@jbrowse/plugin-alignments 2.4.2 → 2.6.0

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

@@ -11,6 +11,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -47,7 +51,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>; /**
+             * #getter
+             */
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -57,11 +63,33 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            /**
+             * #getter
+             */
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -73,13 +101,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
-     * #action
-     */
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
         min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    configuration: AnyConfigurationSchemaType;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
     /**
      * #property
@@ -119,6 +148,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -128,6 +158,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             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]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -135,6 +166,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -143,14 +175,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined; /**
-             * #getter
-             */
+            rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            rendererTypeName: string;
             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]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -158,6 +187,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -167,21 +197,49 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    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;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -195,49 +253,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    setMessage(message: string): void;
 } & {
-    afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
 } & {
-    afterAttach(): void;
-} & {
-    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(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     message: string | undefined;
     stats: {
@@ -246,7 +277,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | undefined;
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -267,25 +298,25 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     toggleCrossHatches(): void;
     setCrossHatches(cross: boolean): void;
 } & {
-    readonly TooltipComponent: import("react").FC<{}>;
     readonly adapterTypeName: any;
     readonly rendererTypeNameSimple: any;
-    readonly rendererTypeName: string;
     readonly filters: undefined;
     readonly scaleType: any;
     readonly maxScore: any;
     readonly minScore: any;
 } & {
+    readonly adapterCapabilities: string[];
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+    readonly autoscaleType: any;
 } & {
-    readonly filled: any;
-    readonly summaryScoreModeSetting: any;
     readonly domain: number[] | undefined;
-    readonly needsScalebar: boolean;
+} & {
+    readonly filled: boolean;
+    readonly summaryScoreModeSetting: string;
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
@@ -297,8 +328,36 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         inverted: any;
     };
     readonly canHaveFill: boolean;
-    readonly autoscaleType: any;
-    readonly displayCrossHatchesSetting: any;
+    readonly displayCrossHatchesSetting: boolean;
+    readonly hasResolution: boolean;
+    readonly hasGlobalStats: boolean;
+} & {
+    scoreTrackMenuItems(): ({
+        label: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+    } | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+    } | {
+        label: string;
+        onClick: () => void;
+        subMenu?: undefined;
+    })[];
+} & {
+    reload(): Promise<void>;
+} & {
+    readonly TooltipComponent: import("react").FC<{}>;
+    readonly rendererTypeName: string;
 } & {
     readonly ticks: {
         range: number[];
@@ -306,14 +365,38 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         format: (d: import("d3-scale").NumberValue) => string;
         position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
     } | undefined;
-    readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
-    readonly hasResolution: boolean;
-    readonly hasGlobalStats: boolean;
+    readonly needsScalebar: boolean;
     readonly fillSetting: 0 | 1 | 2;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: ({
+            label: string;
+            subMenu: {
+                label: string;
+                onClick: () => void;
+            }[];
+            onClick?: undefined;
+        } | {
+            label: string;
+            subMenu: {
+                label: string;
+                type: string;
+                checked: boolean;
+                onClick: () => void;
+            }[];
+            onClick?: undefined;
+        } | {
+            label: string;
+            onClick: () => void;
+            subMenu?: undefined;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
         label: string;
         subMenu: {
             label: string;
@@ -327,19 +410,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | {
         type: string;
         label: string;
-        checked: any;
+        checked: boolean;
         onClick: () => void;
         subMenu?: undefined;
     })[];
 } & {
-    reload(): Promise<void>;
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
 } & {
-    modificationTagMap: Record<string, string> | undefined;
+    modificationTagMap: import("mobx").ObservableMap<string, string>;
+    modificationsReady: boolean;
 } & {
     /**
      * #action
@@ -392,12 +472,18 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly modificationsReady: boolean;
+    readonly autorunReady: boolean;
+    readonly renderReady: boolean;
+    readonly ready: boolean;
     /**
      * #method
      */
     renderProps(): any;
 } & {
+    /**
+     * #action
+     */
+    setModificationsReady(flag: boolean): void;
     /**
      * #action
      */
@@ -410,6 +496,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      * #action
      */
     toggleDrawArcs(): void;
+} & {
     afterAttach(): void;
 } & {
     /**
@@ -423,7 +510,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];
         clientRect?: DOMRect | undefined;
-    }) => JSX.Element | null;
+    }) => import("react").JSX.Element | null;
     /**
      * #getter
      */

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -1,12 +1,13 @@
-import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree';
-import clone from 'clone';
-import { autorun } from 'mobx';
+import { types, cast, getEnv, getSnapshot, isAlive } from 'mobx-state-tree';
+import { observable } from 'mobx';
 import { getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
 import { getContainingView } from '@jbrowse/core/util';
 // locals
 import Tooltip from '../components/Tooltip';
 import { FilterModel, getUniqueModificationValues } from '../../shared';
+import { createAutorun, modificationColors } from '../../util';
+import { randomColor } from '../../util';
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
 /**
@@ -45,7 +46,8 @@ function stateModelFactory(pluginManager, configSchema) {
         })),
     }))
         .volatile(() => ({
-        modificationTagMap: undefined,
+        modificationTagMap: observable.map({}),
+        modificationsReady: false,
     }))
         .actions(self => ({
         /**
@@ -70,16 +72,11 @@ function stateModelFactory(pluginManager, configSchema) {
          * #action
          */
         updateModificationColorMap(uniqueModifications) {
-            const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
-            let i = 0;
-            const newMap = clone(self.modificationTagMap) || {};
             uniqueModifications.forEach(value => {
-                if (!newMap[value]) {
-                    const newColor = colorPalette[i++];
-                    newMap[value] = newColor;
+                if (!self.modificationTagMap.has(value)) {
+                    self.modificationTagMap.set(value, modificationColors[value] || randomColor());
                 }
             });
-            self.modificationTagMap = newMap;
         },
     }))
         .views(self => {
@@ -122,11 +119,19 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #getter
              */
-            get modificationsReady() {
-                var _a;
-                return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
-                    ? self.modificationTagMap !== undefined
-                    : true;
+            get autorunReady() {
+                const view = getContainingView(self);
+                return (view.initialized &&
+                    self.featureDensityStatsReady &&
+                    !self.regionTooLarge &&
+                    !self.error);
+            },
+            get renderReady() {
+                const superProps = superRenderProps();
+                return !superProps.notReady && self.modificationsReady;
+            },
+            get ready() {
+                return this.renderReady;
             },
             /**
              * #method
@@ -136,8 +141,8 @@ function stateModelFactory(pluginManager, configSchema) {
                 const { colorBy, filterBy, modificationTagMap } = self;
                 return {
                     ...superProps,
-                    notReady: superProps.notReady || !this.modificationsReady,
-                    modificationTagMap: modificationTagMap,
+                    notReady: !this.ready,
+                    modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
                     // must use getSnapshot because otherwise changes to e.g. just the
                     // colorBy.type are not read
                     colorBy: colorBy ? getSnapshot(colorBy) : undefined,
@@ -147,6 +152,12 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => ({
+        /**
+         * #action
+         */
+        setModificationsReady(flag) {
+            self.modificationsReady = flag;
+        },
         /**
          * #action
          */
@@ -165,27 +176,29 @@ function stateModelFactory(pluginManager, configSchema) {
         toggleDrawArcs() {
             self.drawArcs = !self.drawArcsSetting;
         },
+    }))
+        .actions(self => ({
         afterAttach() {
-            addDisposer(self, autorun(async () => {
-                try {
-                    const { colorBy } = self;
-                    const view = getContainingView(self);
-                    if (!view.initialized ||
-                        !self.estimatedStatsReady ||
-                        self.regionTooLarge) {
-                        return;
-                    }
-                    const { staticBlocks } = view;
-                    if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                        const adapter = getConf(self.parentTrack, 'adapter');
-                        self.updateModificationColorMap(await getUniqueModificationValues(self, adapter, colorBy, staticBlocks));
+            createAutorun(self, async () => {
+                self.setModificationsReady(false);
+                if (!self.autorunReady) {
+                    return;
+                }
+                const view = getContainingView(self);
+                const { staticBlocks } = view;
+                const { colorBy } = self;
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    const adapter = getConf(self.parentTrack, 'adapter');
+                    const vals = await getUniqueModificationValues(self, adapter, colorBy, staticBlocks);
+                    if (isAlive(self)) {
+                        self.updateModificationColorMap(vals);
+                        self.setModificationsReady(true);
                     }
                 }
-                catch (error) {
-                    console.error(error);
-                    self.setError(error);
+                else {
+                    self.setModificationsReady(true);
                 }
-            }, { delay: 1000 }));
+            }, { delay: 1000 });
         },
     }))
         .views(self => {

package/esm/LinearSNPCoverageDisplay/models/model.js.map

@@ -1 +1 @@
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package/esm/MismatchParser/index.d.ts

@@ -13,12 +13,17 @@ export interface Mismatch {
 export declare function parseCigar(cigar?: string): string[];
 export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
- * parse a SAM MD tag to find mismatching bases of the template versus the reference
- * @returns array of mismatches and their positions
+ * parse a SAM MD tag to find mismatching bases of the template versus the
+ * reference @returns array of mismatches and their positions
  */
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
 export declare function getMismatches(cigar: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
+export declare function getModificationProbabilities(feature: Feature): number[] | undefined;
+export declare function getMethBins(feature: Feature): {
+    methBins: number[];
+    methProbs: number[];
+};
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): {
     type: string;
     positions: number[];