@jbrowse/plugin-alignments 2.12.0 → 2.12.2

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SNPCoverageConfigFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -75,4 +76,3 @@ function SNPCoverageConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-exports.default = SNPCoverageConfigFactory;

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

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import PluginManager from '@jbrowse/core/PluginManager';
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 /**
@@ -34,7 +33,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
@@ -45,12 +44,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode; /**
-                 * #property
-                 */
-                filled?: boolean | undefined;
-                status?: string | undefined;
-                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+                message: import("react").ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: import("react").ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -61,7 +58,7 @@ 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;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -92,14 +89,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             description: string;
             defaultValue: string;
             contextVariable: string[];
-        }; /**
-         * #property
-         */
+        };
         jexlFilters: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: never[];
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
@@ -146,9 +139,7 @@ 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>>; /**
-         * #property
-         */
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         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/dist/MismatchParser/index.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import { Feature } from '@jbrowse/core/util';
 export interface Mismatch {
     qual?: number;

package/dist/MismatchParser/index.js

@@ -1,6 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.featurizeSA = exports.getTag = exports.getClip = exports.getLengthSansClipping = exports.getLength = exports.getLengthOnRef = exports.getOrientedMismatches = exports.getOrientedCigar = exports.getModificationTypes = exports.getModificationPositions = exports.getMethBins = exports.getModificationProbabilities = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
+exports.parseCigar = parseCigar;
+exports.cigarToMismatches = cigarToMismatches;
+exports.mdToMismatches = mdToMismatches;
+exports.getMismatches = getMismatches;
+exports.getNextRefPos = getNextRefPos;
+exports.getModificationProbabilities = getModificationProbabilities;
+exports.getMethBins = getMethBins;
+exports.getModificationPositions = getModificationPositions;
+exports.getModificationTypes = getModificationTypes;
+exports.getOrientedCigar = getOrientedCigar;
+exports.getOrientedMismatches = getOrientedMismatches;
+exports.getLengthOnRef = getLengthOnRef;
+exports.getLength = getLength;
+exports.getLengthSansClipping = getLengthSansClipping;
+exports.getClip = getClip;
+exports.getTag = getTag;
+exports.featurizeSA = featurizeSA;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("../util");
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
@@ -11,7 +27,6 @@ const endClip = new RegExp(/^(\d+)([SH])/);
 function parseCigar(cigar = '') {
     return cigar.split(cigarRegex).slice(0, -1);
 }
-exports.parseCigar = parseCigar;
 function cigarToMismatches(ops, seq, ref, qual) {
     let roffset = 0; // reference offset
     let soffset = 0; // seq offset
@@ -102,7 +117,6 @@ function cigarToMismatches(ops, seq, ref, qual) {
     }
     return mismatches;
 }
-exports.cigarToMismatches = cigarToMismatches;
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the
  * reference @returns array of mismatches and their positions
@@ -184,7 +198,6 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
     }
     return mismatchRecords;
 }
-exports.mdToMismatches = mdToMismatches;
 function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];
     const ops = parseCigar(cigar);
@@ -198,7 +211,6 @@ function getMismatches(cigar, md, seq, ref, qual) {
     }
     return mismatches;
 }
-exports.getMismatches = getMismatches;
 // get relative reference sequence positions for positions given relative to
 // the read sequence
 function* getNextRefPos(cigarOps, positions) {
@@ -231,7 +243,6 @@ function* getNextRefPos(cigarOps, positions) {
         }
     }
 }
-exports.getNextRefPos = getNextRefPos;
 function getModificationProbabilities(feature) {
     var _a;
     const m = (0, util_2.getTagAlt)(feature, 'ML', 'Ml') || [];
@@ -239,7 +250,6 @@ function getModificationProbabilities(feature) {
         ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
