npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.0 → 2.4.1 - Mend

@jbrowse/plugin-alignments 2.4.0 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (112) hide show

package/dist/BamAdapter/BamAdapter.js +2 -2
package/dist/BamAdapter/BamAdapter.js.map +1 -1
package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/CramAdapter.js +2 -2
package/dist/CramAdapter/CramAdapter.js.map +1 -1
package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/dist/CramAdapter/util.js +10 -10
package/dist/CramAdapter/util.js.map +1 -1
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -3
package/dist/LinearAlignmentsDisplay/models/model.js +3 -4
package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/dist/LinearPileupDisplay/index.d.ts +2 -3
package/dist/LinearPileupDisplay/index.js +4 -2
package/dist/LinearPileupDisplay/index.js.map +1 -1
package/dist/LinearPileupDisplay/model.d.ts +7 -9
package/dist/LinearPileupDisplay/model.js +4 -4
package/dist/LinearPileupDisplay/model.js.map +1 -1
package/dist/LinearReadArcsDisplay/model.d.ts +2 -2
package/dist/LinearReadCloudDisplay/model.d.ts +2 -2
package/dist/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
package/dist/MismatchParser/index.js +4 -6
package/dist/MismatchParser/index.js.map +1 -1
package/dist/NestedFrequencyTable.js +3 -13
package/dist/NestedFrequencyTable.js.map +1 -1
package/dist/PileupRPC/rpcMethods.d.ts +3 -4
package/dist/PileupRPC/rpcMethods.js +6 -6
package/dist/PileupRPC/rpcMethods.js.map +1 -1
package/dist/PileupRenderer/PileupRenderer.d.ts +6 -4
package/dist/PileupRenderer/PileupRenderer.js +30 -34
package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
package/dist/PileupRenderer/components/PileupRendering.js +2 -2
package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
package/dist/PileupRenderer/configSchema.js +1 -1
package/dist/PileupRenderer/configSchema.js.map +1 -1
package/dist/PileupRenderer/sortUtil.js +5 -4
package/dist/PileupRenderer/sortUtil.js.map +1 -1
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/dist/index.d.ts +3 -5
package/dist/index.js +6 -6
package/dist/index.js.map +1 -1
package/esm/BamAdapter/BamAdapter.js +2 -2
package/esm/BamAdapter/BamAdapter.js.map +1 -1
package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
package/esm/CramAdapter/CramAdapter.js +2 -2
package/esm/CramAdapter/CramAdapter.js.map +1 -1
package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
package/esm/CramAdapter/util.js +10 -10
package/esm/CramAdapter/util.js.map +1 -1
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -3
package/esm/LinearAlignmentsDisplay/models/model.js +3 -4
package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
package/esm/LinearPileupDisplay/index.d.ts +2 -3
package/esm/LinearPileupDisplay/index.js +2 -1
package/esm/LinearPileupDisplay/index.js.map +1 -1
package/esm/LinearPileupDisplay/model.d.ts +7 -9
package/esm/LinearPileupDisplay/model.js +4 -4
package/esm/LinearPileupDisplay/model.js.map +1 -1
package/esm/LinearReadArcsDisplay/model.d.ts +2 -2
package/esm/LinearReadCloudDisplay/model.d.ts +2 -2
package/esm/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
package/esm/MismatchParser/index.js +4 -6
package/esm/MismatchParser/index.js.map +1 -1
package/esm/NestedFrequencyTable.js +3 -13
package/esm/NestedFrequencyTable.js.map +1 -1
package/esm/PileupRPC/rpcMethods.d.ts +3 -4
package/esm/PileupRPC/rpcMethods.js +3 -4
package/esm/PileupRPC/rpcMethods.js.map +1 -1
package/esm/PileupRenderer/PileupRenderer.d.ts +6 -4
package/esm/PileupRenderer/PileupRenderer.js +30 -34
package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
package/esm/PileupRenderer/components/PileupRendering.js +2 -2
package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
package/esm/PileupRenderer/configSchema.js +1 -1
package/esm/PileupRenderer/configSchema.js.map +1 -1
package/esm/PileupRenderer/sortUtil.js +5 -4
package/esm/PileupRenderer/sortUtil.js.map +1 -1
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
package/esm/index.d.ts +3 -5
package/esm/index.js +3 -3
package/esm/index.js.map +1 -1
package/package.json +2 -2
package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
package/src/BamAdapter/BamAdapter.ts +2 -2
package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
package/src/CramAdapter/CramAdapter.ts +2 -2
package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
package/src/CramAdapter/util.ts +10 -10
package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +2 -2
package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
package/src/LinearAlignmentsDisplay/models/model.tsx +3 -4
package/src/LinearPileupDisplay/index.ts +2 -4
package/src/LinearPileupDisplay/model.ts +4 -4
package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
package/src/MismatchParser/index.ts +3 -5
package/src/NestedFrequencyTable.ts +3 -11
package/src/PileupRPC/rpcMethods.ts +3 -9
package/src/PileupRenderer/PileupRenderer.ts +47 -61
package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
package/src/PileupRenderer/configSchema.ts +1 -1
package/src/PileupRenderer/sortUtil.ts +5 -4
package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
package/src/index.ts +5 -10

