@jbrowse/plugin-alignments 1.5.8 → 1.6.2

package/dist/plugin-alignments.cjs.development.js

@@ -157,14 +157,14 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
+  subClass.prototype = Object.create(superClass && superClass.prototype, {
+    constructor: {
+      value: subClass,
+      writable: true,
+      configurable: true
+    }
+  });
   Object.defineProperty(subClass, "prototype", {
-    value: Object.create(superClass && superClass.prototype, {
-      constructor: {
-        value: subClass,
-        writable: true,
-        configurable: true
-      }
-    }),
     writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
@@ -1604,9 +1604,12 @@ var MismatchParser = {
 };
 
 var configSchemaF = (function (pluginManager) {
-  var types = pluginManager.lib['mobx-state-tree'].types;
-  return types.late(function () {
+  return mobxStateTree.types.late(function () {
     return configuration.ConfigurationSchema('CramAdapter', {
+      fetchSizeLimit: {
+        type: 'number',
+        defaultValue: 3000000
+      },
       cramLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -1671,7 +1674,7 @@ var configSchema = /*#__PURE__*/mobxStateTree.types.late(function () {
     },
     fetchSizeLimit: {
       type: 'number',
-      defaultValue: 500000000
+      defaultValue: 5000000
     },
     sequenceAdapter: {
       type: 'frozen',
@@ -1993,28 +1996,24 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       }(), opts.signal);
     }
   }, {
-    key: "getRefNames",
+    key: "estimateRegionsStats",
     value: function () {
-      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
-        var opts,
-            _yield$this$configure,
-            subadapter,
-            _args3 = arguments;
+      var _estimateRegionsStats = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(regions, opts) {
+        var _yield$this$configure, subadapter;
 
         return runtime_1.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
-                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
-                _context3.next = 3;
+                _context3.next = 2;
                 return this.configure();
 
-              case 3:
+              case 2:
                 _yield$this$configure = _context3.sent;
                 subadapter = _yield$this$configure.subadapter;
-                return _context3.abrupt("return", subadapter.getRefNames(opts));
+                return _context3.abrupt("return", subadapter.estimateRegionsStats(regions, opts));
 
-              case 6:
+              case 5:
               case "end":
                 return _context3.stop();
             }
@@ -2022,6 +2021,42 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }, _callee3, this);
       }));
 
+      function estimateRegionsStats(_x2, _x3) {
+        return _estimateRegionsStats.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
+        var opts,
+            _yield$this$configure2,
+            subadapter,
+            _args4 = arguments;
+
+        return runtime_1.wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                opts = _args4.length > 0 && _args4[0] !== undefined ? _args4[0] : {};
+                _context4.next = 3;
+                return this.configure();
+
+              case 3:
+                _yield$this$configure2 = _context4.sent;
+                subadapter = _yield$this$configure2.subadapter;
+                return _context4.abrupt("return", subadapter.getRefNames(opts));
+
+              case 6:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
       function getRefNames() {
         return _getRefNames.apply(this, arguments);
       }
@@ -2045,20 +2080,20 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "generateCoverageBins",
     value: function () {
-      var _generateCoverageBins = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4(features, region, opts) {
-        var colorBy, _yield$this$configure2, sequenceAdapter, originalRefName, refName, start, end, binMax, skipmap, initBins, regionSeq, _yield$sequenceAdapte, _yield$sequenceAdapte2, feat, bins;
+      var _generateCoverageBins = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5(features, region, opts) {
+        var colorBy, _yield$this$configure3, sequenceAdapter, originalRefName, refName, start, end, binMax, skipmap, initBins, regionSeq, _yield$sequenceAdapte, _yield$sequenceAdapte2, feat, bins;
 
-        return runtime_1.wrap(function _callee4$(_context4) {
+        return runtime_1.wrap(function _callee5$(_context5) {
           while (1) {
-            switch (_context4.prev = _context4.next) {
+            switch (_context5.prev = _context5.next) {
               case 0:
                 colorBy = opts.colorBy;
-                _context4.next = 3;
+                _context5.next = 3;
                 return this.configure();
 
               case 3:
-                _yield$this$configure2 = _context4.sent;
-                sequenceAdapter = _yield$this$configure2.sequenceAdapter;
+                _yield$this$configure3 = _context5.sent;
+                sequenceAdapter = _yield$this$configure3.sequenceAdapter;
                 originalRefName = region.originalRefName, refName = region.refName, start = region.start, end = region.end;
                 binMax = Math.ceil(region.end - region.start);
                 skipmap = {};
@@ -2076,11 +2111,11 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 }); // request an extra +1 on the end to get CpG crossing region boundary
 
                 if (!sequenceAdapter) {
-                  _context4.next = 16;
+                  _context5.next = 16;
                   break;
                 }
 
-                _context4.next = 12;
+                _context5.next = 12;
                 return sequenceAdapter.getFeatures({
                   refName: originalRefName || refName,
                   start: start,
@@ -2089,13 +2124,13 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 }).pipe(operators.toArray()).toPromise();
 
               case 12:
-                _yield$sequenceAdapte = _context4.sent;
+                _yield$sequenceAdapte = _context5.sent;
                 _yield$sequenceAdapte2 = _slicedToArray(_yield$sequenceAdapte, 1);
                 feat = _yield$sequenceAdapte2[0];
                 regionSeq = feat === null || feat === void 0 ? void 0 : feat.get('seq');
 
               case 16:
-                _context4.next = 18;
+                _context5.next = 18;
                 return features.pipe(operators.reduce(function (bins, feature) {
                   var cigar = feature.get('CIGAR');
                   var fstart = feature.get('start');
@@ -2286,21 +2321,21 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 }, initBins)).toPromise();
 
               case 18:
-                bins = _context4.sent;
-                return _context4.abrupt("return", {
+                bins = _context5.sent;
+                return _context5.abrupt("return", {
                   bins: bins,
                   skipmap: skipmap
                 });
 
               case 20:
               case "end":
-                return _context4.stop();
+                return _context5.stop();
             }
           }
-        }, _callee4, this);
+        }, _callee5, this);
       }));
 