         : (_a = (0, util_2.getTagAlt)(feature, 'MP', 'Mp')) === null || _a === void 0 ? void 0 : _a.split('').map(s => s.charCodeAt(0) - 33).map(elt => Math.min(1, elt / 50));
 }
-exports.getModificationProbabilities = getModificationProbabilities;
 function getMethBins(feature) {
     const fstart = feature.get('start');
     const fend = feature.get('end');
@@ -269,7 +279,6 @@ function getMethBins(feature) {
     }
     return { methBins, methProbs };
 }
-exports.getMethBins = getMethBins;
 function getModificationPositions(mm, fseq, fstrand) {
     const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
     const mods = mm.split(';').filter(mod => !!mod);
@@ -319,7 +328,6 @@ function getModificationPositions(mm, fseq, fstrand) {
     }
     return result;
 }
-exports.getModificationPositions = getModificationPositions;
 function getModificationTypes(mm) {
     return mm
         .split(';')
@@ -336,7 +344,6 @@ function getModificationTypes(mm) {
         return typestr.split(/(\d+|.)/).filter(f => !!f);
     });
 }
-exports.getModificationTypes = getModificationTypes;
 function getOrientedCigar(flip, cigar) {
     if (flip) {
         const ret = [];
@@ -357,12 +364,10 @@ function getOrientedCigar(flip, cigar) {
         return cigar;
     }
 }
-exports.getOrientedCigar = getOrientedCigar;
 function getOrientedMismatches(flip, cigar) {
     const p = parseCigar(cigar);
     return cigarToMismatches(flip ? getOrientedCigar(flip, p) : p);
 }
-exports.getOrientedMismatches = getOrientedMismatches;
 function getLengthOnRef(cigar) {
     const cigarOps = parseCigar(cigar);
     let lengthOnRef = 0;
@@ -375,7 +380,6 @@ function getLengthOnRef(cigar) {
     }
     return lengthOnRef;
 }
-exports.getLengthOnRef = getLengthOnRef;
 function getLength(cigar) {
     const cigarOps = parseCigar(cigar);
     let length = 0;
@@ -388,7 +392,6 @@ function getLength(cigar) {
     }
     return length;
 }
-exports.getLength = getLength;
 function getLengthSansClipping(cigar) {
     const cigarOps = parseCigar(cigar);
     let length = 0;
@@ -401,18 +404,15 @@ function getLengthSansClipping(cigar) {
     }
     return length;
 }
-exports.getLengthSansClipping = getLengthSansClipping;
 function getClip(cigar, strand) {
     return strand === -1
         ? +(cigar.match(startClip) || [])[1] || 0
         : +(cigar.match(endClip) || [])[1] || 0;
 }
-exports.getClip = getClip;
 function getTag(f, tag) {
     const tags = f.get('tags');
     return tags ? tags[tag] : f.get(tag);
 }
-exports.getTag = getTag;
 // produces a list of "feature-like" object from parsing supplementary
 // alignments in the SA tag
 //
@@ -445,4 +445,3 @@ function featurizeSA(SA, id, strand, readName, normalize) {
         };
     })) || []);
 }
-exports.featurizeSA = featurizeSA;

package/dist/PileupRPC/index.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = PileupRPCMethodsF;
 const rpcMethods_1 = require("./rpcMethods");
 function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
 }
-exports.default = PileupRPCMethodsF;

package/dist/PileupRPC/util.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.filterForPairs = exports.getInsertSizeStats = void 0;
+exports.getInsertSizeStats = getInsertSizeStats;
+exports.filterForPairs = filterForPairs;
 function getInsertSizeStats(features) {
     const filtered = features.map(f => Math.abs(f.tlen));
     const sum = filtered.reduce((a, b) => a + b, 0);
@@ -12,8 +13,6 @@ function getInsertSizeStats(features) {
     const lower = avg - 3 * sd;
     return { upper, lower, avg, sd };
 }
-exports.getInsertSizeStats = getInsertSizeStats;
 function filterForPairs(features) {
     return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
 }
-exports.filterForPairs = filterForPairs;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Feature, Region } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
@@ -42,8 +41,8 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         canvasRecordedData: any;
-        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        html?: string | undefined;
+        reactElement?: import("react").ReactElement;
+        html?: string;
     } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
@@ -51,7 +50,7 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         reactElement: import("react").JSX.Element;
-        html?: string | undefined;
+        html?: string;
     } | {
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
@@ -59,8 +58,8 @@ export default class PileupRenderer extends BoxRendererType {
         width: number;
         maxHeightReached: boolean;
         imageData: any;
-        reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        html?: string | undefined;
+        reactElement?: import("react").ReactElement;
+        html?: string;
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }

package/dist/PileupRenderer/colorBy.js

@@ -1,6 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.colorByStrandedRnaSeq = exports.colorByOrientation = exports.colorByStrand = exports.colorByMappingQuality = exports.colorByInsertSize = void 0;
+exports.colorByInsertSize = colorByInsertSize;
+exports.colorByMappingQuality = colorByMappingQuality;
+exports.colorByStrand = colorByStrand;
+exports.colorByOrientation = colorByOrientation;
+exports.colorByStrandedRnaSeq = colorByStrandedRnaSeq;
 const configuration_1 = require("@jbrowse/core/configuration");
 const color_1 = require("../shared/color");
 const util_1 = require("../util");
@@ -10,11 +14,9 @@ function colorByInsertSize(feature) {
         ? '#555'
         : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`;
 }
-exports.colorByInsertSize = colorByInsertSize;
 function colorByMappingQuality(feature) {
     return `hsl(${feature.get('score')},50%,50%)`;
 }
-exports.colorByMappingQuality = colorByMappingQuality;
 function getOrientation(feature, config) {
     const orientationType = (0, configuration_1.readConfObject)(config, 'orientationType');
     const type = util_1.orientationTypes[orientationType];
@@ -29,11 +31,9 @@ function getOrientation(feature, config) {
 function colorByStrand(feature) {
     return feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B';
 }
-exports.colorByStrand = colorByStrand;
 function colorByOrientation(feature, config) {
     return color_1.fillColor[getOrientation(feature, config) || 'color_nostrand'];
 }
-exports.colorByOrientation = colorByOrientation;
 function getStranded(feature) {
     const flags = feature.get('flags');
     const strand = feature.get('strand');
@@ -67,4 +67,3 @@ function getStranded(feature) {
 function colorByStrandedRnaSeq(feature) {
     return color_1.fillColor[getStranded(feature)];
 }
-exports.colorByStrandedRnaSeq = colorByStrandedRnaSeq;

package/dist/PileupRenderer/getAlignmentShapeColor.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getAlignmentShapeColor = void 0;
+exports.getAlignmentShapeColor = getAlignmentShapeColor;
 const configuration_1 = require("@jbrowse/core/configuration");
 const color_1 = require("../shared/color");
 const colorBy_1 = require("./colorBy");
@@ -56,4 +56,3 @@ function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor,
                 : (0, configuration_1.readConfObject)(config, 'color', { feature });
     }
 }
-exports.getAlignmentShapeColor = getAlignmentShapeColor;

package/dist/PileupRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = register;
 const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
@@ -17,4 +18,3 @@ function register(pluginManager) {
         });
     });
 }
-exports.default = register;

package/dist/PileupRenderer/layoutFeature.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.layoutFeature = void 0;
+exports.layoutFeature = layoutFeature;
 const util_1 = require("@jbrowse/core/util");
 function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }) {
     let expansionBefore = 0;
@@ -36,4 +36,3 @@ function layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightP
         heightPx,
     };
 }
-exports.layoutFeature = layoutFeature;

package/dist/PileupRenderer/layoutFeatures.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.layoutFeats = void 0;
+exports.layoutFeats = layoutFeats;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 // locals
@@ -31,4 +31,3 @@ function layoutFeats(props) {
         displayMode,
     }), featureMap.size);
 }
-exports.layoutFeats = layoutFeats;