package/esm/LinearAlignmentsDisplay/models/model.js CHANGED Viewed

@@ -9,9 +9,9 @@ const minDisplayHeight = 20;
 function getLowerPanelDisplays(pluginManager) {
     return (pluginManager
         .getDisplayElements()
-        // @ts-ignore
+        // @ts-expect-error
         .filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
-        // @ts-ignore
+        // @ts-expect-error
         .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
 }
 function deepSnap(x1, x2) {
@@ -49,7 +49,6 @@ function AlignmentsModel(pluginManager, configSchema) {
          * #property
          * refers to LinearPileupDisplay sub-display model
          */
-        // @ts-ignore
         PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)),
         /**
          * #property
@@ -297,7 +296,7 @@ function stateModelFactory(pluginManager, configSchema) {
         if (!snap) {
             return snap;
         }
-        // @ts-ignore
+        // @ts-expect-error
         const { height, ...rest } = snap;
         return { heightPreConfig: height, ...rest };
     });

package/esm/LinearAlignmentsDisplay/models/model.js.map CHANGED Viewed

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package/esm/LinearPileupDisplay/index.d.ts CHANGED Viewed

@@ -1,5 +1,4 @@
-import configSchemaFactory from './configSchema';
-import modelFactory from './model';
 import PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;
-export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
+export { default as linearPileupDisplayStateModelFactory } from './model';
+export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';

package/esm/LinearPileupDisplay/index.js CHANGED Viewed

@@ -17,5 +17,6 @@ export default function register(pluginManager) {
         });
     });
 }
-export { modelFactory as linearPileupDisplayStateModelFactory, configSchemaFactory as linearPileupDisplayConfigSchemaFactory, };
+export { default as linearPileupDisplayStateModelFactory } from './model';
+export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
 //# sourceMappingURL=index.js.map

package/esm/LinearPileupDisplay/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,oCAAoC,EAAE,MAAM,SAAS,CAAA;AACzE,OAAO,EAAE,OAAO,IAAI,sCAAsC,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/LinearPileupDisplay/model.d.ts CHANGED Viewed

@@ -157,7 +157,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -187,7 +187,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
     updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -206,9 +206,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     reload(): Promise<void>;
     afterAttach(): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features"; /**
-     * #action
-     */
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
@@ -470,7 +468,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            features: Map<string, Feature>;
+            features: Map<string, Feature>; /**
+             * #getter
+             */
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -486,9 +486,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     id: string;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
-    userBpPerPxLimit: number | undefined; /**
-     * #method
-     */
+    userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
 export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;

package/esm/LinearPileupDisplay/model.js CHANGED Viewed

@@ -208,7 +208,7 @@ function stateModelFactory(configSchema) {
                     if (sortedBy) {
                         const { pos, refName, assemblyName } = sortedBy;
                         // render just the sorted region first
-                        // @ts-ignore
+                        // @ts-expect-error
                         await self.rendererType.renderInClient(rpcManager, {
                             assemblyName,
                             regions: [
@@ -263,9 +263,9 @@ function stateModelFactory(configSchema) {
                             // feature.id that was returned e.g. that the user hasn't
                             // moused over to a new position during the async operation
                             // above
-                            // @ts-ignore
+                            // @ts-expect-error
                             if (self.featureIdUnderMouse === feature.uniqueId) {
-                                // @ts-ignore
+                                // @ts-expect-error
                                 self.setFeatureUnderMouse(new SimpleFeature(feature));
                             }
                         }
@@ -493,7 +493,7 @@ function stateModelFactory(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (feature) {
-                                    // @ts-ignore
+                                    // @ts-expect-error
                                     self.selectFeature(new SimpleFeature(feature));
                                 }
                             }

package/esm/LinearPileupDisplay/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearReadArcsDisplay/model.d.ts CHANGED Viewed

