@jbrowse/plugin-alignments 1.7.7 → 1.7.10

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -76,15 +76,24 @@ function Formatter(_ref) {
       show = _useState2[0],
       setShow = _useState2[1];
 
+  var _useState3 = (0, _react.useState)(false),
+      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
+      copied = _useState4[0],
+      setCopied = _useState4[1];
+
   var display = String(value);
 
   if (display.length > 100) {
     return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
-        return (0, _copyToClipboard.default)(display);
+        (0, _copyToClipboard.default)(display);
+        setCopied(true);
+        setTimeout(function () {
+          setCopied(false);
+        }, 700);
       }
-    }, "Copy"), /*#__PURE__*/_react.default.createElement("button", {
+    }, copied ? 'Copied to clipboard' : 'Copy'), /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
         return setShow(function (val) {
@@ -142,7 +151,8 @@ function SupplementaryAlignments(props) {
     return /*#__PURE__*/_react.default.createElement("li", {
       key: "".concat(locString, "-").concat(index)
     }, /*#__PURE__*/_react.default.createElement(_core.Link, {
-      onClick: function onClick() {
+      onClick: function onClick(event) {
+        event.preventDefault();
         var view = model.view;
 
         try {

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -2,12 +2,37 @@ import PluginManager from '@jbrowse/core/PluginManager';
 declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
     featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
-    setFeatureData(data: unknown): void;
+    setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+    setFormattedData(feat: Record<string, unknown>): void;
+} & {
+    afterCreate(): void;
+}, {
+    type: "BaseFeatureWidget";
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}>> & import("mobx-state-tree")._NotCustomized, {
+    id: string;
+    type: "BaseFeatureWidget";
+    formattedFields: any;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    finalizedFeatureData: any;
+} & import("mobx-state-tree")._NotCustomized>;
 export default function register(pluginManager: PluginManager): void;
 export { configSchema };

package/dist/AlignmentsFeatureDetail/index.js

@@ -15,12 +15,12 @@ var _react = require("react");
 
 var _configuration = require("@jbrowse/core/configuration");
 
-var _mst = require("@jbrowse/core/util/types/mst");
-
 var _mobxStateTree = require("mobx-state-tree");
 
 var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 
+var _BaseFeatureWidget = require("@jbrowse/core/BaseFeatureWidget");
+
 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; }
@@ -29,21 +29,10 @@ var configSchema = (0, _configuration.ConfigurationSchema)('AlignmentsFeatureWid
 exports.configSchema = configSchema;
 
 function stateModelFactory(pluginManager) {
-  return _mobxStateTree.types.model('AlignmentsFeatureWidget', {
-    id: _mst.ElementId,
-    type: _mobxStateTree.types.literal('AlignmentsFeatureWidget'),
-    featureData: _mobxStateTree.types.frozen(),
-    view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
-  }).actions(function (self) {
-    return {
-      setFeatureData: function setFeatureData(data) {
-        self.featureData = data;
-      },
-      clearFeatureData: function clearFeatureData() {
-        self.featureData = undefined;
-      }
-    };
-  });
+  var baseModel = (0, _BaseFeatureWidget.stateModelFactory)(pluginManager);
+  return _mobxStateTree.types.compose(baseModel, _mobxStateTree.types.model('AlignmentsFeatureWidget', {
+    type: _mobxStateTree.types.literal('AlignmentsFeatureWidget')
+  }));
 }
 
 function register(pluginManager) {

package/dist/BamAdapter/BamAdapter.d.ts

@@ -28,7 +28,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
                 tag: string;
                 value: unknown;
             };
-            name: string;
+            readName: string;
         };
     }): import("rxjs").Observable<Feature>;
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {

package/dist/BamAdapter/BamAdapter.js

@@ -406,7 +406,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
         var _ref5 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(observer) {
-          var _yield$_this3$configu, bam, records, _ref6, _ref6$flagInclude, flagInclude, _ref6$flagExclude, flagExclude, tagFilter, name, _iterator, _step, record, ref, flags, val;
+          var _yield$_this3$configu, bam, records, _ref6, _ref6$flagInclude, flagInclude, _ref6$flagExclude, flagExclude, tagFilter, readName, _iterator, _step, record, ref, flags, val;
 
           return _regenerator.default.wrap(function _callee8$(_context8) {
             while (1) {
@@ -428,7 +428,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 case 9:
                   records = _context8.sent;
-                  _ref6 = filterBy || {}, _ref6$flagInclude = _ref6.flagInclude, flagInclude = _ref6$flagInclude === void 0 ? 0 : _ref6$flagInclude, _ref6$flagExclude = _ref6.flagExclude, flagExclude = _ref6$flagExclude === void 0 ? 0 : _ref6$flagExclude, tagFilter = _ref6.tagFilter, name = _ref6.name;
+                  _ref6 = filterBy || {}, _ref6$flagInclude = _ref6.flagInclude, flagInclude = _ref6$flagInclude === void 0 ? 0 : _ref6$flagInclude, _ref6$flagExclude = _ref6.flagExclude, flagExclude = _ref6$flagExclude === void 0 ? 0 : _ref6$flagExclude, tagFilter = _ref6.tagFilter, readName = _ref6.readName;
                   _iterator = _createForOfIteratorHelper(records);
                   _context8.prev = 12;
 
@@ -480,7 +480,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   return _context8.abrupt("continue", 31);
 
                 case 28:
-                  if (!(name && record.get('name') !== name)) {
+                  if (!(readName && record.get('name') !== readName)) {
                     _context8.next = 30;
                     break;
                   }

package/dist/BamAdapter/MismatchParser.d.ts

@@ -18,11 +18,8 @@ export declare function cigarToMismatches(ops: string[], seq: string, ref?: stri
 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): ({
+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

@@ -24,6 +24,7 @@ var _util = require("@jbrowse/core/util");
 var _marked = /*#__PURE__*/_regenerator.default.mark(getNextRefPos);
 
 var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
+var modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
 
 function parseCigar(cigar) {
   return (cigar || '').split(/([MIDNSHPX=])/);
@@ -50,6 +51,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
               start: roffset + j,
               type: 'mismatch',
               base: seq[soffset + j],
+              altbase: ref[roffset + j],
               length: 1
             });
           }
@@ -243,47 +245,91 @@ function getMismatches(cigar, md, seq, ref, qual) {
 
 
 function getNextRefPos(cigarOps, positions) {
-  var cigarIdx, readPos, refPos, i, pos, len, op;
+  var readPos, refPos, currPos, i, len, op, _i, _i2;
+
   return _regenerator.default.wrap(function getNextRefPos$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
-          cigarIdx = 0;
           readPos = 0;
           refPos = 0;
+          currPos = 0;
           i = 0;
 
         case 4:
-          if (!(i < positions.length)) {
-            _context.next = 12;
+          if (!(i < cigarOps.length && currPos < positions.length)) {
+            _context.next = 31;
             break;
           }
 
-          pos = positions[i];
+          len = +cigarOps[i];
+          op = cigarOps[i + 1];
 
-          for (; cigarIdx < cigarOps.length && readPos < pos; cigarIdx += 2) {
-            len = +cigarOps[cigarIdx];
-            op = cigarOps[cigarIdx + 1];
+          if (!(op === 'S' || op === 'I')) {
+            _context.next = 12;
+            break;
+          }
 
-            if (op === 'S' || op === 'I') {
-              readPos += len;
-            } else if (op === 'D' || op === 'N') {
-              refPos += len;
-            } else if (op === 'M' || op === 'X' || op === '=') {
-              readPos += len;
-              refPos += len;
+          for (_i = 0; _i < len && currPos < positions.length; _i++) {
+            if (positions[currPos] === readPos + _i) {
+              currPos++;
             }
           }
 