-      function generateCoverageBins(_x2, _x3, _x4) {
+      function generateCoverageBins(_x4, _x5, _x6) {
         return _generateCoverageBins.apply(this, arguments);
       }
 
@@ -3395,10 +3430,12 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           var _baseColor = colorForBase.deletion;
           ctx.fillStyle = _baseColor;
           ctx.fillRect(leftPx, topPx, widthPx, heightPx);
+          var txt = "".concat(mismatch.length);
+          var rect = ctx.measureText(txt);
 
-          if (widthPx >= charWidth && heightPx >= heightLim) {
+          if (widthPx >= rect.width && heightPx >= heightLim) {
             ctx.fillStyle = theme.palette.getContrastText(_baseColor);
-            ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+            ctx.fillText(txt, leftPx + (rightPx - leftPx) / 2 - rect.width / 2, topPx + heightPx);
           }
         } else if (mismatch.type === 'insertion' && drawIndels) {
           ctx.fillStyle = 'purple';
@@ -3458,19 +3495,20 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
 
           var _len = +_mismatch.base || _mismatch.length;
 
-          var txt = "".concat(_len);
+          var _txt = "".concat(_len);
 
           if (_mismatch.type === 'insertion' && _len >= 10) {
             if (bpPerPx > largeInsertionIndicatorScale) {
               ctx.fillStyle = 'purple';
               ctx.fillRect(_leftPx2 - 1, topPx, 2, heightPx);
             } else if (heightPx > charHeight) {
-              var rect = ctx.measureText(txt);
+              var _rect = ctx.measureText(_txt);
+
               var padding = 5;
               ctx.fillStyle = 'purple';
-              ctx.fillRect(_leftPx2 - rect.width / 2 - padding, topPx, rect.width + 2 * padding, heightPx);
+              ctx.fillRect(_leftPx2 - _rect.width / 2 - padding, topPx, _rect.width + 2 * padding, heightPx);
               ctx.fillStyle = 'white';
-              ctx.fillText(txt, _leftPx2 - rect.width / 2, topPx + heightPx);
+              ctx.fillText(_txt, _leftPx2 - _rect.width / 2, topPx + heightPx);
             } else {
               var _padding = 2;
               ctx.fillStyle = 'purple';
@@ -4096,7 +4134,8 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
     configuration: configuration.ConfigurationReference(configSchema),
     height: 250,
     showCoverage: true,
-    showPileup: true
+    showPileup: true,
+    userFeatureScreenDensity: mobxStateTree.types.maybe(mobxStateTree.types.number)
   }))["volatile"](function () {
     return {
       scrollTop: 0
@@ -4189,9 +4228,9 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
           height: self.snpCovHeight
         };
       },
-      setUserBpPerPxLimit: function setUserBpPerPxLimit(limit) {
-        self.PileupDisplay.setUserBpPerPxLimit(limit);
-        self.SNPCoverageDisplay.setUserBpPerPxLimit(limit);
+      setUserFeatureScreenDensity: function setUserFeatureScreenDensity(limit) {
+        self.PileupDisplay.setUserFeatureScreenDensity(limit);
+        self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit);
       },
       setPileupDisplay: function setPileupDisplay(displayConfig) {
         self.PileupDisplay = {
@@ -4382,11 +4421,6 @@ function SNPCoverageConfigFactory(pluginManager) {
       description: 'draw upside down',
       defaultValue: false
     },
-    maxDisplayedBpPerPx: {
-      type: 'number',
-      description: 'maximum bpPerPx that is displayed in the view',
-      defaultValue: 100
-    },
     headroom: {
       type: 'number',
       description: 'round the upper value of the domain scale to the nearest N',
@@ -4593,8 +4627,9 @@ var stateModelFactory$1 = function stateModelFactory(pluginManager, configSchema
       },
 
       renderProps: function renderProps() {
-        return _objectSpread2(_objectSpread2({}, superRenderProps()), {}, {
-          notReady: !self.ready || !this.modificationsReady,
+        var superProps = superRenderProps();
+        return _objectSpread2(_objectSpread2({}, superProps), {}, {
+          notReady: superProps.notReady || !this.modificationsReady,
           filters: self.filters,
           modificationTagMap: JSON.parse(JSON.stringify(self.modificationTagMap)),
           // must use getSnapshot because otherwise changes to e.g. just the
@@ -4773,10 +4808,10 @@ function PileupConfigFactory(pluginManager) {
       SvgFeatureRenderer: SvgFeatureRendererConfigSchema
     }),
     renderer: '',
-    maxDisplayedBpPerPx: {
+    maxFeatureScreenDensity: {
       type: 'number',
-      description: 'maximum bpPerPx that is displayed in the view',
-      defaultValue: 100
+      description: 'maximum features per pixel that is displayed in the view',
+      defaultValue: 5
     },
     colorScheme: {
       type: 'stringEnum',
@@ -4863,17 +4898,13 @@ var stateModelFactory$2 = function stateModelFactory(configSchema) {
     return {
       colorTagMap: mobx.observable.map({}),
       modificationTagMap: mobx.observable.map({}),
-      ready: false,
-      currBpPerPx: 0
+      ready: false
     };
   }).actions(function (self) {
     return {
       setReady: function setReady(flag) {
         self.ready = flag;
       },
-      setCurrBpPerPx: function setCurrBpPerPx(n) {
-        self.currBpPerPx = n;
-      },
       setMaxHeight: function setMaxHeight(n) {
         self.trackMaxHeight = n;
       },
@@ -5176,14 +5207,14 @@ var stateModelFactory$2 = function stateModelFactory(configSchema) {
 
