@jbrowse/plugin-alignments 1.6.7 → 1.7.0

package/dist/LinearPileupDisplay/components/FilterByTag.js

@@ -0,0 +1,203 @@
+"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 _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+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 (theme) {
+  return {
+    paper: {
+      padding: theme.spacing(2),
+      margin: theme.spacing(2)
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    field: {
+      margin: theme.spacing(2)
+    }
+  };
+});
+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'];
+
+function Bitmask(props) {
+  var _props$flag = props.flag,
+      flag = _props$flag === void 0 ? 0 : _props$flag,
+      setFlag = props.setFlag;
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    type: "number",
+    value: flag,
+    onChange: function onChange(event) {
+      return setFlag(+event.target.value);
+    }
+  }), flagNames.map(function (name, index) {
+    var val = flag & 1 << index;
+    var key = "".concat(name, "_").concat(val);
+    return /*#__PURE__*/_react["default"].createElement("div", {
+      key: key
+    }, /*#__PURE__*/_react["default"].createElement("input", {
+      type: "checkbox",
+      checked: Boolean(val),
+      onChange: function onChange(event) {
+        if (event.target.checked) {
+          setFlag(flag | 1 << index);
+        } else {
+          setFlag(flag & ~(1 << index));
+        }
+      }
+    }), /*#__PURE__*/_react["default"].createElement("label", {
+      htmlFor: key
+    }, name));
+  }));
+}
+
+function FilterByTagDlg(props) {
+  var _filterBy$tagFilter, _filterBy$tagFilter2;
+
+  var model = props.model,
+      handleClose = props.handleClose;
+  var classes = useStyles();
+  var filterBy = model.filterBy;
+
+  var _useState = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      flagInclude = _useState2[0],
+      setFlagInclude = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      flagExclude = _useState4[0],
+      setFlagExclude = _useState4[1];
+
+  var _useState5 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter = filterBy.tagFilter) === null || _filterBy$tagFilter === void 0 ? void 0 : _filterBy$tagFilter.tag) || ''),
+      _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
+      tag = _useState6[0],
+      setTag = _useState6[1];
+
+  var _useState7 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter2 = filterBy.tagFilter) === null || _filterBy$tagFilter2 === void 0 ? void 0 : _filterBy$tagFilter2.value) || ''),
+      _useState8 = (0, _slicedToArray2["default"])(_useState7, 2),
+      tagValue = _useState8[0],
+      setTagValue = _useState8[1];
+
+  var _useState9 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || ''),
+      _useState10 = (0, _slicedToArray2["default"])(_useState9, 2),
+      readName = _useState10[0],
+      setReadName = _useState10[1];
+
+  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+  var site = 'https://broadinstitute.github.io/picard/explain-flags.html';
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set filter bitmask options. Refer to ", /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    href: site
+  }, site), ' ', "for details"), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement("div", {
+    style: {
+      display: 'flex'
+    }
+  }, /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have ALL these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+    flag: flagInclude,
+    setFlag: setFlagInclude
+  })), /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have NONE of these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+    flag: flagExclude,
+    setFlag: setFlagExclude
+  })))), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: tag,
+    onChange: function onChange(event) {
+      setTag(event.target.value);
+    },
+    placeholder: "Enter tag name",
+    inputProps: {
+      maxLength: 2,
+      'data-testid': 'color-tag-name-input'
+    },
+    error: tag.length === 2 && !validTag,
+    helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
+    "data-testid": "color-tag-name"
+  }), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: tagValue,
+    onChange: function onChange(event) {
+      setTagValue(event.target.value);
+    },
+    placeholder: "Enter tag value",
+    inputProps: {
+      'data-testid': 'color-tag-name-input'
+    },
+    "data-testid": "color-tag-value"
+  })), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+    className: classes.paper,
+    variant: "outlined"
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by read name"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    className: classes.field,
+    value: readName,
+    onChange: function onChange(event) {
+      setReadName(event.target.value);
+    },
+    placeholder: "Enter read name",
+    inputProps: {
+      'data-testid': 'color-tag-readname-input'
+    },
+    "data-testid": "color-tag-readname"
+  })), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    autoFocus: true,
+    type: "submit",
+    onClick: function onClick() {
+      model.setFilterBy({
+        flagInclude: flagInclude,
+        flagExclude: flagExclude,
+        readName: readName,
+        tagFilter: tag !== '' ? {
+          tag: tag,
+          value: tagValue
+        } : undefined
+      });
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(FilterByTagDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -0,0 +1,32 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _react = _interopRequireDefault(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _Typography = _interopRequireDefault(require("@material-ui/core/Typography"));
+
+function LinearPileupDisplayBlurb(props) {
+  var model = props.model;
+  var sortedBy = model.sortedBy;
+  return sortedBy ? /*#__PURE__*/_react["default"].createElement("div", {
+    "data-testid": "blurb-".concat(model.sortedBy),
+    style: {
+      backgroundColor: 'white'