@@ -156,7 +156,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -186,7 +186,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
     updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;

package/esm/LinearReadCloudDisplay/model.d.ts CHANGED Viewed

@@ -163,7 +163,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -193,7 +193,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
     updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;

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

@@ -175,7 +175,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: any;
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -205,7 +205,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;
-    setHeight(displayHeight: number): any;
+    setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
     updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;

package/esm/MismatchParser/index.js CHANGED Viewed

@@ -278,18 +278,17 @@ export function getModificationTypes(mm) {
     const mods = mm.split(';');
     return mods
         .filter(mod => !!mod)
-        .map(mod => {
+        .flatMap(mod => {
         const [basemod] = mod.split(',');
         const matches = basemod.match(modificationRegex);
         if (!matches) {
             throw new Error(`bad format for MM tag: ${mm}`);
         }
-        const [, , , typestr] = matches;
+        const typestr = matches[3];
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
         // split, and they can also be chemical codes (ChEBI) e.g. C+16061
         return typestr.split(/(\d+|.)/).filter(f => !!f);
-    })
-        .flat();
+    });
 }
 export function getOrientedCigar(flip, cigar) {
     if (flip) {
@@ -303,8 +302,7 @@ export function getOrientedCigar(flip, cigar) {
             else if (op === 'I') {
                 op = 'D';
             }
-            ret.push(len);
-            ret.push(op);
+            ret.push(len, op);
         }
         return ret;
     }

package/esm/MismatchParser/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/NestedFrequencyTable.js CHANGED Viewed

@@ -20,12 +20,7 @@ export default class NestedFrequencyTable {
         if (!amount) {
             amount = 1;
         }
-        if (!slotName) {
-            slotName = 'default';
-        }
-        else {
-            slotName = slotName.toString();
-        }
+        slotName = slotName ? slotName.toString() : 'default';
         if (this.categories[slotName]) {
             this.categories[slotName] = Math.max(0, this.categories[slotName] - amount);
             return this.categories[slotName];
@@ -37,12 +32,7 @@ export default class NestedFrequencyTable {
         if (!amount) {
             amount = 1;
         }
-        if (!slotName) {
-            slotName = 'default';
-        }
-        else {
-            slotName = slotName.toString();
-        }
+        slotName = slotName ? slotName.toString() : 'default';
         this.categories[slotName] = (this.categories[slotName] || 0) + amount;
         return this.categories[slotName];
     }
@@ -56,7 +46,7 @@ export default class NestedFrequencyTable {
         if (typeof path === 'string') {
             path = path.split('/');
         }
-        if (!path.length) {
+        if (path.length === 0) {
             return this;
         }
         const slotName = path[0].toString();

package/esm/NestedFrequencyTable.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/PileupRPC/rpcMethods.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-import PileupGetReducedFeatures from './methods/GetReducedFeatures';
-import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
-import PileupGetVisibleModifications from './methods/GetVisibleModifications';
-export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
+export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
+export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
+export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';

package/esm/PileupRPC/rpcMethods.js CHANGED Viewed

@@ -1,5 +1,4 @@
-import PileupGetReducedFeatures from './methods/GetReducedFeatures';
-import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
-import PileupGetVisibleModifications from './methods/GetVisibleModifications';
-export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
+export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
+export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
+export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';
 //# sourceMappingURL=rpcMethods.js.map

package/esm/PileupRPC/rpcMethods.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/PileupRenderer/PileupRenderer.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { Theme } from '@mui/material/styles';
-import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Region, Feature } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
@@ -100,7 +100,7 @@ export default class PileupRenderer extends BoxRendererType {
         canvasWidth: number;
     }): void;
     drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
         feat: LayoutFeature;
         renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -110,8 +110,9 @@ export default class PileupRenderer extends BoxRendererType {
         charHeight: number;
         defaultColor: boolean;
         canvasWidth: number;
+        theme: Theme;
     }): void;
-    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
+    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, theme, }: {
         ctx: CanvasRenderingContext2D;
         feat: LayoutFeature;
         renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -129,6 +130,7 @@ export default class PileupRenderer extends BoxRendererType {
         charWidth: number;
         charHeight: number;
         canvasWidth: number;
+        theme: Theme;
     }): void;
     drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
         ctx: CanvasRenderingContext2D;
@@ -175,4 +177,4 @@ export default class PileupRenderer extends BoxRendererType {
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+export { type RenderArgs, type RenderResults, type RenderArgsSerialized, type ResultsSerialized, type ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';