       renderProps: function renderProps() {
         var view = util.getContainingView(self);
-        var ready = self.ready,
-            colorTagMap = self.colorTagMap,
+        var colorTagMap = self.colorTagMap,
             modificationTagMap = self.modificationTagMap,
             sortedBy = self.sortedBy,
             colorBy = self.colorBy,
             rpcDriverName = self.rpcDriverName;
-        return _objectSpread2(_objectSpread2({}, superRenderProps()), {}, {
-          notReady: !ready || sortedBy && self.currBpPerPx !== view.bpPerPx,
+        var superProps = superRenderProps();
+        return _objectSpread2(_objectSpread2({}, superProps), {}, {
+          notReady: superProps.notReady || !self.ready || sortedBy && self.currBpPerPx !== view.bpPerPx,
           rpcDriverName: rpcDriverName,
           displayModel: self,
           sortedBy: sortedBy,
@@ -5676,13 +5707,16 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.cram$/i;
           var adapterName = 'CramAdapter';
           var fileName = tracks.getFileName(file);
+          var obj = {
+            type: adapterName,
+            cramLocation: file,
+            craiLocation: index || tracks.makeIndex(file, '.crai')
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              cramLocation: file,
-              craiLocation: index || tracks.makeIndex(file, '.crai')
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -5694,16 +5728,19 @@ var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
           var adapterName = 'BamAdapter';
           var fileName = tracks.getFileName(file);
           var indexName = index && tracks.getFileName(index);
+          var obj = {
+            type: adapterName,
+            bamLocation: file,
+            index: {
+              location: index || tracks.makeIndex(file, '.bai'),
+              indexType: tracks.makeIndexType(indexName, 'CSI', 'BAI')
+            }
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bamLocation: file,
-              index: {
-                location: index || tracks.makeIndex(file, '.bai'),
-                indexType: tracks.makeIndexType(indexName, 'CSI', 'BAI')
-              }
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -6174,7 +6211,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "configure",
     value: function () {
       var _configure = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
-        var cramLocation, craiLocation, sequenceAdapterType, _yield$this$getSubAda, dataAdapter;
+        var cramLocation, craiLocation, cram$1, sequenceAdapterType, seqConf, _yield$this$getSubAda, sequenceAdapter;
 
         return runtime_1.wrap(function _callee$(_context) {
           while (1) {
@@ -6199,14 +6236,15 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 throw new Error('missing craiLocation argument');
 
               case 6:
-                this.cram = new cram.IndexedCramFile({
+                // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                cram$1 = new cram.IndexedCramFile({
                   cramFilehandle: io.openLocation(cramLocation, this.pluginManager),
                   index: new cram.CraiIndex({
                     filehandle: io.openLocation(craiLocation, this.pluginManager)
                   }),
                   seqFetch: this.seqFetch.bind(this),
                   checkSequenceMD5: false,
-                  fetchSizeLimit: this.config.fetchSizeLimit || 600000000
+                  fetchSizeLimit: 200000000
                 }); // instantiate the sequence adapter
 
                 sequenceAdapterType = configuration.readConfObject(this.config, ['sequenceAdapter', 'type']);
@@ -6219,31 +6257,28 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 throw new Error('Error getting subadapter');
 
               case 10:
-                _context.next = 12;
-                return this.getSubAdapter(configuration.readConfObject(this.config, 'sequenceAdapter'));
+                seqConf = configuration.readConfObject(this.config, 'sequenceAdapter');
+                _context.next = 13;
+                return this.getSubAdapter(seqConf);
 
-              case 12:
+              case 13:
                 _yield$this$getSubAda = _context.sent;
-                dataAdapter = _yield$this$getSubAda.dataAdapter;
+                sequenceAdapter = _yield$this$getSubAda.dataAdapter;
 
-                if (!(dataAdapter instanceof BaseAdapter.BaseFeatureDataAdapter)) {
-                  _context.next = 18;
+                if (sequenceAdapter instanceof BaseAdapter.BaseFeatureDataAdapter) {
+                  _context.next = 17;
                   break;
                 }
 
-                this.sequenceAdapter = dataAdapter;
-                _context.next = 19;
-                break;
-
-              case 18:
                 throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(sequenceAdapterType, "'"));
 
-              case 19:
+              case 17:
                 return _context.abrupt("return", {
-                  sequenceAdapter: this.sequenceAdapter
+                  cram: cram$1,
+                  sequenceAdapter: sequenceAdapter
                 });
 
-              case 20:
+              case 18:
               case "end":
                 return _context.stop();
             }
@@ -6261,6 +6296,8 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "getHeader",
     value: function () {
       var _getHeader = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2(opts) {
+        var _yield$this$configure, cram;
+
         return runtime_1.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
@@ -6269,9 +6306,11 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 return this.configure();
 
               case 2:
-                return _context2.abrupt("return", this.cram.cram.getHeaderText(opts));
+                _yield$this$configure = _context2.sent;
+                cram = _yield$this$configure.cram;
+                return _context2.abrupt("return", cram.cram.getHeaderText(opts));
 
-              case 3:
+              case 5:
               case "end":
                 return _context2.stop();
             }
@@ -6289,69 +6328,63 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "seqFetch",
     value: function () {
       var _seqFetch = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(seqId, start, end) {
-        var refSeqStore, refName, features, seqChunks, trimmed, sequence;
+        var _yield$this$configure2, sequenceAdapter, refName, seqChunks, sequence;
+
         return runtime_1.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
                 start -= 1; // convert from 1-based closed to interbase
 
-                refSeqStore = this.sequenceAdapter;
-
-                if (refSeqStore) {
-                  _context3.next = 4;
-                  break;
-                }
-
-                return _context3.abrupt("return", undefined);
+                _context3.next = 3;
+                return this.configure();
 
-              case 4:
+              case 3:
+                _yield$this$configure2 = _context3.sent;
+                sequenceAdapter = _yield$this$configure2.sequenceAdapter;
                 refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId);
 
                 if (refName) {
-                  _context3.next = 7;
+                  _context3.next = 8;
                   break;
                 }
 
                 return _context3.abrupt("return", undefined);
 
-              case 7:
-                features = refSeqStore.getFeatures({
+              case 8:
+                _context3.next = 10;
+                return sequenceAdapter.getFeatures({
                   refName: refName,
                   start: start,
                   end: end,
                   assemblyName: ''
-                }, {});
-                _context3.next = 10;
-                return features.pipe(operators.toArray()).toPromise();
+                }).pipe(operators.toArray()).toPromise();
 
               case 10:
                 seqChunks = _context3.sent;
-                trimmed = [];
-                seqChunks.sort(function (a, b) {
+                sequence = seqChunks.sort(function (a, b) {
                   return a.get('start') - b.get('start');
-                }).forEach(function (chunk) {
+                }).map(function (chunk) {
                   var chunkStart = chunk.get('start');
                   var chunkEnd = chunk.get('end');
                   var trimStart = Math.max(start - chunkStart, 0);
                   var trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
                   var trimLength = trimEnd - trimStart;
                   var chunkSeq = chunk.get('seq') || chunk.get('residues');
-                  trimmed.push(chunkSeq.substr(trimStart, trimLength));
-                });
-                sequence = trimmed.join('');
+                  return chunkSeq.substr(trimStart, trimLength);
+                }).join('');
 
                 if (!(sequence.length !== end - start)) {
-                  _context3.next = 16;
+                  _context3.next = 14;
                   break;
                 }
 
                 throw new Error("sequence fetch failed: fetching ".concat(refName, ":").concat((start - 1).toLocaleString(), "-").concat(end.toLocaleString(), " returned ").concat(sequence.length.toLocaleString(), " bases, but should have returned ").concat((end - start).toLocaleString()));
 
-              case 16:
+              case 14:
                 return _context3.abrupt("return", sequence);
 
-              case 17:
+              case 15:
               case "end":
                 return _context3.stop();
             }
@@ -6365,77 +6398,91 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       return seqFetch;
     }()
+  }, {
+    key: "setupPre",
+    value: function () {
+      var _setupPre = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4(opts) {
+        var _ref, _ref$statusCallback, statusCallback, configured, cram, samHeader, idToName, nameToId, readGroups, data;
+
+        return runtime_1.wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _ref = opts || {}, _ref$statusCallback = _ref.statusCallback, statusCallback = _ref$statusCallback === void 0 ? function () {} : _ref$statusCallback;
+                _context4.next = 3;
+                return this.configure();
+
+              case 3:
+                configured = _context4.sent;
+                statusCallback('Downloading index');
+                cram = configured.cram;
+                _context4.next = 8;
+                return cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
+
+              case 8:
+                samHeader = _context4.sent;
+                // use the @SQ lines in the header to figure out the
+                // mapping between ref ID numbers and names
+                idToName = [];
+                nameToId = {};
+                samHeader.filter(function (l) {
+                  return l.tag === 'SQ';
+                }).forEach(function (sqLine, refId) {
+                  sqLine.data.forEach(function (item) {
+                    if (item.tag === 'SN') {
+                      // this is the ref name
+                      var refName = item.value;
+                      nameToId[refName] = refId;
+                      idToName[refId] = refName;
+                    }
+                  });
+                });
+                readGroups = samHeader.filter(function (l) {
+                  return l.tag === 'RG';
+                }).map(function (rgLine) {
+                  var _rgLine$data$find;
+
+                  return (_rgLine$data$find = rgLine.data.find(function (item) {
+                    return item.tag === 'ID';
+                  })) === null || _rgLine$data$find === void 0 ? void 0 : _rgLine$data$find.value;
+                });
+                data = {
+                  idToName: idToName,
+                  nameToId: nameToId,
+                  readGroups: readGroups
+                };
+                statusCallback('');
+                this.samHeader = data;
+                return _context4.abrupt("return", _objectSpread2({
+                  samHeader: data
+                }, configured));
+
+              case 17:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function setupPre(_x5) {
+        return _setupPre.apply(this, arguments);
+      }
+
+      return setupPre;
+    }()
   }, {
     key: "setup",
     value: function () {
       var _setup = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5(opts) {
         var _this2 = this;
 
-        var _ref, _ref$statusCallback, statusCallback;
-
         return runtime_1.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
-                _ref = opts || {}, _ref$statusCallback = _ref.statusCallback, statusCallback = _ref$statusCallback === void 0 ? function () {} : _ref$statusCallback;
-
                 if (!this.setupP) {
-                  this.setupP = this.configure().then( /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
-                    var samHeader, idToName, nameToId, readGroups;
-                    return runtime_1.wrap(function _callee4$(_context4) {
-                      while (1) {
-                        switch (_context4.prev = _context4.next) {
-                          case 0:
-                            statusCallback('Downloading index');
-                            _context4.next = 3;
-                            return _this2.cram.cram.getSamHeader(opts === null || opts === void 0 ? void 0 : opts.signal);
-
-                          case 3:
-                            samHeader = _context4.sent;
-                            // use the @SQ lines in the header to figure out the
-                            // mapping between ref ID numbers and names
-                            idToName = [];
-                            nameToId = {};
-                            samHeader.filter(function (l) {
-                              return l.tag === 'SQ';
-                            }).forEach(function (sqLine, refId) {
-                              sqLine.data.forEach(function (item) {
-                                if (item.tag === 'SN') {
-                                  // this is the ref name
-                                  var refName = item.value;
-                                  nameToId[refName] = refId;
-                                  idToName[refId] = refName;
-                                }
-                              });
-                            });
-                            readGroups = samHeader.filter(function (l) {
-                              return l.tag === 'RG';
-                            }).map(function (rgLine) {
-                              var _rgLine$data$find;
-
-                              return (_rgLine$data$find = rgLine.data.find(function (item) {
-                                return item.tag === 'ID';
-                              })) === null || _rgLine$data$find === void 0 ? void 0 : _rgLine$data$find.value;
-                            });
-
-                            if (idToName.length) {
-                              _this2.samHeader = {
-                                idToName: idToName,
-                                nameToId: nameToId,
-                                readGroups: readGroups
-                              };
-                            }
-
-                            statusCallback('');
-                            return _context4.abrupt("return", _this2.samHeader);
-
-                          case 11:
-                          case "end":
-                            return _context4.stop();
-                        }
-                      }
-                    }, _callee4);
-                  })))["catch"](function (e) {
+                  this.setupP = this.setupPre(opts)["catch"](function (e) {
                     _this2.setupP = undefined;
                     throw e;
                   });
@@ -6443,7 +6490,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 return _context5.abrupt("return", this.setupP);
 
