@jbrowse/plugin-alignments 2.9.0 → 2.10.1

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -5,7 +5,11 @@ import { IFilter } from '../shared';
 import { ChainData } from '../shared/fetchChains';
 /**
  * #stateModel LinearReadCloudDisplay
- * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
+ * it is not a block based track, hence not BaseLinearDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
+ * - [TrackHeightMixin](../trackheightmixin)
+ * - [FeatureDensityMixin](../featuredensitymixin)
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -51,11 +55,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }, {
-            rendererTypeName: string; /**
+            /**
              * #property
              */
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -72,11 +77,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #action
-             * internal, a reference to a HTMLCanvas because we use a autorun to draw
-             * the canvas
-             */
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -105,9 +106,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     setScrollTop(scrollTop: number): void;
     setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number; /**
-     * #property
-     */
+    resizeHeight(distance: number): number;
 } & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
@@ -124,15 +123,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void; /**
-     * #method
-     */
+    setFeatureDensityStatsP(arg: any): void;
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    /**
+     * #method
+     */
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
 } & {

package/esm/LinearReadCloudDisplay/model.js

@@ -13,7 +13,11 @@ import { FilterModel } from '../shared';
 const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
 /**
  * #stateModel LinearReadCloudDisplay
- * extends `BaseDisplay`, it is not a block based track, hence not BaseLinearDisplay
+ * it is not a block based track, hence not BaseLinearDisplay
+ * extends
+ * - [BaseDisplay](../basedisplay)
+ * - [TrackHeightMixin](../trackheightmixin)
+ * - [FeatureDensityMixin](../featuredensitymixin)
  */
 function stateModelFactory(configSchema) {
     return types

package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -62,15 +62,14 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
         defaultValue: number;
     };
     fetchSizeLimit: {
-        /**
-         * #slot
-         */
         type: string;
         defaultValue: number;
         description: string;
     };
     height: {
-        type: string;
+        type: string; /**
+         * #slot
+         */
         defaultValue: number;
         description: string;
     };

package/esm/LinearSNPCoverageDisplay/models/configSchema.js

@@ -3,6 +3,9 @@ import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-vie
 import { types } from 'mobx-state-tree';
 /**
  * #config LinearSNPCoverageDisplay
+ *
+ * extends
+ * - [BaseLinearDisplay](../baselineardisplay)
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export default function SNPCoverageConfigFactory(pluginManager) {

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

@@ -3,7 +3,8 @@ import PluginManager from '@jbrowse/core/PluginManager';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
  * #stateModel LinearSNPCoverageDisplay
- * extends `LinearWiggleDisplay`
+ * extends
+ * - [LinearWiggleDisplay](../linearwiggledisplay)
  */
 declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -19,9 +20,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
             refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property
-             */
+            start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
@@ -37,9 +36,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any; /**
-         * #property
-         */
+        layout: any;
         status: string;
         error: unknown;
         message: string | undefined;
@@ -85,9 +82,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             type: string;
             description: string;
             defaultValue: string;
-            contextVariable: string[]; /**
-             * #property
-             */
+            contextVariable: string[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
@@ -133,7 +128,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>; /**
+         * #property
+         */
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
             value: import("mobx-state-tree").ISimpleType<string>;

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -13,7 +13,8 @@ import { randomColor } from '../../util';
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
 /**
  * #stateModel LinearSNPCoverageDisplay
- * extends `LinearWiggleDisplay`
+ * extends
+ * - [LinearWiggleDisplay](../linearwiggledisplay)
  */
 function stateModelFactory(pluginManager, configSchema) {
     return types

package/esm/PileupRenderer/PileupRenderer.js

@@ -1,12 +1,11 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { notEmpty, renderToAbstractCanvas, } from '@jbrowse/core/util';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { PileupLayoutSession, } from './PileupLayoutSession';
 // locals
 import { fetchSequence, shouldFetchReferenceSequence } from '../util';
 import { layoutFeats } from './layoutFeatures';
-import { makeImageData } from './makeImageData';
-import { readConfObject } from '@jbrowse/core/configuration';
 export default class PileupRenderer extends BoxRendererType {
     constructor() {
         super(...arguments);
@@ -53,6 +52,7 @@ export default class PileupRenderer extends BoxRendererType {
             : undefined;
         const width = (region.end - region.start) / bpPerPx;
         const height = Math.max(layout.getTotalHeight(), 1);
+        const { makeImageData } = await import('./makeImageData');
         const res = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
             ctx,
             layoutRecords: layoutRecords.filter(notEmpty),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.9.0",
+  "version": "2.10.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@gmod/bam": "^2.0.0",
-    "@gmod/cram": "^1.7.1",
+    "@gmod/cram": "^2.0.0",
     "@mui/icons-material": "^5.0.1",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
+  "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
 }