@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,20 +1,20 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    scaleOpts: ScaleOpts;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
-}
-export default class SNPCoverageRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
-}
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    scaleOpts: ScaleOpts;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    modificationTagMap?: Record<string, string>;
+}
+export default class SNPCoverageRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
+}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -0,0 +1,296 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+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 _ui = require("@jbrowse/core/ui");
+
+var _util = require("@jbrowse/core/util");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _pluginWiggle = require("@jbrowse/plugin-wiggle");
+
+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 SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
+  (0, _inherits2["default"])(SNPCoverageRenderer, _WiggleBaseRenderer);
+
+  var _super = _createSuper(SNPCoverageRenderer);
+
+  function SNPCoverageRenderer() {
+    (0, _classCallCheck2["default"])(this, SNPCoverageRenderer);
+    return _super.apply(this, arguments);
+  }
+
+  (0, _createClass2["default"])(SNPCoverageRenderer, [{
+    key: "draw",
+    value: // note: the snps are drawn on linear scale even if the data is drawn in log
+    // scape hence the two different scales being used
+    function draw(ctx, props) {
+      var features = props.features,
+          regions = props.regions,
+          bpPerPx = props.bpPerPx,
+          displayCrossHatches = props.displayCrossHatches,
+          _props$modificationTa = props.modificationTagMap,
+          modificationTagMap = _props$modificationTa === void 0 ? {} : _props$modificationTa,
+          scaleOpts = props.scaleOpts,
+          unadjustedHeight = props.height,
+          configTheme = props.theme,
+          cfg = props.config,
+          ticks = props.ticks;
+      var theme = (0, _ui.createJBrowseTheme)(configTheme);
+
+      var _regions = (0, _slicedToArray2["default"])(regions, 1),
+          region = _regions[0];
+
+      var width = (region.end - region.start) / bpPerPx; // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+      // wiggle display, and makes the height of the actual drawn area add
+      // "padding" to the top and bottom of the display
+
+      var offset = _pluginWiggle.YSCALEBAR_LABEL_OFFSET;
+      var height = unadjustedHeight - offset * 2;
+      var domain = scaleOpts.domain;
+
+      if (!domain) {
+        return;
+      }
+
+      var opts = _objectSpread(_objectSpread({}, scaleOpts), {}, {
+        range: [0, height]
+      });
+
+      var viewScale = (0, _pluginWiggle.getScale)(opts); // clipping and insertion indicators, uses a smaller height/2 scale
+
+      var indicatorViewScale = (0, _pluginWiggle.getScale)(_objectSpread(_objectSpread({}, opts), {}, {
+        range: [0, height / 2],
+        scaleType: 'linear'
+      }));
+      var originY = (0, _pluginWiggle.getOrigin)(scaleOpts.scaleType);
+      var indicatorThreshold = (0, _configuration.readConfObject)(cfg, 'indicatorThreshold');
+      var drawInterbaseCounts = (0, _configuration.readConfObject)(cfg, 'drawInterbaseCounts');
+      var drawArcs = (0, _configuration.readConfObject)(cfg, 'drawArcs');
+      var drawIndicators = (0, _configuration.readConfObject)(cfg, 'drawIndicators'); // get the y coordinate that we are plotting at, this can be log scale
+
+      var toY = function toY(n) {
+        return height - (viewScale(n) || 0) + offset;
+      };
+
+      var toHeight = function toHeight(n) {
+        return toY(originY) - toY(n);
+      };
+
+      var indicatorToY = function indicatorToY(n) {
+        return height - (indicatorViewScale(n) || 0) + offset;
+      };
+
+      var indicatorToHeight = function indicatorToHeight(n) {
+        return indicatorToY((0, _pluginWiggle.getOrigin)('linear')) - indicatorToY(n);
+      };
+
+      var colorForBase = {
+        A: theme.palette.bases.A.main,
+        C: theme.palette.bases.C.main,
+        G: theme.palette.bases.G.main,
+        T: theme.palette.bases.T.main,
+        total: 'lightgrey',
+        insertion: 'purple',
+        softclip: 'blue',
+        hardclip: 'red',
+        meth: 'red',
+        unmeth: 'blue',
+        ref: 'lightgrey'
+      };
+      var feats = (0, _toConsumableArray2["default"])(features.values());
+      var coverage = feats.filter(function (f) {
+        return f.get('type') !== 'skip';
+      });
+      var skips = feats.filter(function (f) {
+        return f.get('type') === 'skip';
+      }); // Use two pass rendering, which helps in visualizing the SNPs at higher
+      // bpPerPx First pass: draw the gray background
+
+      ctx.fillStyle = colorForBase.total;
+
+      for (var i = 0; i < coverage.length; i++) {
+        var feature = coverage[i];
+
+        var _featureSpanPx = (0, _util.featureSpanPx)(feature, region, bpPerPx),
+            _featureSpanPx2 = (0, _slicedToArray2["default"])(_featureSpanPx, 2),
+            leftPx = _featureSpanPx2[0],
+            rightPx = _featureSpanPx2[1];
+
+        var w = rightPx - leftPx + 0.3;
+        var score = feature.get('score');