-              case 3:
+              case 2:
               case "end":
                 return _context5.stop();
             }
@@ -6451,7 +6498,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }, _callee5, this);
       }));
 
-      function setup(_x5) {
+      function setup(_x6) {
         return _setup.apply(this, arguments);
       }
 
@@ -6461,6 +6508,8 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "getRefNames",
     value: function () {
       var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(opts) {
+        var _yield$this$setup, samHeader;
+
         return runtime_1.wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
@@ -6469,23 +6518,18 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 return this.setup(opts);
 
               case 2:
-                if (!this.samHeader.idToName) {
-                  _context6.next = 4;
-                  break;
-                }
-
-                return _context6.abrupt("return", this.samHeader.idToName);
+                _yield$this$setup = _context6.sent;
+                samHeader = _yield$this$setup.samHeader;
 
-              case 4:
-                if (!this.sequenceAdapter) {
+                if (samHeader.idToName) {
                   _context6.next = 6;
                   break;
                 }
 
-                return _context6.abrupt("return", this.sequenceAdapter.getRefNames());
+                throw new Error('CRAM file has no header lines');
 
               case 6:
-                throw new Error('unable to get refnames');
+                return _context6.abrupt("return", samHeader.idToName);
 
               case 7:
               case "end":
@@ -6495,7 +6539,7 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }, _callee6, this);
       }));
 
-      function getRefNames(_x6) {
+      function getRefNames(_x7) {
         return _getRefNames.apply(this, arguments);
       }
 
@@ -6541,18 +6585,19 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     value: function getFeatures(region, opts) {
       var _this3 = this;
 
-      var _ref3 = opts || {},
-          signal = _ref3.signal,
-          _ref3$statusCallback = _ref3.statusCallback,
-          statusCallback = _ref3$statusCallback === void 0 ? function () {} : _ref3$statusCallback;
+      var _ref2 = opts || {},
+          signal = _ref2.signal,
+          _ref2$statusCallback = _ref2.statusCallback,
+          statusCallback = _ref2$statusCallback === void 0 ? function () {} : _ref2$statusCallback;
 
       var refName = region.refName,
           start = region.start,
           end = region.end,
           originalRefName = region.originalRefName;
       return rxjs.ObservableCreate( /*#__PURE__*/function () {
-        var _ref4 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(observer) {
-          var refId, records;
+        var _ref3 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(observer) {
+          var _yield$_this3$setup, cram, sequenceAdapter, refId, records;
+
           return runtime_1.wrap(function _callee7$(_context7) {
             while (1) {
               switch (_context7.prev = _context7.next) {
@@ -6561,22 +6606,27 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   return _this3.setup(opts);
 
                 case 2:
-                  if (!(_this3.sequenceAdapter && !_this3.seqIdToRefName)) {
-                    _context7.next = 6;
+                  _yield$_this3$setup = _context7.sent;
+                  cram = _yield$_this3$setup.cram;
+                  sequenceAdapter = _yield$_this3$setup.sequenceAdapter;
+                  statusCallback('Downloading alignments');
+
+                  if (_this3.seqIdToRefName) {
+                    _context7.next = 10;
                     break;
                   }
 
-                  _context7.next = 5;
-                  return _this3.sequenceAdapter.getRefNames(opts);
+                  _context7.next = 9;
+                  return sequenceAdapter.getRefNames(opts);
 
-                case 5:
+                case 9:
                   _this3.seqIdToRefName = _context7.sent;
 
-                case 6:
+                case 10:
                   refId = _this3.refNameToId(refName);
 
                   if (!(refId !== undefined)) {
-                    _context7.next = 15;
+                    _context7.next = 20;
                     break;
                   }
 
@@ -6584,23 +6634,27 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                     _this3.seqIdToOriginalRefName[refId] = originalRefName;
                   }
 
-                  statusCallback('Downloading alignments');
-                  _context7.next = 12;
-                  return _this3.cram.getRecordsForRange(refId, start, end, opts);
+                  _context7.next = 15;
+                  return cram.getRecordsForRange(refId, start, end, opts);
 
-                case 12:
+                case 15:
                   records = _context7.sent;
                   util.checkAbortSignal(signal); // eslint-disable-next-line @typescript-eslint/no-explicit-any
 
                   records.forEach(function (record) {
                     observer.next(_this3.cramRecordToFeature(record));
                   });
+                  _context7.next = 21;
+                  break;
 
-                case 15:
+                case 20:
+                  console.warn('Unknown refName', refName);
+
+                case 21:
                   statusCallback('');
                   observer.complete();
 
-                case 17:
+                case 23:
                 case "end":
                   return _context7.stop();
               }
@@ -6608,8 +6662,8 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
           }, _callee7);
         }));
 
