@jbrowse/plugin-alignments 1.7.8 → 1.7.9

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -142,7 +142,8 @@ function SupplementaryAlignments(props) {
     return /*#__PURE__*/_react.default.createElement("li", {
       key: "".concat(locString, "-").concat(index)
     }, /*#__PURE__*/_react.default.createElement(_core.Link, {
-      onClick: function onClick() {
+      onClick: function onClick(event) {
+        event.preventDefault();
         var view = model.view;
 
         try {

package/dist/BamAdapter/MismatchParser.js

@@ -24,6 +24,7 @@ var _util = require("@jbrowse/core/util");
 var _marked = /*#__PURE__*/_regenerator.default.mark(getNextRefPos);
 
 var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
+var modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
 
 function parseCigar(cigar) {
   return (cigar || '').split(/([MIDNSHPX=])/);
@@ -351,7 +352,7 @@ function getModificationPositions(mm, fseq, fstrand) {
         skips = _mod$split2.slice(1); // regexes based on parse_mm.pl from hts-specs
 
 
-    var matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');
@@ -426,7 +427,7 @@ function getModificationTypes(mm) {
         _mod$split4 = (0, _slicedToArray2.default)(_mod$split3, 1),
         basemod = _mod$split4[0];
 
-    var matches = basemod.match(/([A-Z])([-+])([^,]+)/);
+    var matches = basemod.match(modificationRegex);
 
     if (!matches) {
       throw new Error('bad format for MM tag');

package/dist/LinearPileupDisplay/model.d.ts

@@ -233,7 +233,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     toggleSoftClipping(): void;
     toggleMismatchAlpha(): void;
     setConfig(configuration: AnyConfigurationModel): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
+    setSortedBy(type: string, tag?: string): void;
     setFilterBy(filter: {
         flagInclude: number;
         flagExclude: number;

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -305,8 +305,8 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     }): void;
     setColorBy(colorBy?: {
         type: string;
-        tag?: string | undefined;
-    } | undefined): void;
+        tag?: string;
+    }): void;
     updateModificationColorMap(uniqueModifications: string[]): void;
 } & {
     readonly rendererConfig: any;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -102,12 +102,23 @@ export default class PileupRenderer extends BoxRendererType {
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
     fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<any, any>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
         maxHeightReached: boolean;
         reactElement: JSX.Element;
+        canvasRecordedData?: undefined;
         imageData?: undefined;
         html?: string | undefined;
     } | {
@@ -116,7 +127,8 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
-        imageData: import("@jbrowse/core/util/offscreenCanvas/types").AbstractImageBitmap;
+        imageData: any;
+        canvasRecordedData?: undefined;
         reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         html?: string | undefined;
     }>;

package/dist/PileupRenderer/PileupRenderer.js

@@ -137,8 +137,8 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
     value: // get width and height of chars the height is an approximation: width
     // letter M is approximately the height
     function getCharWidthHeight(ctx) {
-      var charWidth = ctx.measureText('A').width;
-      var charHeight = ctx.measureText('M').width;
+      var charWidth = (0, _util.measureText)('A');
+      var charHeight = (0, _util.measureText)('M');
       return {
         charWidth: charWidth,
         charHeight: charHeight

package/dist/SNPCoverageRenderer/configSchema.d.ts

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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.7.8",
+  "version": "1.7.9",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "b429fa2bb5734fc8a5380988f6dfdd3f7a41a39f"
+  "gitHead": "a6504c385d703ce6e755d05652ef659ffe28c864"
 }

package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx

@@ -134,7 +134,8 @@ function SupplementaryAlignments(props: { tag: string; model: any }) {
             return (
               <li key={`${locString}-${index}`}>
                 <Link
-                  onClick={() => {
+                  onClick={event => {
+                    event.preventDefault()
                     const { view } = model
                     try {
                       if (view) {

package/src/BamAdapter/MismatchParser.ts

@@ -10,6 +10,7 @@ export interface Mismatch {
   cliplen?: number
 }
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
+const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/)
 export function parseCigar(cigar: string) {
   return (cigar || '').split(/([MIDNSHPX=])/)
 }
@@ -273,7 +274,7 @@ export function getModificationPositions(
     const [basemod, ...skips] = mod.split(',')
 
     // regexes based on parse_mm.pl from hts-specs
-    const matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/)
+    const matches = basemod.match(modificationRegex)
     if (!matches) {
       throw new Error('bad format for MM tag')
     }
@@ -328,7 +329,7 @@ export function getModificationTypes(mm: string) {
     .map(mod => {
       const [basemod] = mod.split(',')
 
-      const matches = basemod.match(/([A-Z])([-+])([^,]+)/)
+      const matches = basemod.match(modificationRegex)
       if (!matches) {
         throw new Error('bad format for MM tag')
       }

package/src/PileupRenderer/PileupRenderer.tsx

@@ -132,8 +132,8 @@ export default class PileupRenderer extends BoxRendererType {
   // get width and height of chars the height is an approximation: width
   // letter M is approximately the height
   getCharWidthHeight(ctx: CanvasRenderingContext2D) {
-    const charWidth = ctx.measureText('A').width
-    const charHeight = ctx.measureText('M').width
+    const charWidth = measureText('A')
+    const charHeight = measureText('M')
     return { charWidth, charHeight }
   }
 
@@ -1097,7 +1097,6 @@ export default class PileupRenderer extends BoxRendererType {
 
     const width = (end - start) / bpPerPx
     const height = Math.max(layout.getTotalHeight(), 1)
-
     const res = await renderToAbstractCanvas(
       width,
       height,