@jbrowse/plugin-alignments 1.6.7 → 1.7.0

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -0,0 +1,216 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _core = require("@material-ui/core");
+
+var _mobxReact = require("mobx-react");
+
+var _util = require("@jbrowse/core/util");
+
+var _copyToClipboard = _interopRequireDefault(require("copy-to-clipboard"));
+
+var _BaseFeatureDetail = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+
+var _MismatchParser = require("../BamAdapter/MismatchParser");
+
+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 || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+var useStyles = (0, _core.makeStyles)(function () {
+  return {
+    compact: {
+      paddingRight: 0,
+      paddingTop: 0,
+      paddingBottom: 0
+    }
+  };
+});
+var omit = ['clipPos', 'flags']; // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+function AlignmentFlags(props) {
+  var classes = useStyles();
+  var feature = props.feature;
+  var flags = feature.flags;
+  var flagNames = ['read paired', 'read mapped in proper pair', 'read unmapped', 'mate unmapped', 'read reverse strand', 'mate reverse strand', 'first in pair', 'second in pair', 'not primary alignment', 'read fails platform/vendor quality checks', 'read is PCR or optical duplicate', 'supplementary alignment'];
+  return /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.BaseCard, (0, _extends2["default"])({}, props, {
+    title: "Flags"
+  }), /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.SimpleValue, {
+    name: 'Flag',
+    value: flags
+  }), /*#__PURE__*/_react["default"].createElement(_core.FormGroup, null, flagNames.map(function (name, index) {
+    var val = flags & 1 << index;
+    var key = "".concat(name, "_").concat(val);
+    return /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
+      key: key,
+      control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
+        className: classes.compact,
+        checked: Boolean(val),
+        name: name,
+        readOnly: true
+      }),
+      label: name
+    });
+  })));
+}
+
+function Formatter(_ref) {
+  var value = _ref.value;
+
+  var _useState = (0, _react.useState)(false),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      show = _useState2[0],
+      setShow = _useState2[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);
+      }
+    }, "Copy"), /*#__PURE__*/_react["default"].createElement("button", {
+      type: "button",
+      onClick: function onClick() {
+        return setShow(function (val) {
+          return !val;
+        });
+      }
+    }, show ? 'Show less' : 'Show more'), /*#__PURE__*/_react["default"].createElement("div", null, show ? display : "".concat(display.slice(0, 100), "...")));
+  }
+
+  return /*#__PURE__*/_react["default"].createElement("div", null, display);
+} // utility function to get length of alignment from cigar
+
+
+function getLengthOnRef(cigar) {
+  var cigarOps = (0, _MismatchParser.parseCigar)(cigar);
+  var lengthOnRef = 0;
+
+  for (var i = 0; i < cigarOps.length; i += 2) {
+    var len = +cigarOps[i];
+    var op = cigarOps[i + 1];
+
+    if (op !== 'H' && op !== 'S' && op !== 'I') {
+      lengthOnRef += len;
+    }
+  }
+
+  return lengthOnRef;
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function SupplementaryAlignments(props) {
+  var tag = props.tag,
+      model = props.model;
+  var session = (0, _util.getSession)(model);
+  return /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.BaseCard, (0, _extends2["default"])({}, props, {
+    title: "Supplementary alignments"
+  }), /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "List of supplementary alignment locations"), /*#__PURE__*/_react["default"].createElement("ul", null, tag.split(';').filter(function (SA) {
+    return !!SA;
+  }).map(function (SA, index) {
+    var _SA$split = SA.split(','),
+        _SA$split2 = (0, _slicedToArray2["default"])(_SA$split, 4),
+        saRef = _SA$split2[0],
+        saStart = _SA$split2[1],
+        saStrand = _SA$split2[2],
+        saCigar = _SA$split2[3];
+
+    var saLength = getLengthOnRef(saCigar);
+    var extra = Math.floor(saLength / 5);
+    var start = +saStart;
+    var end = +saStart + saLength;
+    var locString = "".concat(saRef, ":").concat(Math.max(1, start - extra), "-").concat(end + extra);
+    var displayStart = start.toLocaleString('en-US');
+    var displayEnd = end.toLocaleString('en-US');
+    var displayString = "".concat(saRef, ":").concat(displayStart, "-").concat(displayEnd, " (").concat(saStrand, ")");
+    return /*#__PURE__*/_react["default"].createElement("li", {
+      key: "".concat(locString, "-").concat(index)
+    }, /*#__PURE__*/_react["default"].createElement(_core.Link, {
+      onClick: function onClick() {
+        var view = model.view;
+
+        try {
+          if (view) {
+            view.navToLocString(locString);
+          } else {
+            throw new Error('No view associated with this view anymore');
+          }
+        } catch (e) {
+          console.error(e);
+          session.notify("".concat(e));
+        }
+      },
+      href: "#"
+    }, displayString));
+  })));
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function PairLink(_ref2) {
+  var locString = _ref2.locString,
+      model = _ref2.model;
+  var session = (0, _util.getSession)(model);
+  return /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    onClick: function onClick() {
+      var view = model.view;
+
+      try {
+        if (view) {
+          view.navToLocString(locString);
+        } else {
+          session.notify('No view associated with this feature detail panel anymore', 'warning');
+        }
+      } catch (e) {
+        console.error(e);
+        session.notify("".concat(e));
+      }
+    },
+    href: "#"
+  }, locString);
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function AlignmentFeatureDetails(props) {
+  var model = props.model;
+  var feat = JSON.parse(JSON.stringify(model.featureData));
+  var SA = feat.tags && feat.tags.SA || feat.SA;
+  return /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    "data-testid": "alignment-side-drawer"
+  }, /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.FeatureDetails, (0, _extends2["default"])({}, props, {
+    omit: omit,
+    feature: feat,
+    formatter: function formatter(value, key) {
+      return key === 'next_segment_position' ? /*#__PURE__*/_react["default"].createElement(PairLink, {
+        model: model,
+        locString: value
+      }) : /*#__PURE__*/_react["default"].createElement(Formatter, {
+        value: value
+      });
+    }
+  })), SA ? /*#__PURE__*/_react["default"].createElement(SupplementaryAlignments, {
+    model: model,
+    tag: SA
+  }) : null, /*#__PURE__*/_react["default"].createElement(AlignmentFlags, (0, _extends2["default"])({
+    feature: feat
+  }, props)));
+}
+
+var _default = (0, _mobxReact.observer)(AlignmentFeatureDetails);
+
+exports["default"] = _default;