-        return function (_x7) {
-          return _ref4.apply(this, arguments);
+        return function (_x8) {
+          return _ref3.apply(this, arguments);
         };
       }(), signal);
     }
@@ -6617,13 +6671,102 @@ var CramAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     key: "freeResources",
     value: function
       /* { region } */
-    freeResources() {} // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
+    freeResources() {}
   }, {
     key: "cramRecordToFeature",
     value: function cramRecordToFeature(record) {
       return new CramSlightlyLazyFeature(record, this);
-    }
+    } // we return the configured fetchSizeLimit, and the bytes for the region
+
+  }, {
+    key: "estimateRegionsStats",
+    value: function () {
+      var _estimateRegionsStats = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee8(regions, opts) {
+        var bytes, fetchSizeLimit;
+        return runtime_1.wrap(function _callee8$(_context8) {
+          while (1) {
+            switch (_context8.prev = _context8.next) {
+              case 0:
+                _context8.next = 2;
+                return this.bytesForRegions(regions, opts);
+
+              case 2:
+                bytes = _context8.sent;
+                fetchSizeLimit = configuration.readConfObject(this.config, 'fetchSizeLimit');
+                return _context8.abrupt("return", {
+                  bytes: bytes,
+                  fetchSizeLimit: fetchSizeLimit
+                });
+
+              case 5:
+              case "end":
+                return _context8.stop();
+            }
+          }
+        }, _callee8, this);
+      }));
+
+      function estimateRegionsStats(_x9, _x10) {
+        return _estimateRegionsStats.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
+    /**
+     * get the approximate number of bytes queried from the file for the given
+     * query regions
+     * @param regions - list of query regions
+     */
+
+  }, {
+    key: "bytesForRegions",
+    value: function () {
+      var _bytesForRegions = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee9(regions, _opts) {
+        var _this4 = this;
+
+        var _yield$this$configure3, cram, blockResults;
+
+        return runtime_1.wrap(function _callee9$(_context9) {
+          while (1) {
+            switch (_context9.prev = _context9.next) {
+              case 0:
+                _context9.next = 2;
+                return this.configure();
+
+              case 2:
+                _yield$this$configure3 = _context9.sent;
+                cram = _yield$this$configure3.cram;
+                _context9.next = 6;
+                return Promise.all(regions.map(function (region) {
+                  var refName = region.refName,
+                      start = region.start,
+                      end = region.end;
+
+                  var chrId = _this4.refNameToId(refName);
+
+                  return cram.index.getEntriesForRange(chrId, start, end);
+                }));
+
+              case 6:
+                blockResults = _context9.sent;
+                return _context9.abrupt("return", blockResults.flat().reduce(function (a, b) {
+                  return a + b.sliceBytes;
+                }, 0));
+
+              case 8:
+              case "end":
+                return _context9.stop();
+            }
+          }
+        }, _callee9, this);
+      }));
+
+      function bytesForRegions(_x11, _x12) {
+        return _bytesForRegions.apply(this, arguments);
+      }
+
+      return bytesForRegions;
+    }()
   }]);
 
   return CramAdapter;
@@ -6661,7 +6804,6 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
   }, {
     key: "_get_flags",
     value: function _get_flags() {
-      // @ts-ignore
       return this.record.flags;
     }
   }, {
@@ -6669,12 +6811,6 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
     value: function _get_strand() {
       return this.record.isReverseComplemented() ? -1 : 1;
     }
-  }, {
-    key: "_get_read_group_id",
-    value: function _get_read_group_id() {
-      // @ts-ignore
-      return this.record.readGroupId;
-    }
   }, {
     key: "_get_pair_orientation",
     value: function _get_pair_orientation() {
@@ -6699,7 +6835,9 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
   }, {
     key: "_get_next_segment_position",
     value: function _get_next_segment_position() {
-      return this.record.isPaired() ? "".concat(this.adapter.refIdToName(this.record._next_refid()), ":").concat(this.record._next_pos() + 1) : undefined;
+      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",
@@ -6871,7 +7009,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     // configure method allows derived classes to override this behavior
     function () {
       var _configure = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
-        var bamLocation, location, indexType, chunkSizeLimit, fetchSizeLimit, bam$1, adapterConfig;
+        var bamLocation, location, indexType, chunkSizeLimit, bam$1, adapterConfig;
         return runtime_1.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
@@ -6881,13 +7019,12 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   location = configuration.readConfObject(this.config, ['index', 'location']);
                   indexType = configuration.readConfObject(this.config, ['index', 'indexType']);
                   chunkSizeLimit = configuration.readConfObject(this.config, 'chunkSizeLimit');
-                  fetchSizeLimit = configuration.readConfObject(this.config, 'fetchSizeLimit');
                   bam$1 = new bam.BamFile({
                     bamFilehandle: io.openLocation(bamLocation, this.pluginManager),
                     csiFilehandle: indexType === 'CSI' ? io.openLocation(location, this.pluginManager) : undefined,
                     baiFilehandle: indexType !== 'CSI' ? io.openLocation(location, this.pluginManager) : undefined,
                     chunkSizeLimit: chunkSizeLimit,
-                    fetchSizeLimit: fetchSizeLimit
+                    fetchSizeLimit: 100000000
                   });
                   adapterConfig = configuration.readConfObject(this.config, 'sequenceAdapter');
 
@@ -6955,87 +7092,109 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       return getHeader;
     }()
   }, {
-    key: "setup",
+    key: "setupPre",
     value: function () {
-      var _setup = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4(opts) {
-        var _this = this;
-
-        var _ref2, _ref2$statusCallback, statusCallback;
+      var _setupPre = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4(opts) {
+        var _ref2, _ref2$statusCallback, statusCallback, _yield$this$configure2, bam;
 
         return runtime_1.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
-                // note that derived classes may not provide a BAM directly so this is
-                // conditional
                 _ref2 = opts || {}, _ref2$statusCallback = _ref2.statusCallback, statusCallback = _ref2$statusCallback === void 0 ? function () {} : _ref2$statusCallback;
+                _context4.next = 3;
+                return this.configure();
 