+    }
+  }, /*#__PURE__*/_react["default"].createElement(_Typography["default"], {
+    color: "secondary",
+    variant: "caption"
+  }, model.sortedBy ? "Sorted by ".concat(sortedBy.type.toLowerCase(), " at ").concat(sortedBy.refName, ":").concat(sortedBy.pos) : null)) : null;
+}
+
+var _default = (0, _mobxReact.observer)(LinearPileupDisplayBlurb);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -0,0 +1,99 @@
+"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 _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+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 (theme) {
+  return {
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    }
+  };
+});
+
+function SetFeatureHeightDlg(props) {
+  var classes = useStyles();
+  var model = props.model,
+      handleClose = props.handleClose;
+  var featureHeightSetting = model.featureHeightSetting,
+      noSpacingSetting = model.noSpacing;
+
+  var _useState = (0, _react.useState)("".concat(featureHeightSetting)),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      height = _useState2[0],
+      setHeight = _useState2[1];
+
+  var _useState3 = (0, _react.useState)(noSpacingSetting),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      noSpacing = _useState4[0],
+      setNoSpacing = _useState4[1];
+
+  var ok = height !== '' && !Number.isNaN(+height);
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Set feature height", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: height,
+    helperText: "Feature height",
+    onChange: function onChange(event) {
+      setHeight(event.target.value);
+    }
+  }), /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
+    control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
+      checked: !!noSpacing,
+      onChange: function onChange() {
+        return setNoSpacing(function (val) {
+          return !val;
+        });
+      }
+    }),
+    label: "Remove spacing between features in y-direction?"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    disabled: !ok,
+    onClick: function onClick() {
+      model.setFeatureHeight(height !== '' && !Number.isNaN(+height) ? +height : undefined);
+      model.setNoSpacing(noSpacing);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SetFeatureHeightDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -0,0 +1,90 @@
+"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 _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+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 (theme) {
+  return {
+    root: {
+      width: 500
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    },
+    field: {
+      margin: theme.spacing(2)
+    }
+  };
+});
+
+function SetMaxHeightDlg(props) {
+  var model = props.model,
+      handleClose = props.handleClose;
+  var classes = useStyles();
+  var _model$maxHeight = model.maxHeight,
+      maxHeight = _model$maxHeight === void 0 ? '' : _model$maxHeight;
+
+  var _useState = (0, _react.useState)("".concat(maxHeight)),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      max = _useState2[0],
+      setMax = _useState2[1];
+
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, {
+    className: classes.root
+  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: max,
+    onChange: function onChange(event) {
+      setMax(event.target.value);
+    },
+    placeholder: "Enter max height for layout"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    onClick: function onClick() {
+      model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SetMaxHeightDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -0,0 +1,95 @@
+"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 _react = _interopRequireWildcard(require("react"));
+
+var _mobxReact = require("mobx-react");
+
+var _core = require("@material-ui/core");
+
+var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
+
+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 (theme) {
+  return {
+    root: {
+      margin: 0,
+      padding: theme.spacing(2)
+    },
+    closeButton: {
+      position: 'absolute',
+      right: theme.spacing(1),
+      top: theme.spacing(1),
+      color: theme.palette.grey[500]
+    }
+  };
+});
+
+function SortByTagDlg(props) {
+  var classes = useStyles();
+  var model = props.model,
+      handleClose = props.handleClose;
+
+  var _useState = (0, _react.useState)(''),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      tag = _useState2[0],
+      setTag = _useState2[1];
+
+  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+    open: true,
+    onClose: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Sort by tag", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+    "aria-label": "close",
+    className: classes.closeButton,
+    onClick: handleClose
+  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set the tag to sort by"), /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+    color: "textSecondary"
+  }, "Examples: HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+    value: tag,
+    onChange: function onChange(event) {
+      return setTag(event.target.value);
+    },
+    placeholder: "Enter tag name",
+    inputProps: {
+      maxLength: 2,
+      'data-testid': 'sort-tag-name-input'
+    },
+    error: tag.length === 2 && !validTag,
+    helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
+    autoComplete: "off",
+    "data-testid": "sort-tag-name"
+  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "primary",
+    type: "submit",
+    autoFocus: true,
+    onClick: function onClick() {
+      model.setSortedBy('tag', tag);
+      handleClose();
+    }
+  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+    variant: "contained",
+    color: "secondary",
+    onClick: function onClick() {
+      return handleClose();
+    }
+  }, "Cancel"))));
+}
+
+var _default = (0, _mobxReact.observer)(SortByTagDlg);
+
+exports["default"] = _default;