+        ctx.fillRect(leftPx, toY(score), w, toHeight(score));
+      } // Keep track of previous total which we will use it to draw the interbase
+      // indicator (if there is a sudden clip, there will be no read coverage but
+      // there will be "clip" coverage) at that position beyond the read. if the
+      // clip is right at a block boundary then prevTotal will not be available,
+      // so this is a best attempt to plot interbase indicator at the "cliffs"
+
+
+      var prevTotal = 0; // extraHorizontallyFlippedOffset is used to draw interbase items, which
+      // are located to the left when forward and right when reversed
+
+      var extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0; // Second pass: draw the SNP data, and add a minimum feature width of 1px
+      // which can be wider than the actual bpPerPx This reduces overdrawing of
+      // the grey background over the SNPs
+
+      for (var _i = 0; _i < coverage.length; _i++) {
+        var _feature = coverage[_i];
+
+        var _featureSpanPx3 = (0, _util.featureSpanPx)(_feature, region, bpPerPx),
+            _featureSpanPx4 = (0, _slicedToArray2["default"])(_featureSpanPx3, 2),
+            _leftPx = _featureSpanPx4[0],
+            _rightPx = _featureSpanPx4[1];
+
+        var _score = _feature.get('score');
+
+        var snpinfo = _feature.get('snpinfo');
+
+        var _w = Math.max(_rightPx - _leftPx + 0.3, 1);
+
+        var totalScore = snpinfo.total;
+        var keys = Object.keys(snpinfo.cov).sort();
+        var curr = 0;
+
+        for (var _i2 = 0; _i2 < keys.length; _i2++) {
+          var base = keys[_i2];
+          var total = snpinfo.cov[base].total;
+          ctx.fillStyle = colorForBase[base] || modificationTagMap[base.replace('mod_', '')] || '#888';
+
+          var _height = toHeight(_score);
+
+          var bottom = toY(_score) + _height;
+
+          ctx.fillRect(_leftPx, bottom - (total + curr) / _score * _height, _w, total / _score * _height);
+          curr += total;
+        }
+
+        var interbaseEvents = Object.keys(snpinfo.noncov);
+        var indicatorHeight = 4.5;
+
+        if (drawInterbaseCounts) {
+          var _curr = 0;
+
+          for (var _i3 = 0; _i3 < interbaseEvents.length; _i3++) {
+            var _base = interbaseEvents[_i3];
+            var _total = snpinfo.noncov[_base].total;
+            ctx.fillStyle = colorForBase[_base];
+            ctx.fillRect(_leftPx - 0.6 + extraHorizontallyFlippedOffset, indicatorHeight + indicatorToHeight(_curr), 1.2, indicatorToHeight(_total));
+            _curr += _total;
+          }
+        }
+
+        if (drawIndicators) {
+          var accum = 0;
+          var max = 0;
+          var maxBase = '';
+
+          for (var _i4 = 0; _i4 < interbaseEvents.length; _i4++) {
+            var _base2 = interbaseEvents[_i4];
+            var _total2 = snpinfo.noncov[_base2].total;
+            accum += _total2;
+
+            if (_total2 > max) {
+              max = _total2;
+              maxBase = _base2;
+            }
+          } // avoid drawing a bunch of indicators if coverage is very low e.g.
+          // less than 7, uses the prev total in the case of the "cliff"
+
+
+          var indicatorComparatorScore = Math.max(totalScore, prevTotal);
+
+          if (accum > indicatorComparatorScore * indicatorThreshold && indicatorComparatorScore > 7) {
+            ctx.fillStyle = colorForBase[maxBase];
+            ctx.beginPath();
+            var l = _leftPx + extraHorizontallyFlippedOffset;
+            ctx.moveTo(l - 3.5, 0);
+            ctx.lineTo(l + 3.5, 0);
+            ctx.lineTo(l, indicatorHeight);
+            ctx.fill();
+          }
+        }
+
+        prevTotal = totalScore;
+      }
+
+      if (drawArcs) {
+        for (var _i5 = 0; _i5 < skips.length; _i5++) {
+          var f = skips[_i5];
+
+          var _bpSpanPx = (0, _util.bpSpanPx)(f.get('start'), f.get('end'), region, bpPerPx),
+              _bpSpanPx2 = (0, _slicedToArray2["default"])(_bpSpanPx, 2),
+              left = _bpSpanPx2[0],
+              right = _bpSpanPx2[1];
+
+          ctx.beginPath();
+          var str = f.get('strand');
+          var xs = f.get('xs');
+          var pos = 'rgba(255,200,200,0.7)';
+          var neg = 'rgba(200,200,255,0.7)';
+          var neutral = 'rgba(200,200,200,0.7)';
+
+          if (xs === '+') {
+            ctx.strokeStyle = pos;
+          } else if (xs === '-') {
+            ctx.strokeStyle = neg;
+          } else if (str === 1) {
+            ctx.strokeStyle = pos;
+          } else if (str === -1) {
+            ctx.strokeStyle = neg;
+          } else {
+            ctx.strokeStyle = neutral;
+          }
+
+          ctx.lineWidth = Math.log(f.get('score') + 1);
+          ctx.moveTo(left, height - offset * 2);
+          ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2);
+          ctx.stroke();
+        }
+      }
+
+      if (displayCrossHatches) {
+        ctx.lineWidth = 1;
+        ctx.strokeStyle = 'rgba(140,140,140,0.8)';
+        ticks.values.forEach(function (tick) {
+          ctx.beginPath();
+          ctx.moveTo(0, Math.round(toY(tick)));
+          ctx.lineTo(width, Math.round(toY(tick)));
+          ctx.stroke();
+        });
+      }
+    }
+  }]);
+  return SNPCoverageRenderer;
+}(_pluginWiggle.WiggleBaseRenderer);
+
+exports["default"] = SNPCoverageRenderer;

