@jbrowse/plugin-bed 1.6.7 → 1.7.0

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -0,0 +1,295 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _bed = _interopRequireDefault(require("@gmod/bed"));
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _tabix = require("@gmod/tabix");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("../util");
+
+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 _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 BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(BedTabixAdapter, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(BedTabixAdapter);
+
+  function BedTabixAdapter(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, BedTabixAdapter);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "parser", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "bed", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "columnNames", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "scoreColumn", void 0);
+    var bedGzLocation = (0, _configuration.readConfObject)(config, 'bedGzLocation');
+    var index = (0, _configuration.readConfObject)(config, 'index');
+    var autoSql = (0, _configuration.readConfObject)(config, 'autoSql');
+    var location = index.location,
+        indexType = index.indexType;
+    _this.bed = new _tabix.TabixIndexedFile({
+      filehandle: (0, _io.openLocation)(bedGzLocation, _this.pluginManager),
+      csiFilehandle: indexType === 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
+      tbiFilehandle: indexType !== 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
+      chunkCacheSize: 50 * Math.pow(2, 20)
+    });
+    _this.columnNames = (0, _configuration.readConfObject)(config, 'columnNames');
+    _this.scoreColumn = (0, _configuration.readConfObject)(config, 'scoreColumn');
+    _this.parser = new _bed["default"]({
+      autoSql: autoSql
+    });
+    return _this;
+  }
+
+  (0, _createClass2["default"])(BedTabixAdapter, [{
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var opts,
+            _args = arguments;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
+                return _context.abrupt("return", this.bed.getReferenceSequenceNames(opts));
+
+              case 2:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                return _context2.abrupt("return", this.bed.getHeader());
+
+              case 1:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "defaultParser",
+    value: function defaultParser(fields, line) {
+      return Object.fromEntries(line.split('\t').map(function (f, i) {
+        return [fields[i], f];
+      }));
+    }
+  }, {
+    key: "getNames",
+    value: function () {
+      var _getNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+        var header, defs, defline;
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                if (!this.columnNames.length) {
+                  _context3.next = 2;
+                  break;
+                }
+
+                return _context3.abrupt("return", this.columnNames);
+
+              case 2:
+                _context3.next = 4;
+                return this.bed.getHeader();
+
+              case 4:
+                header = _context3.sent;
+                defs = header.split('\n').filter(function (f) {
+                  return !!f;
+                });
+                defline = defs[defs.length - 1];
+                return _context3.abrupt("return", defline && defline.includes('\t') ? defline.slice(1).split('\t').map(function (field) {
+                  return field.trim();
+                }) : null);
+
+              case 8:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getNames() {
+        return _getNames.apply(this, arguments);
+      }
+
+      return getNames;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this2 = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(observer) {
+          var meta, columnNumbers, colRef, colStart, colEnd, colSame, names;
+          return _regenerator["default"].wrap(function _callee4$(_context4) {
+            while (1) {
+              switch (_context4.prev = _context4.next) {
+                case 0:
+                  _context4.next = 2;
+                  return _this2.bed.getMetadata();
+
+                case 2:
+                  meta = _context4.sent;
+                  columnNumbers = meta.columnNumbers;
+                  colRef = columnNumbers.ref - 1;
+                  colStart = columnNumbers.start - 1;
+                  colEnd = columnNumbers.end - 1; // colSame handles special case for tabix where a single column is both
+                  // the start and end, this is assumed to be covering the base at this
+                  // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
+
