@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearSNPCoverageDisplay/configSchema.js

@@ -4,74 +4,58 @@ 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");
-/**
- * #config LinearSNPCoverageDisplay
- *
- * extends
- * - [BaseLinearDisplay](../baselineardisplay)
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const util_1 = require("../shared/util");
+function x() { }
 function SNPCoverageConfigFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
-        /**
-         * #slot
-         */
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',
             model: mobx_state_tree_1.types.enumeration('Autoscale type', ['local']),
             description: 'performs local autoscaling (no other options for SNP Coverage available)',
         },
-        /**
-         * #slot
-         */
         minScore: {
             type: 'number',
             defaultValue: Number.MIN_VALUE,
             description: 'minimum value for the y-scale',
         },
-        /**
-         * #slot
-         */
         maxScore: {
             type: 'number',
             description: 'maximum value for the y-scale',
             defaultValue: Number.MAX_VALUE,
         },
-        /**
-         * #slot
-         */
         scaleType: {
             type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']), // todo zscale
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
             description: 'The type of scale to use',
             defaultValue: 'linear',
         },
-        /**
-         * #slot
-         */ inverted: {
+        inverted: {
             type: 'boolean',
             description: 'draw upside down',
             defaultValue: false,
         },
-        /**
-         * #slot
-         */
         multiTicks: {
             type: 'boolean',
             description: 'Display multiple values for the ticks',
             defaultValue: false,
         },
-        /**
-         * #slot
-         */
         renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
             SNPCoverageRenderer: pluginManager.getRendererType('SNPCoverageRenderer').configSchema,
         }),
+        colorBy: {
+            type: 'frozen',
+            description: 'color scheme to use',
+            defaultValue: {
+                type: 'normal',
+            },
+        },
+        filterBy: {
+            type: 'frozen',
+            description: 'default filters to use',
+            defaultValue: util_1.defaultFilterFlags,
+        },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/dist/LinearSNPCoverageDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function register(pluginManager: PluginManager): void;

package/dist/LinearSNPCoverageDisplay/index.js

@@ -4,9 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = register;
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
 function register(pluginManager) {

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -1,11 +1,6 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ColorBy, FilterBy } from '../shared/types';
-/**
- * #stateModel LinearSNPCoverageDisplay
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
+import type { ColorBy, FilterBy } from '../shared/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -18,21 +13,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -50,21 +36,15 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -118,33 +98,12 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    /**
-     * #property
-     */
-    drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    /**
-     * #property
-     */
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    /**
-     * #property
-     */
+    showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    showInterbaseIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    showArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
 }, never, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;