package/dist/PileupRenderer/makeImageData.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeImageData = void 0;
+exports.makeImageData = makeImageData;
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("./util");
@@ -60,4 +60,3 @@ function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
         }
     }
 }
-exports.makeImageData = makeImageData;

package/dist/PileupRenderer/renderAlignment.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderAlignment = void 0;
+exports.renderAlignment = renderAlignment;
 const getAlignmentShapeColor_1 = require("./getAlignmentShapeColor");
 const renderAlignmentShape_1 = require("./renderAlignmentShape");
 const renderPerBaseQuality_1 = require("./renderPerBaseQuality");
@@ -68,4 +68,3 @@ function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase,
             break;
     }
 }
-exports.renderAlignment = renderAlignment;

package/dist/PileupRenderer/renderAlignmentShape.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderAlignmentShape = void 0;
+exports.renderAlignmentShape = renderAlignmentShape;
 const util_1 = require("@jbrowse/core/util");
 function renderAlignmentShape({ ctx, feat, renderArgs, }) {
     const { regions, bpPerPx } = renderArgs;
@@ -37,4 +37,3 @@ function renderAlignmentShape({ ctx, feat, renderArgs, }) {
         ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
     }
 }
-exports.renderAlignmentShape = renderAlignmentShape;

package/dist/PileupRenderer/renderMethylation.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderMethylation = void 0;
+exports.renderMethylation = renderMethylation;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
@@ -54,4 +54,3 @@ function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth
         }
     }
 }
-exports.renderMethylation = renderMethylation;

package/dist/PileupRenderer/renderMismatches.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderMismatches = void 0;
+exports.renderMismatches = renderMismatches;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./util");
 const colord_1 = require("@jbrowse/core/util/colord");
@@ -128,4 +128,3 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
         }
     }
 }
-exports.renderMismatches = renderMismatches;

package/dist/PileupRenderer/renderModifications.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderModifications = void 0;
+exports.renderModifications = renderModifications;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("../util");
@@ -46,4 +46,3 @@ function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWid
         }
     }
 }
-exports.renderModifications = renderModifications;

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseLettering = void 0;
+exports.renderPerBaseLettering = renderPerBaseLettering;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
@@ -43,4 +43,3 @@ function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, cont
         }
     }
 }
-exports.renderPerBaseLettering = renderPerBaseLettering;

package/dist/PileupRenderer/renderPerBaseQuality.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderPerBaseQuality = void 0;
+exports.renderPerBaseQuality = renderPerBaseQuality;
 const util_1 = require("@jbrowse/core/util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("./util");
@@ -35,4 +35,3 @@ function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
         }
     }
 }
-exports.renderPerBaseQuality = renderPerBaseQuality;

package/dist/PileupRenderer/renderSoftClipping.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSoftClipping = void 0;
+exports.renderSoftClipping = renderSoftClipping;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 // locals
@@ -61,4 +61,3 @@ function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase
         }
     }
 }
-exports.renderSoftClipping = renderSoftClipping;

package/dist/PileupRenderer/util.js

@@ -1,6 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getCharWidthHeight = exports.shouldDrawIndels = exports.shouldDrawSNPsMuted = exports.getContrastBaseMap = exports.getColorBaseMap = exports.fillRect = void 0;
+exports.fillRect = fillRect;
+exports.getColorBaseMap = getColorBaseMap;
+exports.getContrastBaseMap = getContrastBaseMap;
+exports.shouldDrawSNPsMuted = shouldDrawSNPsMuted;
+exports.shouldDrawIndels = shouldDrawIndels;
+exports.getCharWidthHeight = getCharWidthHeight;
 const util_1 = require("@jbrowse/core/util");
 function fillRect(ctx, l, t, w, h, cw, color) {
     if (l + w < 0 || l > cw) {
@@ -13,7 +18,6 @@ function fillRect(ctx, l, t, w, h, cw, color) {
         ctx.fillRect(l, t, w, h);
     }
 }
-exports.fillRect = fillRect;
 function getColorBaseMap(theme) {
     const { bases } = theme.palette;
     return {
@@ -24,22 +28,18 @@ function getColorBaseMap(theme) {
         deletion: '#808080', // gray
     };
 }
-exports.getColorBaseMap = getColorBaseMap;
 function getContrastBaseMap(theme) {
     return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
         key,
         theme.palette.getContrastText(value),
     ]));
 }
-exports.getContrastBaseMap = getContrastBaseMap;
 function shouldDrawSNPsMuted(type) {
     return ['methylation', 'modifications'].includes(type || '');
 }
-exports.shouldDrawSNPsMuted = shouldDrawSNPsMuted;
 function shouldDrawIndels() {
     return true;
 }
-exports.shouldDrawIndels = shouldDrawIndels;
 // get width and height of chars the height is an approximation: width letter M
 // is approximately the height
 function getCharWidthHeight() {
@@ -47,4 +47,3 @@ function getCharWidthHeight() {
     const charHeight = (0, util_1.measureText)('M') - 2;
     return { charWidth, charHeight };
 }
-exports.getCharWidthHeight = getCharWidthHeight;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = generateCoverageBins;
 const util_1 = require("../util");
 const MismatchParser_1 = require("../MismatchParser");
 const util_2 = require("@jbrowse/core/util");
@@ -208,4 +209,3 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
     }
     return { bins, skipmap };
 }
-exports.default = generateCoverageBins;

package/dist/SNPCoverageAdapter/index.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SNPCoverageAdapterF;
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function SNPCoverageAdapterF(pluginManager) {
@@ -41,4 +42,3 @@ function SNPCoverageAdapterF(pluginManager) {
         });
     });
 }
-exports.default = SNPCoverageAdapterF;

package/dist/SNPCoverageRenderer/index.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = register;
 const configSchema_1 = __importDefault(require("./configSchema"));
 const SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
@@ -14,4 +15,3 @@ function register(pluginManager) {
         pluginManager,
     }));
 }
-exports.default = register;

package/dist/shared/afterAttach.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.doAfterAttach = void 0;
+exports.doAfterAttach = doAfterAttach;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("../util");
 const fetchChains_1 = require("./fetchChains");
@@ -40,4 +40,3 @@ function doAfterAttach(self, cb) {
         draw(view);
     }, { delay: 1000 });
 }
-exports.doAfterAttach = doAfterAttach;

package/dist/shared/color.js

@@ -1,6 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ColorByModel = exports.getPairedOrientationColor = exports.getPairedInsertSizeAndOrientationColor = exports.getPairedInsertSizeColor = exports.strokeColor = exports.fillColor = void 0;
+exports.ColorByModel = exports.strokeColor = exports.fillColor = void 0;
+exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
+exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
+exports.getPairedOrientationColor = getPairedOrientationColor;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../util");
 exports.fillColor = {
@@ -61,11 +64,9 @@ function getPairedInsertSizeColor(f1, f2, stats) {
     }
     return undefined;
 }
-exports.getPairedInsertSizeColor = getPairedInsertSizeColor;
 function getPairedInsertSizeAndOrientationColor(f1, f2, stats) {
     return (getPairedInsertSizeColor(f1, f2, stats) || getPairedOrientationColor(f1));
 }
-exports.getPairedInsertSizeAndOrientationColor = getPairedInsertSizeAndOrientationColor;
 function getPairedOrientationColor(f) {
     const type = util_1.orientationTypes.fr;
     const type2 = util_1.pairMap[type[f.pair_orientation || '']];
@@ -74,7 +75,6 @@ function getPairedOrientationColor(f) {
         exports.strokeColor[type2] || exports.strokeColor.color_unknown,
     ];
 }
-exports.getPairedOrientationColor = getPairedOrientationColor;
 exports.ColorByModel = mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({
     type: mobx_state_tree_1.types.string,
     tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),