-          _context.next = 9;
-          return positions[i] - readPos + refPos;
+          readPos += len;
+          _context.next = 28;
+          break;
+
+        case 12:
+          if (!(op === 'D' || op === 'N')) {
+            _context.next = 16;
+            break;
+          }
+
+          refPos += len;
+          _context.next = 28;
+          break;
+
+        case 16:
+          if (!(op === 'M' || op === 'X' || op === '=')) {
+            _context.next = 28;
+            break;
+          }
+
+          _i2 = 0;
+
+        case 18:
+          if (!(_i2 < len && currPos < positions.length)) {
+            _context.next = 26;
+            break;
+          }
+
+          if (!(positions[currPos] === readPos + _i2)) {
+            _context.next = 23;
+            break;
+          }
+
+          _context.next = 22;
+          return refPos + _i2;
+
+        case 22:
+          currPos++;
+
+        case 23:
+          _i2++;
+          _context.next = 18;
+          break;
+
+        case 26:
+          readPos += len;
+          refPos += len;
 
-        case 9:
-          i++;
+        case 28:
+          i += 2;
           _context.next = 4;
           break;
 
-        case 12:
+        case 31:
         case "end":
           return _context.stop();
       }
@@ -293,16 +339,21 @@ function getNextRefPos(cigarOps, positions) {
 
 function getModificationPositions(mm, fseq, fstrand) {
   var seq = fstrand === -1 ? (0, _util.revcom)(fseq) : fseq;
-  return mm.split(';').filter(function (mod) {
+  var mods = mm.split(';').filter(function (mod) {
     return !!mod;
-  }).map(function (mod) {
+  });
+  var result = [];
+
+  for (var i = 0; i < mods.length; i++) {
+    var mod = mods[i];
+
     var _mod$split = mod.split(','),
         _mod$split2 = (0, _toArray2.default)(_mod$split),
         basemod = _mod$split2[0],
         skips = _mod$split2.slice(1); // regexes based on parse_mm.pl from hts-specs
 
 
-    var matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');
@@ -322,39 +373,50 @@ function getModificationPositions(mm, fseq, fstrand) {
     if (strand === '-') {
       console.warn('unsupported negative strand modifications'); // make sure to return a somewhat matching type even in this case
 
-      return {
+      result.push({
         type: 'unsupported',
         positions: []
-      };
+      });
     } // this logic also based on parse_mm.pl from hts-specs is that in the
     // sequence of the read, if we have a modification type e.g. C+m;2 and a
     // sequence ACGTACGTAC we skip the two instances of C and go to the last
     // C
 
 
-    return types.map(function (type) {
-      var i = 0;
-      return {
-        type: type,
-        positions: skips.map(function (score) {
-          return +score;
-        }).map(function (delta) {
-          do {
-            if (base === 'N' || base === seq[i]) {
-              delta--;
-            }
+    for (var j = 0; j < types.length; j++) {
+      var type = types[j];
+      var _i3 = 0;
+      var positions = [];
+
+      for (var k = 0; k < skips.length; k++) {
+        var delta = +skips[k];
+
+        do {
+          if (base === 'N' || base === seq[_i3]) {
+            delta--;
+          }
 
-            i++;
-          } while (delta >= 0 && i < seq.length);
+          _i3++;
+        } while (delta >= 0 && _i3 < seq.length);
 
-          var temp = i - 1;
-          return fstrand === -1 ? seq.length - 1 - temp : temp;
-        }).sort(function (a, b) {
+        var temp = _i3 - 1;
+        positions.push(fstrand === -1 ? seq.length - 1 - temp : temp);
+      }
+
+      if (fstrand === -1) {
+        positions.sort(function (a, b) {
           return a - b;
-        })
-      };
-    });
-  }).flat();
+        });
+      }
+
+      result.push({
+        type: type,
+        positions: positions
+      });
+    }
+  }
+
+  return result;
 }
 
 function getModificationTypes(mm) {
@@ -366,7 +428,7 @@ function getModificationTypes(mm) {
         _mod$split4 = (0, _slicedToArray2.default)(_mod$split3, 1),
         basemod = _mod$split4[0];
 
-    var matches = basemod.match(/([A-Z])([-+])([^,]+)/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');

package/dist/BamAdapter/MismatchParser.test.js

@@ -2,7 +2,7 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-var _toArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toArray"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
 var _MismatchParser = require("./MismatchParser");
 
@@ -216,23 +216,15 @@ test('clipping', function () {
     type: 'mismatch'
   }]);
 });
-test('getNextRefPos basic', function () {
+test('getNextRefPos test 1', 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),
-      vals = _iter.slice(0);
-
-  expect(vals).toEqual([-5, 0, 5, 10, 14, 20, 25]);
+  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5, 15, 20, 25]);
 });
-test('getNextRefPos with many indels', function () {
-  var cigar = (0, _MismatchParser.parseCigar)('10S4M1D1IM10');
+test('getNextRefPos test 2', function () {
+  var cigar = (0, _MismatchParser.parseCigar)('10S15M');
   var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15]);
-
-  var _iter2 = (0, _toArray2.default)(iter),
-      vals = _iter2.slice(0);
-
-  expect(vals).toEqual([-5, 0, 5]);
+  expect((0, _toConsumableArray2.default)(iter)).toEqual([0, 5]);
 });
 test('getModificationPositions', function () {
   var positions = (0, _MismatchParser.getModificationPositions)('C+m,2,2,1,4,1', 'AGCTCTCCAGAGTCGNACGCCATYCGCGCGCCACCA', 1);

package/dist/CramAdapter/CramAdapter.d.ts

@@ -6,6 +6,15 @@ interface Header {
     nameToId?: Record<string, number>;
     readGroups?: number[];
 }
+interface FilterBy {
+    flagInclude: number;
+    flagExclude: number;
+    tagFilter: {
+        tag: string;
+        value: unknown;
+    };
+    readName: string;
+}
 export default class CramAdapter extends BaseFeatureDataAdapter {
     samHeader: Header;
     private setupP?;
@@ -26,15 +35,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: {
-            flagInclude: number;
-            flagExclude: number;
-            tagFilter: {
-                tag: string;
-                value: unknown;
-            };
-            name: string;
-        };
+        filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;

package/dist/CramAdapter/CramAdapter.js

@@ -460,7 +460,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
           originalRefName = region.originalRefName;
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
         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;
+          var _yield$_this3$setup, cram, sequenceAdapter, refId, records, _ref4, _ref4$flagInclude, flagInclude, _ref4$flagExclude, flagExclude, tagFilter, readName, filtered;
 
           return _regenerator.default.wrap(function _callee7$(_context7) {
             while (1) {
@@ -504,7 +504,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 case 15:
                   records = _context7.sent;
                   (0, _util.checkAbortSignal)(signal);
-                  _ref4 = filterBy || {}, _ref4$flagInclude = _ref4.flagInclude, flagInclude = _ref4$flagInclude === void 0 ? 0 : _ref4$flagInclude, _ref4$flagExclude = _ref4.flagExclude, flagExclude = _ref4$flagExclude === void 0 ? 0 : _ref4$flagExclude, tagFilter = _ref4.tagFilter, name = _ref4.name; // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                  _ref4 = filterBy || {}, _ref4$flagInclude = _ref4.flagInclude, flagInclude = _ref4$flagInclude === void 0 ? 0 : _ref4$flagInclude, _ref4$flagExclude = _ref4.flagExclude, flagExclude = _ref4$flagExclude === void 0 ? 0 : _ref4$flagExclude, tagFilter = _ref4.tagFilter, readName = _ref4.readName; // eslint-disable-next-line @typescript-eslint/no-explicit-any
 
                   filtered = records.filter(function (record) {
                     var flags = record.flags;
@@ -519,10 +519,10 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                     });
                   }
 
