@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,34 +1,34 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-export declare class PileupGetGlobalValueForTag extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
-export declare class PileupGetVisibleModifications extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util/types';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+export declare class PileupGetGlobalValueForTag extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}
+export declare class PileupGetVisibleModifications extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}

package/dist/PileupRPC/rpcMethods.js

@@ -41,37 +41,37 @@ var _util2 = require("../util");
 
 var _MismatchParser = require("../BamAdapter/MismatchParser");
 
-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 _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; } }
 
 var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
-  (0, _inherits2["default"])(PileupGetGlobalValueForTag, _RpcMethodType);
+  (0, _inherits2.default)(PileupGetGlobalValueForTag, _RpcMethodType);
 
   var _super = _createSuper(PileupGetGlobalValueForTag);
 
   function PileupGetGlobalValueForTag() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, PileupGetGlobalValueForTag);
+    (0, _classCallCheck2.default)(this, PileupGetGlobalValueForTag);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'PileupGetGlobalValueForTag');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'PileupGetGlobalValueForTag');
     return _this;
   }
 
-  (0, _createClass2["default"])(PileupGetGlobalValueForTag, [{
+  (0, _createClass2.default)(PileupGetGlobalValueForTag, [{
     key: "serializeArguments",
     value: function () {
-      var _serializeArguments = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, rpcDriverClassName) {
+      var _serializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, rpcDriverClassName) {
         var _rootModel$session;
 
         var rootModel, assemblyManager, renamedArgs;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -91,7 +91,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
 
               case 6:
                 renamedArgs = _context.sent;
-                return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+                return _context.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
 
               case 8:
               case "end":
@@ -110,9 +110,9 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
   }, {
     key: "execute",
     value: function () {
-      var _execute = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(args, rpcDriverClassName) {
+      var _execute = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args, rpcDriverClassName) {
         var deserializedArgs, adapterConfig, sessionId, regions, tag, dataAdapter, features, featuresArray, uniqueValues;
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -142,7 +142,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
                     uniqueValues.add("".concat(val));
                   }
                 });
-                return _context2.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+                return _context2.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
 
               case 14:
               case "end":
@@ -160,37 +160,37 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
     }()
   }]);
   return PileupGetGlobalValueForTag;
-}(_RpcMethodType3["default"]);
+}(_RpcMethodType3.default);
 
 exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
 
 var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
-  (0, _inherits2["default"])(PileupGetVisibleModifications, _RpcMethodType2);
+  (0, _inherits2.default)(PileupGetVisibleModifications, _RpcMethodType2);
 
   var _super2 = _createSuper(PileupGetVisibleModifications);
 
   function PileupGetVisibleModifications() {
     var _this2;
 
-    (0, _classCallCheck2["default"])(this, PileupGetVisibleModifications);
+    (0, _classCallCheck2.default)(this, PileupGetVisibleModifications);
 
     for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
       args[_key2] = arguments[_key2];
     }
 
     _this2 = _super2.call.apply(_super2, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'PileupGetVisibleModifications');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "name", 'PileupGetVisibleModifications');
     return _this2;
   }
 
-  (0, _createClass2["default"])(PileupGetVisibleModifications, [{
+  (0, _createClass2.default)(PileupGetVisibleModifications, [{
     key: "serializeArguments",
     value: function () {
-      var _serializeArguments2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(args, rpcDriverClassName) {
+      var _serializeArguments2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(args, rpcDriverClassName) {
         var _rootModel$session2;
 
         var rootModel, assemblyManager, renamedArgs;
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -210,7 +210,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
 
               case 6:
                 renamedArgs = _context3.sent;
-                return _context3.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+                return _context3.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
 
               case 8:
               case "end":
@@ -229,9 +229,9 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
   }, {
     key: "execute",
     value: function () {
-      var _execute2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(args, rpcDriverClassName) {
+      var _execute2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(args, rpcDriverClassName) {
         var deserializedArgs, adapterConfig, sessionId, regions, dataAdapter, features, featuresArray, uniqueValues;
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
@@ -262,7 +262,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
                     });
                   }
                 });
-                return _context4.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+                return _context4.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
 
