@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/dist/CramAdapter/util.js

@@ -26,7 +26,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
         }
         refPos = p - 1 - start;
         if (code === 'X') {
-            // substitution
             mismatches[j++] = {
                 start: refPos,
                 length: 1,
@@ -37,7 +36,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'I') {
-            // insertion
             mismatches[j++] = {
                 start: refPos,
                 type: 'insertion',
@@ -46,7 +44,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'N') {
-            // reference skip
             mismatches[j++] = {
                 type: 'skip',
                 length: data,
@@ -55,7 +52,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'S') {
-            // soft clip
             const len = data.length;
             mismatches[j++] = {
                 start: refPos,
@@ -66,10 +62,8 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'P') {
-            // padding
         }
         else if (code === 'H') {
-            // hard clip
             const len = data;
             mismatches[j++] = {
                 start: refPos,
@@ -80,7 +74,6 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'D') {
-            // deletion
             mismatches[j++] = {
                 type: 'deletion',
                 length: data,
@@ -89,21 +82,15 @@ function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'b') {
-            // stretch of bases
         }
         else if (code === 'q') {
-            // stretch of qual scores
         }
         else if (code === 'B') {
-            // a pair of [base, qual]
         }
         else if (code === 'i') {
-            // single-base insertion, we collect these if there are multiple in a row
-            // into a single insertion entry
             insLen++;
         }
         else if (code === 'Q') {
-            // single quality value
         }
     }
     if (sublen && insLen > 0) {
@@ -125,7 +112,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
     if (!refRegion) {
         return '';
     }
-    // not sure I should access these, but...
     const ref = refRegion.seq;
     const refStart = refRegion.start;
     let lastPos = alignmentStart;
@@ -149,7 +135,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen += sublen;
             }
             if (code === 'b') {
-                // An array of bases stored verbatim
                 const ret = data.split(',');
                 const added = String.fromCharCode(...ret);
                 seq += added;
@@ -157,19 +142,16 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen += added.length;
             }
             else if (code === 'B') {
-                // Single base (+ qual score)
                 seq += sub;
                 lastPos++;
                 oplen++;
             }
             else if (code === 'X') {
-                // Substitution
                 seq += sub;
                 lastPos++;
                 oplen++;
             }
             else if (code === 'D' || code === 'N') {
-                // Deletion or Ref Skip
                 lastPos += data;
                 if (oplen) {
                     cigar += `${oplen}${op}`;
@@ -178,7 +160,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'I' || code === 'S') {
-                // Insertion or soft-clip
                 seq += data;
                 if (oplen) {
                     cigar += `${oplen}${op}`;
@@ -187,8 +168,6 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'i') {
-                // Single base insertion
-                // seq += data
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
@@ -197,20 +176,18 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
                 oplen = 0;
             }
             else if (code === 'P') {
-                // Padding
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
                 cigar += `${data}P`;
             }
             else if (code === 'H') {
-                // Hard clip
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
                 cigar += `${data}H`;
                 oplen = 0;
-            } // else q or Q
+            }
         }
     }
     else {

package/dist/GuessAlignmentsTypes/index.d.ts

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

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,6 +1,6 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
+import type { BamFile } from '@gmod/bam';
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
     protected configurePre(): Promise<{
         bam: BamFile;

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,23 +1,14 @@
 declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     htsgetBase: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     htsgetTrackId: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         description: string;

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,31 +1,18 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config HtsgetBamAdapter
- * Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
-    /**
-     * #slot
-     */
     htsgetBase: {
         type: 'string',
         description: 'the base URL to fetch from',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     htsgetTrackId: {
         type: 'string',
         description: 'the trackId, which is appended to the base URL',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: 'frozen',
         description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',

package/dist/HtsgetBamAdapter/index.d.ts

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

package/dist/HtsgetBamAdapter/index.js

@@ -27,8 +27,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = HtsgetBamAdapterF;
-const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
 function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({

package/dist/LinearAlignmentsDisplay/alignmentsModel.d.ts

@@ -1,8 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearAlignmentsDisplayMixin
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export declare function LinearAlignmentsDisplayMixin(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;