+                  colSame = colStart === colEnd ? 1 : 0;
+                  _context4.next = 10;
+                  return _this2.getNames();
+
+                case 10:
+                  names = _context4.sent;
+                  _context4.next = 13;
+                  return _this2.bed.getLines(query.refName, query.start, query.end, {
+                    lineCallback: function lineCallback(line, fileOffset) {
+                      var l = line.split('\t');
+                      var refName = l[colRef];
+                      var start = +l[colStart];
+                      var end = +l[colEnd] + colSame;
+                      var uniqueId = "".concat(_this2.id, "-").concat(fileOffset);
+                      var data = names ? _this2.defaultParser(names, line) : _this2.parser.parseLine(line, {
+                        uniqueId: uniqueId
+                      });
+                      var blockCount = data.blockCount,
+                          blockSizes = data.blockSizes,
+                          blockStarts = data.blockStarts,
+                          chromStarts = data.chromStarts;
+
+                      if (blockCount) {
+                        var starts = chromStarts || blockStarts || [];
+                        var sizes = blockSizes;
+                        var blocksOffset = start;
+                        data.subfeatures = [];
+
+                        for (var b = 0; b < blockCount; b += 1) {
+                          var bmin = (starts[b] || 0) + blocksOffset;
+                          var bmax = bmin + (sizes[b] || 0);
+                          data.subfeatures.push({
+                            uniqueId: "".concat(uniqueId, "-").concat(b),
+                            start: bmin,
+                            end: bmax,
+                            type: 'block'
+                          });
+                        }
+                      }
+
+                      if (_this2.scoreColumn) {
+                        data.score = +data[_this2.scoreColumn];
+                      }
+
+                      delete data.chrom;
+                      delete data.chromStart;
+                      delete data.chromEnd;
+                      var f = new _simpleFeature["default"](_objectSpread(_objectSpread({}, data), {}, {
+                        start: start,
+                        end: end,
+                        refName: refName,
+                        uniqueId: uniqueId
+                      }));
+                      var r = f.get('thickStart') ? (0, _util.ucscProcessedTranscript)(f) : f;
+                      observer.next(r);
+                    },
+                    signal: opts.signal
+                  });
+
+                case 13:
+                  observer.complete();
+
+                case 14:
+                case "end":
+                  return _context4.stop();
+              }
+            }
+          }, _callee4);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "freeResources",
+    value: function freeResources() {}
+  }]);
+  return BedTabixAdapter;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = BedTabixAdapter;
+(0, _defineProperty2["default"])(BedTabixAdapter, "capabilities", ['getFeatures', 'getRefNames']);

package/dist/BedTabixAdapter/BedTabixAdapter.test.js

@@ -0,0 +1,276 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+var _BedTabixAdapter = _interopRequireDefault(require("./BedTabixAdapter"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+test('adapter can fetch features from volvox-bed12.bed.gz', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+  var adapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee$(_context) {
+    while (1) {
+      switch (_context.prev = _context.next) {
+        case 0:
+          adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
+            bedGzLocation: {
+              localPath: require.resolve('./test_data/volvox-bed12.bed.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('./test_data/volvox-bed12.bed.gz.tbi'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000,
+            assemblyName: 'volvox'
+          });
+          _context.t0 = expect;
+          _context.next = 5;
+          return adapter.hasDataForRefName('ctgA');
+
+        case 5:
+          _context.t1 = _context.sent;
+          (0, _context.t0)(_context.t1).toBe(true);
+          _context.t2 = expect;
+          _context.next = 10;
+          return adapter.hasDataForRefName('ctgB');
+
+        case 10:
+          _context.t3 = _context.sent;
+          (0, _context.t2)(_context.t3).toBe(false);
+          _context.next = 14;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 14:
+          featuresArray = _context.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