               case 14:
               case "end":
@@ -280,6 +280,6 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
     }()
   }]);
   return PileupGetVisibleModifications;
-}(_RpcMethodType3["default"]);
+}(_RpcMethodType3.default);
 
 exports.PileupGetVisibleModifications = PileupGetVisibleModifications;

package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,29 +1,29 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
-export interface PileupLayoutSessionProps {
-    config: AnyConfigurationModel;
-    bpPerPx: number;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: unknown;
-}
-declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
-interface CachedPileupLayout {
-    layout: MyMultiLayout;
-    config: AnyConfigurationModel;
-    filters: SerializableFilterChain;
-    sortedBy: unknown;
-    showSoftClip: boolean;
-}
-export declare class PileupLayoutSession extends LayoutSession {
-    sortedBy: unknown;
-    showSoftClip: boolean;
-    constructor(args: PileupLayoutSessionProps);
-    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
-    cachedLayout: CachedPileupLayout | undefined;
-    get layout(): MyMultiLayout;
-}
-export {};
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+export interface PileupLayoutSessionProps {
+    config: AnyConfigurationModel;
+    bpPerPx: number;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: unknown;
+}
+declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+interface CachedPileupLayout {
+    layout: MyMultiLayout;
+    config: AnyConfigurationModel;
+    filters: SerializableFilterChain;
+    sortedBy: unknown;
+    showSoftClip: boolean;
+}
+export declare class PileupLayoutSession extends LayoutSession {
+    sortedBy: unknown;
+    showSoftClip: boolean;
+    constructor(args: PileupLayoutSessionProps);
+    cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
+    cachedLayout: CachedPileupLayout | undefined;
+    get layout(): MyMultiLayout;
+}
+export {};

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -29,33 +29,33 @@ var _BoxRendererType = require("@jbrowse/core/pluggableElementTypes/renderers/Bo
 
 var _configuration = require("@jbrowse/core/configuration");
 
-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 _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; } }
 
 // Sorting and revealing soft clip changes the layout of Pileup renderer
 // Adds extra conditions to see if cached layout is valid
 var PileupLayoutSession = /*#__PURE__*/function (_LayoutSession) {
-  (0, _inherits2["default"])(PileupLayoutSession, _LayoutSession);
+  (0, _inherits2.default)(PileupLayoutSession, _LayoutSession);
 
   var _super = _createSuper(PileupLayoutSession);
 
   function PileupLayoutSession(args) {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, PileupLayoutSession);
+    (0, _classCallCheck2.default)(this, PileupLayoutSession);
     _this = _super.call(this, args);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "sortedBy", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "showSoftClip", false);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cachedLayout", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "sortedBy", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "showSoftClip", false);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cachedLayout", void 0);
     _this.config = args.config;
     return _this;
   }
 
-  (0, _createClass2["default"])(PileupLayoutSession, [{
+  (0, _createClass2.default)(PileupLayoutSession, [{
     key: "cachedLayoutIsValid",
     value: function cachedLayoutIsValid(cachedLayout) {
-      return (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual["default"])(this.sortedBy, cachedLayout.sortedBy);
+      return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual.default)(this.sortedBy, cachedLayout.sortedBy);
     }
   }, {
     key: "layout",