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/SNPCoverageRenderer/configSchema.js

@@ -0,0 +1,40 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {
+  clipColor: {
+    type: 'color',
+    description: 'the color of the clipping marker',
+    defaultValue: 'red'
+  },
+  indicatorThreshold: {
+    type: 'number',
+    description: 'the proportion of reads containing a insertion/clip indicator',
+    defaultValue: 0.4
+  },
+  drawArcs: {
+    type: 'boolean',
+    description: 'Draw sashimi-style arcs for intron features',
+    defaultValue: true
+  },
+  drawInterbaseCounts: {
+    type: 'boolean',
+    description: 'draw count "upsidedown histogram" of the interbase events that don\'t contribute to the coverage count so are not drawn in the normal histogram',
+    defaultValue: true
+  },
+  drawIndicators: {
+    type: 'boolean',
+    description: 'draw a triangular indicator where an event has been detected',
+    defaultValue: true
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/SNPCoverageRenderer/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;

package/dist/SNPCoverageRenderer/index.js

@@ -0,0 +1,34 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.configSchema = void 0;
+exports["default"] = register;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _SNPCoverageRenderer = _interopRequireDefault(require("./SNPCoverageRenderer"));
+
+var _pluginWiggle = require("@jbrowse/plugin-wiggle");
+
+var configSchema = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {}, {
+  baseConfiguration: _configSchema["default"],
+  explicitlyTyped: true
+});
+exports.configSchema = configSchema;
+
+function register(pluginManager) {
+  pluginManager.addRendererType(function () {
+    return new _SNPCoverageRenderer["default"]({
+      name: 'SNPCoverageRenderer',
+      ReactComponent: _pluginWiggle.WiggleRendering,
+      configSchema: configSchema,
+      pluginManager: pluginManager
+    });
+  });
+}

package/dist/declare.d.js

@@ -0,0 +1 @@
+"use strict";