package/dist/LinearSNPCoverageDisplay/model.js

@@ -15,115 +15,83 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const util_1 = require("@jbrowse/core/util");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-// locals
-const util_2 = require("../util");
+const util_1 = require("@jbrowse/core/util");
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const getUniqueModifications_1 = require("../shared/getUniqueModifications");
-// lazies
+const util_2 = require("../util");
 const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
-// using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-/**
- * #stateModel LinearSNPCoverageDisplay
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-        /**
-         * #property
-         */
-        drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), {
-            flagInclude: 0,
-            flagExclude: 1540,
-        }),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
+        showInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        showInterbaseIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        showArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        filterBySetting: mobx_state_tree_1.types.frozen(),
+        colorBySetting: mobx_state_tree_1.types.frozen(),
         jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
     }))
         .volatile(() => ({
-        /**
-         * #volatile
-         */
         visibleModifications: mobx_1.observable.map({}),
-        /**
-         * #volatile
-         */
         modificationsReady: false,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setConfig(configuration) {
             self.configuration = configuration;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
-        /**
-         * #action
-         */
         setColorScheme(colorBy) {
-            self.colorBy = colorBy
+            self.colorBySetting = colorBy
                 ? {
                     ...colorBy,
                 }
                 : undefined;
         },
-        /**
-         * #action
-         */
         setJexlFilters(filters) {
             self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
         },
-        /**
-         * #action
-         */
         updateVisibleModifications(uniqueModifications) {
             for (const modification of uniqueModifications) {
                 if (!self.visibleModifications.has(modification.type)) {
@@ -138,53 +106,34 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { adapterProps: superAdapterProps } = self;
         return {
-            /**
-             * #getter
-             */
             get rendererConfig() {
                 const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-                const { drawArcs, drawInterbaseCounts, drawIndicators } = self;
+                const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
                 return self.rendererType.configSchema.create({
                     ...configBlob,
-                    drawInterbaseCounts: drawInterbaseCounts !== null && drawInterbaseCounts !== void 0 ? drawInterbaseCounts : configBlob.drawInterbaseCounts,
-                    drawIndicators: drawIndicators !== null && drawIndicators !== void 0 ? drawIndicators : configBlob.drawIndicators,
-                    drawArcs: drawArcs !== null && drawArcs !== void 0 ? drawArcs : configBlob.drawArcs,
+                    showInterbaseCounts: showInterbaseCounts !== null && showInterbaseCounts !== void 0 ? showInterbaseCounts : configBlob.showInterbaseCounts,
+                    showInterbaseIndicators: showInterbaseIndicators !== null && showInterbaseIndicators !== void 0 ? showInterbaseIndicators : configBlob.showInterbaseIndicators,
+                    showArcs: showArcs !== null && showArcs !== void 0 ? showArcs : configBlob.showArcs,
                 }, (0, mobx_state_tree_1.getEnv)(self));
             },
-            /**
-             * #getter
-             */
-            get drawArcsSetting() {
+            get showArcsSetting() {
                 var _a;
-                return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
+                return ((_a = self.showArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showArcs'));
             },
-            /**
-             * #getter
-             */
-            get drawInterbaseCountsSetting() {
+            get showInterbaseCountsSetting() {
                 var _a;
-                return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
+                return ((_a = self.showInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseCounts'));
             },
-            /**
-             * #getter
-             */
-            get drawIndicatorsSetting() {
+            get showInterbaseIndicatorsSetting() {
                 var _a;
-                return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
+                return ((_a = self.showInterbaseIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseIndicators'));
             },
-            /**
-             * #getter
-             */
             get autorunReady() {
                 const view = (0, util_1.getContainingView)(self);
                 return (view.initialized &&
-                    self.featureDensityStatsReady &&
-                    !self.regionTooLarge &&
+                    self.statsReadyAndRegionNotTooLarge &&
                     !self.error);
             },
-            /**
-             * #method
-             */
             adapterProps() {
                 const superProps = superAdapterProps();
                 const { filters, filterBy } = self;
@@ -197,29 +146,17 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         setModificationsReady(flag) {
             self.modificationsReady = flag;
         },
-        /**
-         * #action
-         */
-        toggleDrawIndicators() {
-            self.drawIndicators = !self.drawIndicatorsSetting;
+        setShowInterbaseIndicators(arg) {
+            self.showInterbaseIndicators = arg;
         },
-        /**
-         * #action
-         */
-        toggleDrawInterbaseCounts() {
-            self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
+        setShowInterbaseCounts(arg) {
+            self.showInterbaseCounts = arg;
         },
-        /**
-         * #action
-         */
-        toggleDrawArcs() {
-            self.drawArcs = !self.drawArcsSetting;
+        setShowArcs(arg) {
+            self.showArcs = arg;
         },
     }))
         .actions(self => ({
@@ -252,22 +189,13 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
         return {
-            /**
-             * #getter
-             */
             get renderReady() {
                 const superProps = superRenderProps();
                 return !superProps.notReady && self.modificationsReady;
             },
-            /**
-             * #getter
-             */
             get ready() {
                 return this.renderReady;
             },
-            /**
-             * #method
-             */
             renderProps() {
                 const { colorBy, visibleModifications } = self;
                 return {
@@ -277,15 +205,9 @@ function stateModelFactory(pluginManager, configSchema) {
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
                 };
             },
-            /**
-             * #getter
-             */
             get TooltipComponent() {
                 return Tooltip;
             },
-            /**
-             * #getter
-             */
             get adapterConfig() {
                 const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
                 return {
@@ -293,59 +215,47 @@ function stateModelFactory(pluginManager, configSchema) {
                     subadapter,
                 };
             },
-            /**
-             * #getter
-             */
             get rendererTypeName() {
                 return rendererTypes.get('snpcoverage');
             },
-            /**
-             * #getter
-             */
             get needsScalebar() {
                 return true;
             },
-            /**
-             * #method
-             */
             contextMenuItems() {
                 return [];
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
                     {
-                        label: 'Draw insertion/clipping indicators',
+                        label: 'Show insertion/clipping indicators',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawIndicatorsSetting,
+                        checked: self.showInterbaseIndicatorsSetting,
                         onClick: () => {
-                            self.toggleDrawIndicators();
+                            self.setShowInterbaseIndicators(!self.showInterbaseIndicatorsSetting);
                         },
                     },
                     {
-                        label: 'Draw insertion/clipping counts',
+                        label: 'Show insertion/clipping counts',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawInterbaseCountsSetting,
+                        checked: self.showInterbaseCountsSetting,
                         onClick: () => {
-                            self.toggleDrawInterbaseCounts();
+                            self.setShowInterbaseCounts(self.showInterbaseCountsSetting);
                         },
                     },
                     {
-                        label: 'Draw arcs',
+                        label: 'Show arcs',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawArcsSetting,
+                        checked: self.showArcsSetting,
                         onClick: () => {
-                            self.toggleDrawArcs();
+                            self.setShowArcs(self.showArcsSetting);
                         },
                     },
                 ];
             },
-            /**
-             * #getter
-             */
             get filters() {
                 return new serializableFilterChain_1.default({ filters: self.jexlFilters });
             },

package/dist/MismatchParser/cigarToMismatches.d.ts

@@ -1,3 +1,2 @@
-import { Mismatch } from '../shared/types';
-import type { Buffer } from 'buffer';
-export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
+import type { Mismatch } from '../shared/types';
+export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];

package/dist/MismatchParser/cigarToMismatches.js

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.cigarToMismatches = cigarToMismatches;
 function cigarToMismatches(ops, seq, ref, qual) {
-    let roffset = 0; // reference offset
-    let soffset = 0; // seq offset
+    let roffset = 0;
+    let soffset = 0;
     const mismatches = [];
     const hasRefAndSeq = ref && seq;
     for (let i = 0; i < ops.length; i += 2) {
@@ -12,10 +12,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
         if (op === 'M' || op === '=' || op === 'E') {
             if (hasRefAndSeq) {
                 for (let j = 0; j < len; j++) {
-                    if (
-                    // @ts-ignore in the full yarn build of the repo, this says that
-                    // object is possibly undefined for some reason, ignored
-                    seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()) {
+                    if (seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()) {
                         mismatches.push({
                             start: roffset + j,
                             type: 'mismatch',
@@ -60,7 +57,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
                 mismatches.push({
                     start: roffset + j,
                     type: 'mismatch',
-                    base: r[j],
+                    base: r[j] || 'X',
                     qual: q[j],
                     length: 1,
                 });

package/dist/MismatchParser/getNextRefPos.js

@@ -1,8 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getNextRefPos = getNextRefPos;
-// get relative reference sequence positions for positions given relative to
-// the read sequence
 function getNextRefPos(cigarOps, positions) {
     let readPos = 0;
     let refPos = 0;

package/dist/MismatchParser/index.d.ts

@@ -1,8 +1,7 @@
-import { Feature } from '@jbrowse/core/util';
-import type { Buffer } from 'buffer';
-import { Mismatch } from '../shared/types';
+import type { Mismatch } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
 export declare function parseCigar(cigar?: string): string[];
-export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
 export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
 export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
 export declare function getLengthOnRef(cigar: string): number;