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,125 +1,125 @@
-/// <reference types="react" />
-import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Theme } from '@material-ui/core';
-import { Region, Feature } from '@jbrowse/core/util';
-import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
-export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-    colorTagMap?: Record<string, string>;
-    modificationTagMap?: Record<string, string>;
-    sortedBy?: {
-        type: string;
-        pos: number;
-        refName: string;
-        assemblyName: string;
-        tag?: string;
-    };
-    showSoftClip: boolean;
-    highResolutionScaling: number;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    layout: BaseLayout<Feature>;
-    regionSequence?: string;
-}
-interface LayoutRecord {
-    feature: Feature;
-    leftPx: number;
-    rightPx: number;
-    topPx: number;
-    heightPx: number;
-}
-interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
-export default class PileupRenderer extends BoxRendererType {
-    supportsSVG: boolean;
-    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
-        charWidth: number;
-        charHeight: number;
-    };
-    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
-        feature: Feature;
-        layout: BaseLayout<Feature>;
-        bpPerPx: number;
-        region: Region;
-        showSoftClip?: boolean;
-        heightPx: number;
-        displayMode: string;
-    }): LayoutRecord | null;
-    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
-        start: number;
-        end: number;
-        refName: string;
-        assemblyName: string;
-        reversed?: boolean | undefined;
-    };
-    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
-    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
-    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
-    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
-    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-        defaultColor: boolean;
-    }): void;
-    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
-        colorForBase: {
-            [key: string]: string;
-        };
-        contrastForBase: {
-            [key: string]: string;
-        };
-        mismatchAlpha?: boolean;
-        drawSNPs?: boolean;
-        drawIndels?: boolean;
-        minSubfeatureWidth: number;
-        largeInsertionIndicatorScale: number;
-        charWidth: number;
-        charHeight: number;
-    }): void;
-    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
-    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
-    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
-    render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        reactElement: any;
-        imageData?: undefined;
-        html?: string | undefined;
-    } | {
-        features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
-        height: number;
-        width: number;
-        maxHeightReached: boolean;
-        imageData: any;
-        reactElement?: import("react").ReactElement<any, string | ((props: any) => import("react").ReactElement<any, any> | null) | (new (props: any) => import("react").Component<any, any, any>)> | undefined;
-        html?: string | undefined;
-    }>;
-    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
-}
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
+/// <reference types="react" />
+import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import { Theme } from '@material-ui/core';
+import { Region, Feature } from '@jbrowse/core/util';
+import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    colorBy?: {
+        type: string;
+        tag?: string;
+    };
+    colorTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string>;
+    sortedBy?: {
+        type: string;
+        pos: number;
+        refName: string;
+        assemblyName: string;
+        tag?: string;
+    };
+    showSoftClip: boolean;
+    highResolutionScaling: number;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    layout: BaseLayout<Feature>;
+    regionSequence?: string;
+}
+interface LayoutRecord {
+    feature: Feature;
+    leftPx: number;
+    rightPx: number;
+    topPx: number;
+    heightPx: number;
+}
+interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export default class PileupRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    getCharWidthHeight(ctx: CanvasRenderingContext2D): {
+        charWidth: number;
+        charHeight: number;
+    };
+    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+        feature: Feature;
+        layout: BaseLayout<Feature>;
+        bpPerPx: number;
+        region: Region;
+        showSoftClip?: boolean;
+        heightPx: number;
+        displayMode: string;
+    }): LayoutRecord | null;
+    getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
+        start: number;
+        end: number;
+        refName: string;
+        assemblyName: string;
+        reversed?: boolean | undefined;
+    };
+    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
+    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
+    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
+    colorByPerBaseLettering(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    colorByPerBaseQuality(ctx: CanvasRenderingContext2D, feat: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number): void;
+    colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
+    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
+        colorForBase: Record<string, string>;
+        contrastForBase: Record<string, string>;
+        charWidth: number;
+        charHeight: number;
+        defaultColor: boolean;
+    }): void;
+    drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, opts: {
+        colorForBase: {
+            [key: string]: string;
+        };
+        contrastForBase: {
+            [key: string]: string;
+        };
+        mismatchAlpha?: boolean;
+        drawSNPs?: boolean;
+        drawIndels?: boolean;
+        minSubfeatureWidth: number;
+        largeInsertionIndicatorScale: number;
+        charWidth: number;
+        charHeight: number;
+    }): void;
+    drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
+    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
+    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        reactElement: JSX.Element;
+        imageData?: undefined;
+        html?: string | undefined;
+    } | {
+        features: Map<string, Feature>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
+        height: number;
+        width: number;
+        maxHeightReached: boolean;
+        imageData: import("@jbrowse/core/util/offscreenCanvas/types").AbstractImageBitmap;
+        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        html?: string | undefined;
+    }>;
+    createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };