapter, [{
+  (0, _createClass2.default)(CramAdapter, [{
     key: "configure",
     value: function () {
-      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var cramLocation, craiLocation, cram, sequenceAdapterType, seqConf, _yield$this$getSubAda, sequenceAdapter;
 
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -158,10 +158,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getHeader",
     value: function () {
-      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
         var _yield$this$configure, cram;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -190,10 +190,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "seqFetch",
     value: function () {
-      var _seqFetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(seqId, start, end) {
+      var _seqFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(seqId, start, end) {
         var _yield$this$configure2, sequenceAdapter, refName, seqChunks, sequence;
 
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -264,10 +264,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setupPre",
     value: function () {
-      var _setupPre = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(opts) {
+      var _setupPre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
         var _ref, _ref$statusCallback, statusCallback, configured, cram, samHeader, idToName, nameToId, readGroups, data;
 
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
@@ -337,15 +337,15 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setup",
     value: function () {
-      var _setup = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(opts) {
+      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(opts) {
         var _this2 = this;
 
-        return _regenerator["default"].wrap(function _callee5$(_context5) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
                 if (!this.setupP) {
-                  this.setupP = this.setupPre(opts)["catch"](function (e) {
+                  this.setupP = this.setupPre(opts).catch(function (e) {
                     _this2.setupP = undefined;
                     throw e;
                   });
@@ -370,10 +370,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(opts) {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(opts) {
         var _yield$this$setup, samHeader;
 
-        return _regenerator["default"].wrap(function _callee6$(_context6) {
+        return _regenerator.default.wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
               case 0:
@@ -459,10 +459,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
           end = region.end,
           originalRefName = region.originalRefName;
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref3 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee7(observer) {
+        var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(observer) {
           var _yield$_this3$setup, cram, sequenceAdapter, refId, records, _ref4, _ref4$flagInclude, flagInclude, _ref4$flagExclude, flagExclude, tagFilter, name, filtered;
 
-          return _regenerator["default"].wrap(function _callee7$(_context7) {
+          return _regenerator.default.wrap(function _callee7$(_context7) {
             while (1) {
               switch (_context7.prev = _context7.next) {
                 case 0:
@@ -561,15 +561,15 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "cramRecordToFeature",
     value: function cramRecordToFeature(record) {
-      return new _CramSlightlyLazyFeature["default"](record, this);
+      return new _CramSlightlyLazyFeature.default(record, this);
     } // we return the configured fetchSizeLimit, and the bytes for the region
 
   }, {
     key: "estimateRegionsStats",
     value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee8(regions, opts) {
+      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(regions, opts) {
         var bytes, fetchSizeLimit;
-        return _regenerator["default"].wrap(function _callee8$(_context8) {
+        return _regenerator.default.wrap(function _callee8$(_context8) {
           while (1) {
             switch (_context8.prev = _context8.next) {
               case 0:
@@ -607,12 +607,12 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "bytesForRegions",
     value: function () {
-      var _bytesForRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee9(regions, _opts) {
+      var _bytesForRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(regions, _opts) {
         var _this4 = this;
 
         var _yield$this$configure3, cram, blockResults;
 
-        return _regenerator["default"].wrap(function _callee9$(_context9) {
+        return _regenerator.default.wrap(function _callee9$(_context9) {
           while (1) {
             switch (_context9.prev = _context9.next) {
               case 0:
@@ -657,4 +657,4 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   return CramAdapter;
 }(_BaseAdapter.BaseFeatureDataAdapter);
 
-exports["default"] = CramAdapter;
+exports.default = CramAdapter;