package/dist/index.d.ts

@@ -1,10 +1,10 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-import * as MismatchParser from './BamAdapter/MismatchParser';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-export { MismatchParser };
-export type { LinearPileupDisplayModel };
-export default class AlignmentsPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+import * as MismatchParser from './BamAdapter/MismatchParser';
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export { MismatchParser };
+export type { LinearPileupDisplayModel };
+export default class AlignmentsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -1,8 +1,156 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-alignments.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-alignments.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = exports.MismatchParser = void 0;
+
+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 _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var MismatchParser = _interopRequireWildcard(require("./BamAdapter/MismatchParser"));
+
+exports.MismatchParser = MismatchParser;
+
+var _CramAdapter = _interopRequireDefault(require("./CramAdapter"));
+
+var _BamAdapter = _interopRequireDefault(require("./BamAdapter"));
+
+var _HtsgetBamAdapter = _interopRequireDefault(require("./HtsgetBamAdapter"));
+
+var _SNPCoverageAdapter = _interopRequireDefault(require("./SNPCoverageAdapter"));
+
+var _SNPCoverageRenderer = _interopRequireDefault(require("./SNPCoverageRenderer"));
+
+var _PileupRenderer = _interopRequireDefault(require("./PileupRenderer"));
+
+var _LinearAlignmentsDisplay = _interopRequireDefault(require("./LinearAlignmentsDisplay"));
+
+var _LinearSNPCoverageDisplay = _interopRequireDefault(require("./LinearSNPCoverageDisplay"));
+
+var _LinearPileupDisplay = _interopRequireDefault(require("./LinearPileupDisplay"));
+
+var _AlignmentsTrack = _interopRequireDefault(require("./AlignmentsTrack"));
+
+var _AlignmentsFeatureDetail = _interopRequireDefault(require("./AlignmentsFeatureDetail"));
+
+var _rpcMethods = require("./PileupRPC/rpcMethods");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+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; }
+
+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 AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(AlignmentsPlugin, _Plugin);
+
+  var _super = _createSuper(AlignmentsPlugin);
+
+  function AlignmentsPlugin() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, AlignmentsPlugin);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'AlignmentsPlugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(AlignmentsPlugin, [{
+    key: "install",
+    value: function install(pluginManager) {
+      ;
+      [_BamAdapter["default"], _CramAdapter["default"], _LinearPileupDisplay["default"], _LinearSNPCoverageDisplay["default"], _AlignmentsTrack["default"], _SNPCoverageAdapter["default"], _HtsgetBamAdapter["default"], _PileupRenderer["default"], _SNPCoverageRenderer["default"], _LinearAlignmentsDisplay["default"], _AlignmentsFeatureDetail["default"]].map(function (f) {
+        return f(pluginManager);
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.cram$/i;
+          var adapterName = 'CramAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            cramLocation: file,
+            craiLocation: index || (0, _tracks.makeIndex)(file, '.crai')
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.bam$/i;
+          var adapterName = 'BamAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var indexName = index && (0, _tracks.getFileName)(index);
+          var obj = {
+            type: adapterName,
+            bamLocation: file,
+            index: {
+              location: index || (0, _tracks.makeIndex)(file, '.bai'),
+              indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'BAI')
+            }
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+            return 'AlignmentsTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
+      pluginManager.addRpcMethod(function () {
+        return new _rpcMethods.PileupGetGlobalValueForTag(pluginManager);
+      });
+      pluginManager.addRpcMethod(function () {
+        return new _rpcMethods.PileupGetVisibleModifications(pluginManager);
+      });
+    }
+  }]);
+  return AlignmentsPlugin;
+}(_Plugin2["default"]);
+
+exports["default"] = AlignmentsPlugin;

package/dist/index.test.js

@@ -0,0 +1,26 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
+
+var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _ = _interopRequireDefault(require("."));
+
+test('plugin in a stock JBrowse', function () {
+  console.warn = jest.fn();
+  var pluginManager = new _PluginManager["default"]([new _["default"](), new _pluginSvg["default"]()]);
+  pluginManager.createPluggableElements();
+  pluginManager.configure();
+  expect(function () {
+    return pluginManager.addPlugin(new _["default"]());
+  }).toThrow(/JBrowse already configured, cannot add plugins/);
+  var BamAdapter = pluginManager.getAdapterType('BamAdapter');
+  var config = BamAdapter.configSchema.create({
+    type: 'BamAdapter'
+  });
+  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
+});