+
+        case 17:
+        case "end":
+          return _context.stop();
+      }
+    }
+  }, _callee);
+})));
+test('adapter can fetch features from volvox.sort.bed.gz simple bed3', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+  var adapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee2$(_context2) {
+    while (1) {
+      switch (_context2.prev = _context2.next) {
+        case 0:
+          adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
+            bedGzLocation: {
+              localPath: require.resolve('./test_data/volvox.sort.bed.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('./test_data/volvox.sort.bed.gz.tbi'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: 'contigA',
+            start: 0,
+            end: 20000,
+            assemblyName: 'volvox'
+          });
+          _context2.t0 = expect;
+          _context2.next = 5;
+          return adapter.hasDataForRefName('contigA');
+
+        case 5:
+          _context2.t1 = _context2.sent;
+          (0, _context2.t0)(_context2.t1).toBe(true);
+          _context2.t2 = expect;
+          _context2.next = 10;
+          return adapter.hasDataForRefName('ctgB');
+
+        case 10:
+          _context2.t3 = _context2.sent;
+          (0, _context2.t2)(_context2.t3).toBe(false);
+          _context2.next = 14;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 14:
+          featuresArray = _context2.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
+
+        case 17:
+        case "end":
+          return _context2.stop();
+      }
+    }
+  }, _callee2);
+})));
+test('adapter can fetch features bed with autosql', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+  var adapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee3$(_context3) {
+    while (1) {
+      switch (_context3.prev = _context3.next) {
+        case 0:
+          adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
+            bedGzLocation: {
+              localPath: require.resolve('./test_data/volvox-autosql.bed.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('./test_data/volvox-autosql.bed.gz.tbi'),
+                locationType: 'LocalPathLocation'
+              }
+            },
+            autoSql: "table gdcCancer\n\"somatic variants converted from MAF files obtained through the NCI GDC\"\n    (\n    string chrom;      \"Chromosome (or contig, scaffold, etc.)\"\n    uint   chromStart; \"Start position in chromosome\"\n    uint   chromEnd;   \"End position in chromosome\"\n    string name;       \"Name of item\"\n    uint   score;      \"Score from 0-1000\"\n    char[1] strand;    \"+ or -\"\n    uint thickStart;   \"Start of where display should be thick (start codon)\"\n    uint thickEnd;     \"End of where display should be thick (stop codon)\"\n    uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n    int blockCount;    \"Number of blocks\"\n    int[blockCount] blockSizes; \"Comma separated list of block sizes\"\n    int[blockCount] chromStarts; \"Start positions relative to chromStart\"\n    string sampleCount;    \"Number of samples with this variant\"\n    string freq;                    \"Variant frequency\"\n    lstring Hugo_Symbol;            \"Hugo symbol\"\n    lstring Entrez_Gene_Id;         \"Entrez Gene Id\"\n    lstring Variant_Classification; \"Class of variant\"\n    lstring Variant_Type;           \"Type of variant\"\n    lstring Reference_Allele;       \"Reference allele\"\n    lstring Tumor_Seq_Allele1;      \"Tumor allele 1\"\n    lstring Tumor_Seq_Allele2;      \"Tumor allele 2\"\n    lstring dbSNP_RS;               \"dbSNP RS number\"\n    lstring dbSNP_Val_Status;       \"dbSNP validation status\"\n    lstring days_to_death;          \"Number of days till death\"\n    lstring cigarettes_per_day;     \"Number of cigarettes per day\"\n    lstring weight;                 \"Weight\"\n    lstring alcohol_history;        \"Any alcohol consumption?\"\n    lstring alcohol_intensity;      \"Frequency of alcohol consumption\"\n    lstring bmi;                    \"Body mass index\"\n    lstring years_smoked;           \"Number of years smoked\"\n    lstring height;                 \"Height\"\n    lstring gender;                 \"Gender\"\n    lstring project_id;             \"TCGA Project id\"\n    lstring ethnicity;              \"Ethnicity\"\n    lstring Tumor_Sample_Barcode;   \"Tumor sample barcode\"\n    lstring Matched_Norm_Sample_Barcode;  \"Matcheds normal sample barcode\"\n    lstring case_id;                \"Case ID number\"\n)"
+          }));
+          features = adapter.getFeatures({
+            refName: 'ctgA',
+            start: 0,
+            end: 20000,
+            assemblyName: 'volvox'
+          });
+          _context3.t0 = expect;