-                  if (name) {
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    filtered = filtered.filter(function (record) {
-                      return record.name === name;
+                  if (readName) {
+                    filtered = filtered.filter( // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    function (record) {
+                      return record.readName === readName;
                     });
                   } // eslint-disable-next-line @typescript-eslint/no-explicit-any
 

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -158,11 +158,12 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
 
       if (typeof this.record.readFeatures !== 'undefined') {
         // @ts-ignore
-        this.record.readFeatures.forEach(function (_ref) {
-          var code = _ref.code,
-              refPos = _ref.refPos,
-              sub = _ref.sub,
-              data = _ref.data;
+        for (var i = 0; i < this.record.readFeatures.length; i++) {
+          var _this$record$readFeat = this.record.readFeatures[i],
+              code = _this$record$readFeat.code,
+              refPos = _this$record$readFeat.refPos,
+              sub = _this$record$readFeat.sub,
+              data = _this$record$readFeat.data;
           sublen = refPos - last_pos;
           seq += ref.substring(last_pos - refStart, refPos - refStart);
           last_pos = refPos;
@@ -241,7 +242,7 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
             oplen = 0;
           } // else q or Q
 
-        });
+        }
       } else {
         sublen = this.record.readLength - seq.length;
       }
@@ -359,86 +360,90 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
       }
 
       var start = this.get('start');
-      var mismatches = [];
-      readFeatures.forEach(function (args) {
-        var code = args.code,
-            pos = args.pos,
-            data = args.data,
-            sub = args.sub,
-            ref = args.ref;
-        var refPos = args.refPos - 1 - start;
+      var mismatches = new Array(readFeatures.length);
+      var j = 0;
+
+      for (var i = 0; i < readFeatures.length; i++) {
+        var f = readFeatures[i];
+        var code = f.code,
+            pos = f.pos,
+            data = f.data,
+            sub = f.sub,
+            ref = f.ref;
+        var refPos = f.refPos - 1 - start;
 
         if (code === 'X') {
           // substitution
-          mismatches.push({
+          mismatches[j++] = {
             start: refPos,
             length: 1,
             base: sub,
             qual: qual === null || qual === void 0 ? void 0 : qual[pos],
             altbase: ref,
             type: 'mismatch'
-          });
+          };
         } else if (code === 'I') {
           // insertion
-          mismatches.push({
+          mismatches[j++] = {
             start: refPos,
             type: 'insertion',
             base: "".concat(data.length),
             length: 0
-          });
+          };
         } else if (code === 'N') {
           // reference skip
-          mismatches.push({
+          mismatches[j++] = {
             type: 'skip',
             length: data,
             start: refPos,
             base: 'N'
-          });
+          };
         } else if (code === 'S') {
           // soft clip
           var len = data.length;
-          mismatches.push({
+          mismatches[j++] = {
             start: refPos,
             type: 'softclip',
             base: "S".concat(len),
             cliplen: len,
             length: 1
-          });
+          };
         } else if (code === 'P') {// padding
         } else if (code === 'H') {
           // hard clip
           var _len = data;
-          mismatches.push({
+          mismatches[j++] = {
             start: refPos,
             type: 'hardclip',
             base: "H".concat(_len),
             cliplen: _len,
             length: 1
-          });
+          };
         } else if (code === 'D') {
           // deletion
-          mismatches.push({
+          mismatches[j++] = {
             type: 'deletion',
             length: data,
             start: refPos,
             base: '*'
-          });
+          };
         } else if (code === 'b') {// stretch of bases
         } else if (code === 'q') {// stretch of qual scores
         } else if (code === 'B') {// a pair of [base, qual]
         } else if (code === 'i') {
           // single-base insertion
           // insertion
-          mismatches.push({
+          mismatches[j++] = {
             start: refPos,
             type: 'insertion',
             base: data,
             length: 1
-          });
+          };
         } else if (code === 'Q') {// single quality value
         }
-      });
-      return mismatches;
+      }
+
+      return mismatches.slice(0, j);
     }
   }]);
   return CramSlightlyLazyFeature;