package/dist/LinearPileupDisplay/configSchema.js

@@ -0,0 +1,47 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
+
+var _mobxStateTree = require("mobx-state-tree");
+
+function PileupConfigFactory(pluginManager) {
+  var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
+  var SvgFeatureRendererConfigSchema = pluginManager.getRendererType('SvgFeatureRenderer').configSchema; // modify config schema to take in a sub coverage display
+
+  return (0, _configuration.ConfigurationSchema)('LinearPileupDisplay', {
+    defaultRendering: {
+      type: 'stringEnum',
+      model: _mobxStateTree.types.enumeration('Rendering', ['pileup', 'svg']),
+      defaultValue: 'pileup'
+    },
+    renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
+      PileupRenderer: PileupRendererConfigSchema,
+      SvgFeatureRenderer: SvgFeatureRendererConfigSchema
+    }),
+    renderer: '',
+    maxFeatureScreenDensity: {
+      type: 'number',
+      description: 'maximum features per pixel that is displayed in the view',
+      defaultValue: 5
+    },
+    colorScheme: {
+      type: 'stringEnum',
+      model: _mobxStateTree.types.enumeration('colorScheme', ['strand', 'normal', 'insertSize', 'insertSizeAndOrientation', 'mappingQuality', 'tag']),
+      description: 'color scheme to use',
+      defaultValue: 'normal'
+    }
+  }, {
+    baseConfiguration: (0, _pluginLinearGenomeView.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+    explicitlyTyped: true
+  });
+}
+
+var _default = PileupConfigFactory;
+exports["default"] = _default;

package/dist/LinearPileupDisplay/configSchema.test.js

@@ -0,0 +1,92 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+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 _Plugin3 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+
+var _pluginSvg = require("@jbrowse/plugin-svg");
+
+var _PileupRenderer = _interopRequireDefault(require("../PileupRenderer"));
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+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; } }
+
+// mock warnings to avoid unnecessary outputs
+beforeEach(function () {
+  jest.spyOn(console, 'warn').mockImplementation(function () {});
+});
+afterEach(function () {
+  console.warn.mockRestore();
+});
+
+var PileupRendererPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(PileupRendererPlugin, _Plugin);
+
+  var _super = _createSuper(PileupRendererPlugin);
+
+  function PileupRendererPlugin() {
+    (0, _classCallCheck2["default"])(this, PileupRendererPlugin);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(PileupRendererPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      (0, _PileupRenderer["default"])(pluginManager);
+    }
+  }]);
+  return PileupRendererPlugin;
+}(_Plugin3["default"]);
+
+var SvgFeatureRendererPlugin = /*#__PURE__*/function (_Plugin2) {
+  (0, _inherits2["default"])(SvgFeatureRendererPlugin, _Plugin2);
+
+  var _super2 = _createSuper(SvgFeatureRendererPlugin);
+
+  function SvgFeatureRendererPlugin() {
+    (0, _classCallCheck2["default"])(this, SvgFeatureRendererPlugin);
+    return _super2.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(SvgFeatureRendererPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addRendererType(function () {
+        return new _BoxRendererType["default"]({
+          name: 'SvgFeatureRenderer',
+          ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
+          configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
+          pluginManager: pluginManager
+        });
+      });
+    }
+  }]);
+  return SvgFeatureRendererPlugin;
+}(_Plugin3["default"]);
+
+test('has a type attr', function () {
+  var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
+  var config = configSchema.create({
+    type: 'LinearPileupDisplay',
+    displayId: 'display0',
+    name: 'Zonker Display'
+  });
+  expect(config.type).toEqual('LinearPileupDisplay');
+});