@jbrowse/plugin-variants 1.7.11 → 2.1.0

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap

@@ -2,84 +2,76 @@
 
 exports[`VariantTrack widget renders with just the required model elements 1`] = `
 <div
-  class="MuiPaper-root MuiPaper-elevation1 MuiPaper-rounded"
+  class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 css-1ps6pg7-MuiPaper-root"
   data-testid="variant-side-drawer"
 >
   <div
-    class="MuiPaper-root MuiAccordion-root MuiAccordion-expanded MuiAccordion-rounded MuiPaper-elevation1 MuiPaper-rounded"
+    class="MuiPaper-root MuiPaper-elevation MuiPaper-rounded MuiPaper-elevation1 MuiAccordion-root MuiAccordion-rounded Mui-expanded MuiAccordion-gutters css-1elwnq4-MuiPaper-root-MuiAccordion-root"
   >
     <div
-      aria-disabled="false"
       aria-expanded="true"
-      class="MuiButtonBase-root MuiAccordionSummary-root MuiAccordionSummary-expanded"
+      class="MuiButtonBase-root MuiAccordionSummary-root Mui-expanded MuiAccordionSummary-gutters css-sh22l5-MuiButtonBase-root-MuiAccordionSummary-root"
       role="button"
       tabindex="0"
     >
       <div
-        class="MuiAccordionSummary-content MuiAccordionSummary-expanded"
+        class="MuiAccordionSummary-content Mui-expanded MuiAccordionSummary-contentGutters css-o4b71y-MuiAccordionSummary-content"
       >
         <span
-          class="MuiTypography-root MuiTypography-button"
+          class="MuiTypography-root MuiTypography-button css-1f0on15-MuiTypography-root"
         >
            
           rs123
         </span>
       </div>
       <div
-        aria-disabled="false"
-        aria-hidden="true"
-        class="MuiButtonBase-root MuiIconButton-root MuiAccordionSummary-expandIcon MuiAccordionSummary-expanded MuiIconButton-edgeEnd"
+        class="MuiAccordionSummary-expandIconWrapper Mui-expanded css-yw020d-MuiAccordionSummary-expandIconWrapper"
       >
-        <span
-          class="MuiIconButton-label"
+        <svg
+          aria-hidden="true"
+          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium tss-rb1zhf-expandIcon css-i4bv87-MuiSvgIcon-root"
+          data-testid="ExpandMoreIcon"
+          focusable="false"
+          viewBox="0 0 24 24"
         >
-          <svg
-            aria-hidden="true"
-            class="MuiSvgIcon-root makeStyles-expandIcon"
-            focusable="false"
-            viewBox="0 0 24 24"
-          >
-            <path
-              d="M16.59 8.59L12 13.17 7.41 8.59 6 10l6 6 6-6z"
-            />
-          </svg>
-        </span>
-        <span
-          class="MuiTouchRipple-root"
-        />
+          <path
+            d="M16.59 8.59 12 13.17 7.41 8.59 6 10l6 6 6-6z"
+          />
+        </svg>
       </div>
     </div>
     <div
-      class="MuiCollapse-root MuiCollapse-entered"
+      class="MuiCollapse-root MuiCollapse-vertical MuiCollapse-entered css-pwcg7p-MuiCollapse-root"
       style="min-height: 0px;"
     >
       <div
-        class="MuiCollapse-wrapper"
+        class="MuiCollapse-wrapper MuiCollapse-vertical css-smkl36-MuiCollapse-wrapper"
       >
         <div
-          class="MuiCollapse-wrapperInner"
+          class="MuiCollapse-wrapperInner MuiCollapse-vertical css-9l5vo-MuiCollapse-wrapperInner"
         >
           <div
+            class="MuiAccordion-region"
             role="region"
           >
             <div
-              class="MuiAccordionDetails-root makeStyles-expansionPanelDetails"
+              class="MuiAccordionDetails-root tss-1g973hk-expansionPanelDetails css-15v22id-MuiAccordionDetails-root"
             >
               <p
-                class="MuiTypography-root MuiTypography-body1"
+                class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
               >
                 Core details
               </p>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldName"
+                  class="tss-1y9c7n2-fieldName"
                 >
                   Position
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     ctgA:177..177 
@@ -87,15 +79,15 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldName"
+                  class="tss-1y9c7n2-fieldName"
                 >
                   Name
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     rs123
@@ -103,15 +95,15 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldName"
+                  class="tss-1y9c7n2-fieldName"
                 >
                   Length
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     1
@@ -119,24 +111,25 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <hr
-                class="MuiDivider-root"
+                class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
               />
               <p
-                class="MuiTypography-root MuiTypography-body1"
+                class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
               >
                 Attributes
               </p>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldDescription makeStyles-fieldName"
-                  title="reference base(s): Each base must be one of A,C,G,T,N (case insensitive)."
+                  aria-label="reference base(s): Each base must be one of A,C,G,T,N (case insensitive)."
+                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  data-mui-internal-clone-element="true"
                 >
                   REF
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     A
@@ -144,16 +137,17 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldDescription makeStyles-fieldName"
-                  title="alternate base(s): Comma-separated list of alternate non-reference alleles"
+                  aria-label="alternate base(s): Comma-separated list of alternate non-reference alleles"
+                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  data-mui-internal-clone-element="true"
                 >
                   ALT
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     &lt;TRA&gt;
@@ -161,16 +155,17 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldDescription makeStyles-fieldName"
-                  title="quality: Phred-scaled quality score for the assertion made in ALT"
+                  aria-label="quality: Phred-scaled quality score for the assertion made in ALT"
+                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  data-mui-internal-clone-element="true"
                 >
                   QUAL
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     10.4
@@ -178,16 +173,16 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="makeStyles-field"
+                class="tss-1m8nxnb-field"
               >
                 <div
-                  class="makeStyles-fieldName"
+                  class="tss-1y9c7n2-fieldName"
                   style="width: 62px;"
                 >
                   INFO.MQ
                 </div>
                 <div
-                  class="makeStyles-fieldValue"
+                  class="tss-1omt041-fieldValue"
                 >
                   <div>
                     5
@@ -201,7 +196,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
     </div>
   </div>
   <hr
-    class="MuiDivider-root"
+    class="MuiDivider-root MuiDivider-fullWidth css-9mgopn-MuiDivider-root"
   />
 </div>
 `;