-                if (!this.setupP) {
-                  this.setupP = this.configure().then( /*#__PURE__*/function () {
-                    var _ref4 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(_ref3) {
-                      var bam, samHeader, idToName, nameToId;
-                      return runtime_1.wrap(function _callee3$(_context3) {
-                        while (1) {
-                          switch (_context3.prev = _context3.next) {
-                            case 0:
-                              bam = _ref3.bam;
-                              statusCallback('Downloading index');
-                              _context3.next = 4;
-                              return bam.getHeader(opts);
-
-                            case 4:
-                              samHeader = _context3.sent;
-                              // use the @SQ lines in the header to figure out the
-                              // mapping between ref ref ID numbers and names
-                              idToName = [];
-                              nameToId = {};
-                              samHeader.filter(function (l) {
-                                return l.tag === 'SQ';
-                              }).forEach(function (sqLine, refId) {
-                                sqLine.data.forEach(function (item) {
-                                  if (item.tag === 'SN') {
-                                    // this is the ref name
-                                    var refName = item.value;
-                                    nameToId[refName] = refId;
-                                    idToName[refId] = refName;
-                                  }
-                                });
-                              });
-                              statusCallback('');
-                              _this.samHeader = {
-                                idToName: idToName,
-                                nameToId: nameToId
-                              };
-                              return _context3.abrupt("return", _this.samHeader);
-
-                            case 11:
-                            case "end":
-                              return _context3.stop();
-                          }
-                        }
-                      }, _callee3);
-                    }));
+              case 3:
+                _yield$this$configure2 = _context4.sent;
+                bam = _yield$this$configure2.bam;
+                _context4.next = 7;
+                return util.updateStatus('Downloading index', statusCallback, /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
+                  var samHeader, idToName, nameToId;
+                  return runtime_1.wrap(function _callee3$(_context3) {
+                    while (1) {
+                      switch (_context3.prev = _context3.next) {
+                        case 0:
+                          _context3.next = 2;
+                          return bam.getHeader(opts);
+
+                        case 2:
+                          samHeader = _context3.sent;
+                          // use the @SQ lines in the header to figure out the
+                          // mapping between ref ref ID numbers and names
+                          idToName = [];
+                          nameToId = {};
+                          samHeader.filter(function (l) {
+                            return l.tag === 'SQ';
+                          }).forEach(function (sqLine, refId) {
+                            sqLine.data.forEach(function (item) {
+                              if (item.tag === 'SN') {
+                                // this is the ref name
+                                var refName = item.value;
+                                nameToId[refName] = refId;
+                                idToName[refId] = refName;
+                              }
+                            });
+                          });
+                          return _context3.abrupt("return", {
+                            idToName: idToName,
+                            nameToId: nameToId
+                          });
+
+                        case 7:
+                        case "end":
+                          return _context3.stop();
+                      }
+                    }
+                  }, _callee3);
+                })));
 
-                    return function (_x3) {
-                      return _ref4.apply(this, arguments);
-                    };
-                  }())["catch"](function (e) {
+              case 7:
+                this.samHeader = _context4.sent;
+                return _context4.abrupt("return", this.samHeader);
+
+              case 9:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function setupPre(_x2) {
+        return _setupPre.apply(this, arguments);
+      }
+
+      return setupPre;
+    }()
+  }, {
+    key: "setup",
+    value: function () {
+      var _setup = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5(opts) {
+        var _this = this;
+
+        return runtime_1.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 = undefined;
                     throw e;
                   });
                 }
 
-                return _context4.abrupt("return", this.setupP);
+                return _context5.abrupt("return", this.setupP);
 
-              case 3:
+              case 2:
               case "end":
-                return _context4.stop();
+                return _context5.stop();
             }
           }
-        }, _callee4, this);
+        }, _callee5, this);
       }));
 
-      function setup(_x2) {
+      function setup(_x3) {
         return _setup.apply(this, arguments);
       }
 
@@ -7044,27 +7203,27 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5(opts) {
+      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(opts) {
         var _yield$this$setup, idToName;
 
-        return runtime_1.wrap(function _callee5$(_context5) {
+        return runtime_1.wrap(function _callee6$(_context6) {
           while (1) {
-            switch (_context5.prev = _context5.next) {
+            switch (_context6.prev = _context6.next) {
               case 0:
-                _context5.next = 2;
+                _context6.next = 2;
                 return this.setup(opts);
 
               case 2:
-                _yield$this$setup = _context5.sent;
+                _yield$this$setup = _context6.sent;
                 idToName = _yield$this$setup.idToName;
-                return _context5.abrupt("return", idToName);
+                return _context6.abrupt("return", idToName);
 
               case 5:
               case "end":
-                return _context5.stop();
+                return _context6.stop();
             }
           }
-        }, _callee5, this);
+        }, _callee6, this);
       }));
 
       function getRefNames(_x4) {
@@ -7076,35 +7235,35 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "seqFetch",
     value: function () {
-      var _seqFetch = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(refName, start, end) {
-        var _yield$this$configure2, sequenceAdapter, refSeqStore, features, seqChunks, trimmed, sequence;
+      var _seqFetch = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(refName, start, end) {
+        var _yield$this$configure3, sequenceAdapter, refSeqStore, features, seqChunks, trimmed, sequence;
 
-        return runtime_1.wrap(function _callee6$(_context6) {
+        return runtime_1.wrap(function _callee7$(_context7) {
           while (1) {
-            switch (_context6.prev = _context6.next) {
+            switch (_context7.prev = _context7.next) {
               case 0:
-                _context6.next = 2;
+                _context7.next = 2;
                 return this.configure();
 
               case 2:
-                _yield$this$configure2 = _context6.sent;
-                sequenceAdapter = _yield$this$configure2.sequenceAdapter;
+                _yield$this$configure3 = _context7.sent;
+                sequenceAdapter = _yield$this$configure3.sequenceAdapter;
                 refSeqStore = sequenceAdapter;
 
                 if (refSeqStore) {
-                  _context6.next = 7;
+                  _context7.next = 7;
                   break;
                 }
 
-                return _context6.abrupt("return", undefined);
+                return _context7.abrupt("return", undefined);
 
               case 7:
                 if (refName) {
-                  _context6.next = 9;
+                  _context7.next = 9;
                   break;
                 }
 
-                return _context6.abrupt("return", undefined);
+                return _context7.abrupt("return", undefined);
 
               case 9:
                 features = refSeqStore.getFeatures({
@@ -7113,11 +7272,11 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   end: end,
                   assemblyName: ''
                 });
-                _context6.next = 12;
+                _context7.next = 12;
                 return features.pipe(operators.toArray()).toPromise();
 
               case 12:
-                seqChunks = _context6.sent;
+                seqChunks = _context7.sent;
                 trimmed = [];
                 seqChunks.sort(function (a, b) {
                   return a.get('start') - b.get('start');
@@ -7133,21 +7292,21 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 sequence = trimmed.join('');
 
                 if (!(sequence.length !== end - start)) {
-                  _context6.next = 18;
+                  _context7.next = 18;
                   break;
                 }
 
                 throw new Error("sequence fetch failed: fetching ".concat(refName, ":").concat((start - 1).toLocaleString(), "-").concat(end.toLocaleString(), " returned ").concat(sequence.length.toLocaleString(), " bases, but should have returned ").concat((end - start).toLocaleString()));
 
               case 18:
-                return _context6.abrupt("return", sequence);
+                return _context7.abrupt("return", sequence);
 
               case 19:
               case "end":
-                return _context6.stop();
+                return _context7.stop();
             }
           }
-        }, _callee6, this);
+        }, _callee7, this);
       }));
 
       function seqFetch(_x5, _x6, _x7) {
@@ -7166,44 +7325,44 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
           end = region.end,
           originalRefName = region.originalRefName;
 