+          _context3.next = 5;
+          return adapter.hasDataForRefName('ctgA');
+
+        case 5:
+          _context3.t1 = _context3.sent;
+          (0, _context3.t0)(_context3.t1).toBe(true);
+          _context3.t2 = expect;
+          _context3.next = 10;
+          return adapter.hasDataForRefName('ctgB');
+
+        case 10:
+          _context3.t3 = _context3.sent;
+          (0, _context3.t2)(_context3.t3).toBe(false);
+          _context3.next = 14;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 14:
+          featuresArray = _context3.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
+
+        case 17:
+        case "end":
+          return _context3.stop();
+      }
+    }
+  }, _callee3);
+})));
+test('adapter can fetch bed with header', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+  var adapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee4$(_context4) {
+    while (1) {
+      switch (_context4.prev = _context4.next) {
+        case 0:
+          adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
+            bedGzLocation: {
+              localPath: require.resolve('./test_data/volvox.sort.with.header.bed.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('./test_data/volvox.sort.with.header.bed.gz.tbi'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: 'contigA',
+            start: 0,
+            end: 20000,
+            assemblyName: 'volvox'
+          });
+          _context4.t0 = expect;
+          _context4.next = 5;
+          return adapter.hasDataForRefName('contigA');
+
+        case 5:
+          _context4.t1 = _context4.sent;
+          (0, _context4.t0)(_context4.t1).toBe(true);
+          _context4.t2 = expect;
+          _context4.next = 10;
+          return adapter.hasDataForRefName('ctgB');
+
+        case 10:
+          _context4.t3 = _context4.sent;
+          (0, _context4.t2)(_context4.t3).toBe(false);
+          _context4.next = 14;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 14:
+          featuresArray = _context4.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
+
+        case 17:
+        case "end":
+          return _context4.stop();
+      }
+    }
+  }, _callee4);
+})));
+test('adapter can use gwas header', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
+  var adapter, features, featuresArray, featuresJsonArray;
+  return _regenerator["default"].wrap(function _callee5$(_context5) {
+    while (1) {
+      switch (_context5.prev = _context5.next) {
+        case 0:
+          adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
+            bedGzLocation: {
+              localPath: require.resolve('./test_data/gwas.bed.gz'),
+              locationType: 'LocalPathLocation'
+            },
+            index: {
+              location: {
+                localPath: require.resolve('./test_data/gwas.bed.gz.tbi'),
+                locationType: 'LocalPathLocation'
+              }
+            }
+          }));
+          features = adapter.getFeatures({
+            refName: '1',
+            start: 0,
+            end: 100000,
+            assemblyName: 'hg19'
+          });
+          _context5.next = 4;
+          return features.pipe((0, _operators.toArray)()).toPromise();
+
+        case 4:
+          featuresArray = _context5.sent;
+          featuresJsonArray = featuresArray.map(function (f) {
+            return f.toJSON();
+          });
+          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
+
+        case 7:
+        case "end":
+          return _context5.stop();
+      }
+    }
+  }, _callee5);
+})));

package/dist/BedTabixAdapter/configSchema.js

@@ -0,0 +1,53 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _default = (0, _configuration.ConfigurationSchema)('BedTabixAdapter', {
+  bedGzLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.bed.gz',
+      locationType: 'UriLocation'
+    }
+  },
+  index: (0, _configuration.ConfigurationSchema)('TabixIndex', {
+    indexType: {
+      model: _mobxStateTree.types.enumeration('IndexType', ['TBI', 'CSI']),
+      type: 'stringEnum',
+      defaultValue: 'TBI'
+    },
+    location: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.bed.gz.tbi',
+        locationType: 'UriLocation'
+      }
+    }
+  }),
+  columnNames: {
+    type: 'stringArray',
+    description: 'List of column names',
+    defaultValue: []
+  },
+  scoreColumn: {
+    type: 'string',
+    description: 'The column to use as a "score" attribute',
+    defaultValue: ''
+  },
+  autoSql: {
+    type: 'string',
+    description: 'The autoSql definition for the data fields in the file',
+    defaultValue: ''
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/BedTabixAdapter/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));