package/src/VcfTabixAdapter/VcfFeature.ts

@@ -106,7 +106,7 @@ export default class VCFFeature implements Feature {
     alt: string[],
   ): [string, string] | [undefined, undefined] {
     // it's just a remark if there are no alternate alleles
-    if (!alt || alt === []) {
+    if (!alt || alt.length === 0) {
       return ['remark', 'no alternative alleles']
     }
 

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -118,9 +118,6 @@ export default class extends BaseFeatureDataAdapter {
     regions: Region[],
     opts: BaseOptions = {},
   ) {
-    // TODO: restore commented version below once TSDX supports Rollup v2
-    // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
-    const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions
     return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {
       const { vcf } = await this.configure()
 
@@ -138,10 +135,7 @@ export default class extends BaseFeatureDataAdapter {
           `getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,
         )
       }
-      superGetFeaturesInMultipleRegions
-        .call(this, regions, opts)
-        .subscribe(observer)
-      // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
+      super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
     })
   }
 

package/dist/LinearVariantDisplay/configSchema.test.js

@@ -1,92 +0,0 @@
-"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 _BoxRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
-
-var _Plugin3 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _PileupRenderer = _interopRequireDefault(require("@jbrowse/plugin-alignments/src/PileupRenderer"));
-
-var _SvgFeatureRenderer = require("@jbrowse/plugin-svg/src/SvgFeatureRenderer");
-
-var _configSchema = 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: _SvgFeatureRenderer.ReactComponent,
-          configSchema: _SvgFeatureRenderer.configSchema,
-          pluginManager: pluginManager
-        });
-      });
-    }
-  }]);
-  return SvgFeatureRendererPlugin;
-}(_Plugin3.default);
-
-test('has a viewType attr', function () {
-  var configSchema = (0, _configSchema.LinearVariantDisplayConfigFactory)(new _PluginManager.default([new PileupRendererPlugin(), new SvgFeatureRendererPlugin()]).createPluggableElements().configure());
-  var config = configSchema.create({
-    type: 'LinearVariantDisplay',
-    displayId: 'diplayId0',
-    name: 'Zonker Display'
-  });
-  expect(config.type).toEqual('LinearVariantDisplay');
-});

package/dist/VariantFeatureWidget/VariantFeatureWidget.test.js

@@ -1,56 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _ = require(".");
-
-var _VariantFeatureWidget = _interopRequireDefault(require("./VariantFeatureWidget"));
-
-describe('VariantTrack widget', function () {
-  it('renders with just the required model elements', function () {
-    console.warn = jest.fn();
-    var pluginManager = new _PluginManager.default([]);
-
-    var Session = _mobxStateTree.types.model({
-      rpcManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-      pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-      configuration: (0, _configuration.ConfigurationSchema)('test', {}),
-      widget: (0, _.stateModelFactory)(pluginManager)
-    });
-
-    var model = Session.create({
-      widget: {
-        type: 'VariantFeatureWidget'
-      }
-    });
-    model.widget.setFeatureData({
-      refName: 'ctgA',
-      start: 176,
-      end: 177,
-      name: 'rs123',
-      REF: 'A',
-      ALT: ['<TRA>'],
-      QUAL: 10.4,
-      INFO: {
-        MQ: 5
-      }
-    });
-
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_VariantFeatureWidget.default, {
-      model: model.widget
-    })),
-        container = _render.container;
-
-    expect(container.firstChild).toMatchSnapshot();
-  });
-});