package/dist/LinearAlignmentsDisplay/alignmentsModel.js

@@ -1,48 +1,18 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.LinearAlignmentsDisplayMixin = LinearAlignmentsDisplayMixin;
-const mobx_state_tree_1 = require("mobx-state-tree");
-// jbrowse
 const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("./util");
-/**
- * #stateModel LinearAlignmentsDisplayMixin
- */
 function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
     return mobx_state_tree_1.types.model({
-        /**
-         * #property
-         * refers to LinearPileupDisplay sub-display model
-         */
         PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...(0, util_1.getLowerPanelDisplays)(pluginManager).map(f => f.stateModel))),
-        /**
-         * #property
-         * refers to LinearSNPCoverageDisplay sub-display model
-         */
         SNPCoverageDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
-        /**
-         * #property
-         */
         snpCovHeight: 45,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearAlignmentsDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
         heightPreConfig: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        /**
-         * #property
-         */
         lowerPanelType: 'LinearPileupDisplay',
     });
 }

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearAlignmentsDisplayModel } from '../model';
+import type { LinearAlignmentsDisplayModel } from '../model';
 declare const AlignmentsDisplay: ({ model, }: {
     model: LinearAlignmentsDisplayModel;
 }) => React.JSX.Element | null;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     resizeHandle: {
         height: 5,

package/dist/LinearAlignmentsDisplay/configSchema.d.ts

@@ -1,21 +1,7 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function configModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    /**
-     * #slot
-     */
     snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    /**
-     * #slot
-     */
     height: {
         type: string;
         defaultValue: number;

package/dist/LinearAlignmentsDisplay/configSchema.js

@@ -3,33 +3,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = configModelFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-function configModelFactory(pm) {
+function configModelFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
-        /**
-         * #slot
-         */
-        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
-        /**
-         * #slot
-         */
-        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+        pileupDisplay: pluginManager.getDisplayType('LinearPileupDisplay')
             .configSchema,
-        /**
-         * #slot
-         */
+        snpCoverageDisplay: pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema,
         height: {
             type: 'number',
             defaultValue: 250,
         },
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/dist/LinearAlignmentsDisplay/index.d.ts

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

package/dist/LinearAlignmentsDisplay/index.js

@@ -5,10 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LinearAlignmentsDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
+const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
-const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
 function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);

package/dist/LinearAlignmentsDisplay/model.d.ts

@@ -1,16 +1,10 @@
 import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { MenuItem } from '@jbrowse/core/ui';
-import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { FilterBy } from '../shared/types';
-/**
- * #stateModel LinearAlignmentsDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [LinearAlignmentsDisplayMixin](../linearalignmentsdisplaymixin)
- */
+import type { FilterBy } from '../shared/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { MenuItem } from '@jbrowse/core/ui';
+import type { Instance } from 'mobx-state-tree';
 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>;
@@ -83,98 +77,35 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    /**
-     * #volatile
-     */
     scrollTop: number;
 } & {
-    /**
-     * #action
-     */
     setScrollTop(scrollTop: number): void;
-    /**
-     * #action
-     */
     setSNPCoverageHeight(n: number): void;
 } & {
-    /**
-     * #getter
-     */
     readonly height: any;
-    /**
-     * #getter
-     */
     readonly featureIdUnderMouse: any;
 } & {
-    /**
-     * #getter
-     */
     readonly pileupConf: any;
-    /**
-     * #method
-     */
     getFeatureByID(blockKey: string, id: string): any;
-    /**
-     * #method
-     */
     searchFeatureByID(id: string): any;
-    /**
-     * #getter
-     */
     readonly features: any;
-    /**
-     * #getteralignmentsdisplaymodel
-     */
     readonly DisplayBlurb: any;
-    /**
-     * #getter
-     */
     readonly sortedBy: any;
-    /**
-     * #getter
-     */
     readonly coverageConf: any;
 } & {
-    /**
-     * #action
-     */
     setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
-    /**
-     * #action
-     */
     setPileupDisplay(configuration: AnyConfigurationModel): void;
-    /**
-     * #action
-     */
     setHeight(n: number): number;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
-    /**
-     * #action
-     */
     setLowerPanelType(type: string): void;
-    /**
-     * #action
-     */
     resizeHeight(distance: number): number;
 } & {
     afterAttach(): void;
-    /**
-     * #action
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.JSX.Element>;
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;