package/dist/AlignmentsFeatureDetail/index.js

@@ -0,0 +1,63 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.configSchema = void 0;
+exports["default"] = register;
+exports.stateModelFactory = stateModelFactory;
+
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+
+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"));
+
+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; }
+
+var configSchema = (0, _configuration.ConfigurationSchema)('AlignmentsFeatureWidget', {});
+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;
+      }
+    };
+  });
+}
+
+function register(pluginManager) {
+  pluginManager.addWidgetType(function () {
+    return new _WidgetType["default"]({
+      name: 'AlignmentsFeatureWidget',
+      heading: 'Feature details',
+      configSchema: configSchema,
+      stateModel: stateModelFactory(pluginManager),
+      ReactComponent: /*#__PURE__*/(0, _react.lazy)(function () {
+        return Promise.resolve().then(function () {
+          return _interopRequireWildcard(require('./AlignmentsFeatureDetail'));
+        });
+      })
+    });
+  });
+}

package/dist/AlignmentsFeatureDetail/index.test.js

@@ -0,0 +1,60 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _react = require("@testing-library/react");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _react2 = _interopRequireDefault(require("react"));
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _ = require(".");
+
+var _AlignmentsFeatureDetail = _interopRequireDefault(require("./AlignmentsFeatureDetail"));
+
+test('open up a widget', function () {
+  console.warn = jest.fn();
+  var pluginManager = new _PluginManager["default"]([]);
+
+  var Session = _mobxStateTree.types.model({
+    pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
+    rpcManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
+    configuration: (0, _configuration.ConfigurationSchema)('test', {}),
+    widget: (0, _.stateModelFactory)(pluginManager)
+  });
+
+  var session = Session.create({
+    widget: {
+      type: 'AlignmentsFeatureWidget'
+    }
+  });
+  session.widget.setFeatureData({
+    seq: 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG',
+    start: 2,
+    end: 102,
+    strand: 1,
+    score: 37,
+    qual: '17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17',
+    MQ: 37,
+    CIGAR: '100M',
+    length_on_ref: 100,
+    template_length: 0,
+    seq_length: 100,
+    name: 'ctgA_3_555_0:0:0_2:0:0_102d',
+    refName: 'ctgA',
+    type: 'match'
+  });
+
+  var _render = (0, _react.render)( /*#__PURE__*/_react2["default"].createElement(_AlignmentsFeatureDetail["default"], {
+    model: session.widget
+  })),
+      container = _render.container,
+      getByText = _render.getByText;
+
+  expect(container.firstChild).toMatchSnapshot();
+  expect(getByText('ctgA:3..102 (+)')).toBeTruthy();
+});

package/dist/AlignmentsTrack/index.js

@@ -0,0 +1,37 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = register;
+
+var _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _models = require("@jbrowse/core/pluggableElementTypes/models");
+
+function configSchemaFactory(pluginManager) {
+  return (0, _configuration.ConfigurationSchema)('AlignmentsTrack', {}, {
+    baseConfiguration: (0, _models.createBaseTrackConfig)(pluginManager)
+  });
+}
+
+function register(pluginManager) {
+  pluginManager.addTrackType(function () {
+    var configSchema = configSchemaFactory(pluginManager);
+    var track = new _TrackType["default"]({
+      name: 'AlignmentsTrack',
+      configSchema: configSchema,
+      stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'AlignmentsTrack', configSchema)
+    });
+    var linearAlignmentsDisplay = pluginManager.getDisplayType('LinearAlignmentsDisplay'); // Add LinearAlignmentsDisplay here so that it has priority over the other
+    // linear displays (defaults to order the displays are added, but we have
+    // to add the Pileup and SNPCoverage displays first).
+
+    track.addDisplayType(linearAlignmentsDisplay);
+    return track;
+  });
+}