@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/CramAdapter/util.js

@@ -22,7 +22,6 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
         }
         refPos = p - 1 - start;
         if (code === 'X') {
-            // substitution
             mismatches[j++] = {
                 start: refPos,
                 length: 1,
@@ -33,7 +32,6 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'I') {
-            // insertion
             mismatches[j++] = {
                 start: refPos,
                 type: 'insertion',
@@ -42,7 +40,6 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'N') {
-            // reference skip
             mismatches[j++] = {
                 type: 'skip',
                 length: data,
@@ -51,7 +48,6 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'S') {
-            // soft clip
             const len = data.length;
             mismatches[j++] = {
                 start: refPos,
@@ -62,10 +58,8 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'P') {
-            // padding
         }
         else if (code === 'H') {
-            // hard clip
             const len = data;
             mismatches[j++] = {
                 start: refPos,
@@ -76,7 +70,6 @@ export function readFeaturesToMismatches(readFeatures, start, qual) {
             };
         }
         else if (code === 'D') {
-            // deletion
             mismatches[j++] = {
                 type: 'deletion',
                 length: data,
@@ -85,21 +78,15 @@ export 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) {
@@ -121,7 +108,6 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
     if (!refRegion) {
         return '';
     }
-    // not sure I should access these, but...
     const ref = refRegion.seq;
     const refStart = refRegion.start;
     let lastPos = alignmentStart;
@@ -145,7 +131,6 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
                 oplen += sublen;
             }
             if (code === 'b') {
-                // An array of bases stored verbatim
                 const ret = data.split(',');
                 const added = String.fromCharCode(...ret);
                 seq += added;
@@ -153,19 +138,16 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
                 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}`;
@@ -174,7 +156,6 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
                 oplen = 0;
             }
             else if (code === 'I' || code === 'S') {
-                // Insertion or soft-clip
                 seq += data;
                 if (oplen) {
                     cigar += `${oplen}${op}`;
@@ -183,8 +164,6 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
                 oplen = 0;
             }
             else if (code === 'i') {
-                // Single base insertion
-                // seq += data
                 if (oplen) {
                     cigar += `${oplen}${op}`;
                 }
@@ -193,20 +172,18 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
                 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/esm/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/esm/GuessAlignmentsTypes/index.js

@@ -1,45 +1,30 @@
-import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.cram$/i;
-            const adapterName = 'CramAdapter';
-            const fileName = getFileName(file);
-            const obj = {
-                type: adapterName,
-                cramLocation: file,
-                craiLocation: index || makeIndex(file, '.crai'),
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
-            }
-            if (adapterHint === adapterName) {
-                return obj;
-            }
-            return adapterGuesser(file, index, adapterHint);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.bam$/i;
-            const adapterName = 'BamAdapter';
             const fileName = getFileName(file);
             const indexName = index && getFileName(index);
-            const obj = {
-                type: adapterName,
-                bamLocation: file,
-                index: {
-                    location: index || makeIndex(file, '.bai'),
-                    indexType: makeIndexType(indexName, 'CSI', 'BAI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if (testAdapter(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
+                return {
+                    type: 'BamAdapter',
+                    bamLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.bai'),
+                        indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+                    },
+                };
+            }
+            else if (testAdapter(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
+                return {
+                    type: 'CramAdapter',
+                    cramLocation: file,
+                    craiLocation: index || makeIndex(file, '.crai'),
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {

package/esm/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/esm/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/esm/HtsgetBamAdapter/configSchema.js

@@ -1,29 +1,16 @@
 import { ConfigurationSchema } from '@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 = 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/esm/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/esm/HtsgetBamAdapter/index.js

@@ -1,5 +1,5 @@
-import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
 export default function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({

package/esm/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/esm/LinearAlignmentsDisplay/alignmentsModel.js

@@ -1,45 +1,15 @@
+import { ConfigurationReference } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-// jbrowse
-import { ConfigurationReference, } from '@jbrowse/core/configuration';
 import { getLowerPanelDisplays } from './util';
-/**
- * #stateModel LinearAlignmentsDisplayMixin
- */
 export function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
     return types.model({
-        /**
-         * #property
-         * refers to LinearPileupDisplay sub-display model
-         */
         PileupDisplay: types.maybe(types.union(...getLowerPanelDisplays(pluginManager).map(f => f.stateModel))),
-        /**
-         * #property
-         * refers to LinearSNPCoverageDisplay sub-display model
-         */
         SNPCoverageDisplay: types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
-        /**
-         * #property
-         */
         snpCovHeight: 45,
-        /**
-         * #property
-         */
         type: types.literal('LinearAlignmentsDisplay'),
-        /**
-         * #property
-         */
         configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
         heightPreConfig: types.maybe(types.number),
-        /**
-         * #property
-         */
         userFeatureScreenDensity: types.maybe(types.number),
-        /**
-         * #property
-         */
         lowerPanelType: 'LinearPileupDisplay',
     });
 }

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

@@ -1,6 +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;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default AlignmentsDisplay;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,8 +1,8 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     resizeHandle: {
         height: 5,
@@ -18,17 +18,12 @@ const AlignmentsDisplay = observer(function AlignmentsDisplay({ model, }) {
         return null;
     }
     const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
-    return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
-        React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-            React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-        React.createElement(ResizeHandle, { onDrag: delta => {
-                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                return delta;
-            }, className: classes.resizeHandle, style: { top: top - 4 } }),
-        React.createElement("div", { "data-testid": "Blockset-pileup", style: {
-                position: 'absolute',
-                top,
-            } },
-            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
+    return (_jsxs("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' }, children: [_jsx("div", { "data-testid": "Blockset-snpcoverage", children: _jsx(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay }) }), _jsx(ResizeHandle, { onDrag: delta => {
+                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                    return delta;
+                }, className: classes.resizeHandle, style: { top: top - 4 } }), _jsx("div", { "data-testid": "Blockset-pileup", style: {
+                    position: 'absolute',
+                    top,
+                }, children: _jsx(PileupDisplay.RenderingComponent, { model: PileupDisplay }) })] }));
 });
 export default AlignmentsDisplay;

package/esm/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/esm/LinearAlignmentsDisplay/configSchema.js

@@ -1,32 +1,15 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseLinearDisplayConfigSchema } from '@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
- */
-export default function configModelFactory(pm) {
+export default function configModelFactory(pluginManager) {
     return 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: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/esm/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/esm/LinearAlignmentsDisplay/index.js

@@ -1,8 +1,7 @@
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-// locals
+import ReactComponent from './components/AlignmentsDisplay';
 import configSchemaFactory from './configSchema';
 import modelFactory from './model';
-import ReactComponent from './components/AlignmentsDisplay';
 export default function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);

package/esm/LinearAlignmentsDisplay/model.d.ts

@@ -1,16 +1,9 @@
-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 +76,35 @@ 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>;
+    }): Promise<import("react/jsx-runtime").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]>;