package/dist/VcfAdapter/VcfAdapter.test.js

@@ -1,55 +0,0 @@
-"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 _VcfAdapter = _interopRequireDefault(require("./VcfAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var _webEncoding = require("web-encoding");
-
-window.TextDecoder = _webEncoding.TextDecoder;
-test('adapter can fetch variants from volvox.vcf', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, names, featuresArray;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _VcfAdapter.default(_configSchema.default.create({
-            vcfLocation: {
-              localPath: require.resolve('./test_data/volvox.filtered.vcf'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 4;
-          return adapter.getRefNames();
-
-        case 4:
-          names = _context.sent;
-          expect(names).toMatchSnapshot();
-          _context.next = 8;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 8:
-          featuresArray = _context.sent;
-          expect(featuresArray.slice(0, 5)).toMatchSnapshot();
-
-        case 10:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/VcfTabixAdapter/VcfFeature.test.js

@@ -1,106 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _vcf = _interopRequireDefault(require("@gmod/vcf"));
-
-var _VcfFeature = _interopRequireDefault(require("./VcfFeature"));
-
-test('test usage of the VcfFeature', function () {
-  var parser = new _vcf.default({
-    header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-  });
-  var line = "lcl|Scaffald_1\t80465\trs118266897\tR\tA\t29\tPASS\tNS=3;0,14;AF=0.5;DB;112;PG2.1";
-  var variant = parser.parseLine(line);
-  var f = new _VcfFeature.default({
-    parser: parser,
-    variant: variant,
-    id: 'myuniqueid'
-  });
-  expect(f.id()).toEqual('myuniqueid');
-  expect(f.get('name')).toEqual('rs118266897');
-});
-test('try INS feature with END less than start', function () {
-  var parser = new _vcf.default({
-    header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-  });
-  var line = "chr1\t100\trs123\tR\tA\t29\tPASS\tEND=1;SVTYPE=INS";
-  var variant = parser.parseLine(line);
-  var f = new _VcfFeature.default({
-    parser: parser,
-    variant: variant,
-    id: 'myuniqueid'
-  });
-  expect(f.id()).toEqual('myuniqueid');
-  expect(f.get('start')).toEqual(99);
-  expect(f.get('end')).toEqual(100);
-});
-test('try DEL feature with END info field valid', function () {
-  var parser = new _vcf.default({
-    header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-  });
-  var line = "chr1\t100\trs123\tR\t<DEL>\t29\tPASS\tEND=1000;SVTYPE=DEL";
-  var variant = parser.parseLine(line);
-  var f = new _VcfFeature.default({
-    parser: parser,
-    variant: variant,
-    id: 'myuniqueid'
-  });
-  expect(f.id()).toEqual('myuniqueid');
-  expect(f.get('start')).toEqual(99);
-  expect(f.get('end')).toEqual(1000);
-});
-describe('test SV description', function () {
-  it('multiple SVs', function () {
-    var parser = new _vcf.default({
-      header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-    });
-    var line = "chr1\t100\trs123\tR\t<INVDUP>,<INV>\t29\tPASS\tEND=1000;SVTYPE=DEL";
-    var variant = parser.parseLine(line);
-    var f = new _VcfFeature.default({
-      parser: parser,
-      variant: variant,
-      id: 'myuniqueid'
-    });
-    expect(f.get('description')).toEqual('<INVDUP>,<INV>');
-  });
-  it('BND', function () {
-    var parser = new _vcf.default({
-      header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-    });
-    var line = "chr1\t100\trs123\tR\tG[ctgA:34200[\t29\tPASS\tEND=1000;SVTYPE=BND";
-    var variant = parser.parseLine(line);
-    var f = new _VcfFeature.default({
-      parser: parser,
-      variant: variant,
-      id: 'myuniqueid'
-    });
-    expect(f.get('description')).toEqual('G[ctgA:34200[');
-  });
-  it('multiple BND', function () {
-    var parser = new _vcf.default({
-      header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-    });
-    var line = "chr1\t100\trs123\tR\tG[ctgA:34200[,G[ctgA:44200[\t29\tPASS\tEND=1000;SVTYPE=BND";
-    var variant = parser.parseLine(line);
-    var f = new _VcfFeature.default({
-      parser: parser,
-      variant: variant,
-      id: 'myuniqueid'
-    });
-    expect(f.get('description')).toEqual('G[ctgA:34200[,G[ctgA:44200[');
-  });
-  it('multiple SNV', function () {
-    var parser = new _vcf.default({
-      header: "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam"
-    });
-    var line = "chr1\t100\trs123\tG\tA,C\t29\tPASS\tHELLO=world";
-    var variant = parser.parseLine(line);
-    var f = new _VcfFeature.default({
-      parser: parser,
-      variant: variant,
-      id: 'myuniqueid'
-    });
-    expect(f.get('description')).toEqual('SNV G -> A,C');
-  });
-});