-      var _ref5 = opts || {},
-          signal = _ref5.signal,
-          _ref5$statusCallback = _ref5.statusCallback,
-          statusCallback = _ref5$statusCallback === void 0 ? function () {} : _ref5$statusCallback;
+      var _ref4 = opts || {},
+          signal = _ref4.signal,
+          _ref4$statusCallback = _ref4.statusCallback,
+          statusCallback = _ref4$statusCallback === void 0 ? function () {} : _ref4$statusCallback;
 
       return rxjs.ObservableCreate( /*#__PURE__*/function () {
-        var _ref6 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(observer) {
+        var _ref5 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee8(observer) {
           var _yield$_this2$configu, bam, records, _iterator, _step, record, ref;
 
-          return runtime_1.wrap(function _callee7$(_context7) {
+          return runtime_1.wrap(function _callee8$(_context8) {
             while (1) {
-              switch (_context7.prev = _context7.next) {
+              switch (_context8.prev = _context8.next) {
                 case 0:
-                  _context7.next = 2;
+                  _context8.next = 2;
                   return _this2.configure();
 
                 case 2:
-                  _yield$_this2$configu = _context7.sent;
+                  _yield$_this2$configu = _context8.sent;
                   bam = _yield$_this2$configu.bam;
-                  _context7.next = 6;
+                  _context8.next = 6;
                   return _this2.setup(opts);
 
                 case 6:
                   statusCallback('Downloading alignments');
-                  _context7.next = 9;
+                  _context8.next = 9;
                   return bam.getRecordsForRange(refName, start, end, opts);
 
                 case 9:
-                  records = _context7.sent;
+                  records = _context8.sent;
                   util.checkAbortSignal(signal);
                   _iterator = _createForOfIteratorHelper(records);
-                  _context7.prev = 12;
+                  _context8.prev = 12;
 
                   _iterator.s();
 
                 case 14:
                   if ((_step = _iterator.n()).done) {
-                    _context7.next = 24;
+                    _context8.next = 24;
                     break;
                   }
 
@@ -7211,39 +7370,39 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   ref = void 0;
 
                   if (record.get('md')) {
-                    _context7.next = 21;
+                    _context8.next = 21;
                     break;
                   }
 
-                  _context7.next = 20;
+                  _context8.next = 20;
                   return _this2.seqFetch(originalRefName || refName, record.get('start'), record.get('end'));
 
                 case 20:
-                  ref = _context7.sent;
+                  ref = _context8.sent;
 
                 case 21:
                   observer.next(new BamSlightlyLazyFeature(record, _this2, ref));
 
                 case 22:
-                  _context7.next = 14;
+                  _context8.next = 14;
                   break;
 
                 case 24:
-                  _context7.next = 29;
+                  _context8.next = 29;
                   break;
 
                 case 26:
-                  _context7.prev = 26;
-                  _context7.t0 = _context7["catch"](12);
+                  _context8.prev = 26;
+                  _context8.t0 = _context8["catch"](12);
 
-                  _iterator.e(_context7.t0);
+                  _iterator.e(_context8.t0);
 
                 case 29:
-                  _context7.prev = 29;
+                  _context8.prev = 29;
 
                   _iterator.f();
 
-                  return _context7.finish(29);
+                  return _context8.finish(29);
 
                 case 32:
                   statusCallback('');
@@ -7251,17 +7410,69 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 case 34:
                 case "end":
-                  return _context7.stop();
+                  return _context8.stop();
               }
             }
-          }, _callee7, null, [[12, 26, 29, 32]]);
+          }, _callee8, null, [[12, 26, 29, 32]]);
         }));
 
         return function (_x8) {
-          return _ref6.apply(this, arguments);
+          return _ref5.apply(this, arguments);
         };
       }(), signal);
     }
+  }, {
+    key: "estimateRegionsStats",
+    value: function () {
+      var _estimateRegionsStats = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee9(regions, opts) {
+        var _yield$this$configure4, bam, index, bytes, fetchSizeLimit;
+
+        return runtime_1.wrap(function _callee9$(_context9) {
+          while (1) {
+            switch (_context9.prev = _context9.next) {
+              case 0:
+                _context9.next = 2;
+                return this.configure();
+
+              case 2:
+                _yield$this$configure4 = _context9.sent;
+                bam = _yield$this$configure4.bam;
+                // @ts-ignore
+                index = bam.index; // this is a method to avoid calling on htsget adapters
+
+                if (!(index.filehandle !== '?')) {
+                  _context9.next = 13;
+                  break;
+                }
+
+                _context9.next = 8;
+                return util.bytesForRegions(regions, index);
+
+              case 8:
+                bytes = _context9.sent;
+                fetchSizeLimit = configuration.readConfObject(this.config, 'fetchSizeLimit');
+                return _context9.abrupt("return", {
+                  bytes: bytes,
+                  fetchSizeLimit: fetchSizeLimit
+                });
+
+              case 13:
+                return _context9.abrupt("return", _get(_getPrototypeOf(BamAdapter.prototype), "estimateRegionsStats", this).call(this, regions, opts));
+
+              case 14:
+              case "end":
+                return _context9.stop();
+            }
+          }
+        }, _callee9, this);
+      }));
+
+      function estimateRegionsStats(_x9, _x10) {
+        return _estimateRegionsStats.apply(this, arguments);
+      }
+
+      return estimateRegionsStats;
+    }()
   }, {
     key: "freeResources",
     value: function