@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/esm/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,103 +1,83 @@
 import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util';
+import { cacheGetter } from '../shared/util';
 export default class CramSlightlyLazyFeature {
-    // uses parameter properties to automatically create fields on the class
-    // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
     constructor(record, _store) {
         this.record = record;
         this._store = _store;
     }
-    _get_name() {
+    get name() {
         return this.record.readName;
     }
-    _get_start() {
+    get start() {
         return this.record.alignmentStart - 1;
     }
-    _get_end() {
+    get end() {
         var _a;
-        return this.record.alignmentStart + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1) - 1;
+        return this.start + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1);
     }
-    _get_cram_read_features() {
-        return this.record.readFeatures;
-    }
-    _get_type() {
-        return 'match';
-    }
-    _get_score() {
+    get score() {
         return this.record.mappingQuality;
     }
-    _get_flags() {
+    get flags() {
         return this.record.flags;
     }
-    _get_strand() {
+    get strand() {
         return this.record.isReverseComplemented() ? -1 : 1;
     }
-    _read_group_id() {
-        var _a;
-        return (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
-    }
-    _get_qual() {
+    get qual() {
         return (this.record.qualityScores || []).join(' ');
     }
-    qualRaw() {
+    get qualRaw() {
         return this.record.qualityScores;
     }
-    _get_refName() {
+    get refName() {
         return this._store.refIdToName(this.record.sequenceId);
     }
-    _get_is_paired() {
-        return !!this.record.mate;
-    }
-    _get_pair_orientation() {
+    get pair_orientation() {
         return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
     }
-    _get_template_length() {
+    get template_length() {
         return this.record.templateLength || this.record.templateSize;
     }
-    _get_next_ref() {
+    get next_ref() {
         return this.record.mate
             ? this._store.refIdToName(this.record.mate.sequenceId)
             : undefined;
     }
-    _get_next_segment_position() {
+    get next_segment_position() {
         return this.record.mate
             ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
             : undefined;
     }
-    _get_next_pos() {
+    get is_paired() {
+        return !!this.record.mate;
+    }
+    get next_pos() {
         var _a;
         return (_a = this.record.mate) === null || _a === void 0 ? void 0 : _a.alignmentStart;
     }
-    _get_tags() {
-        const RG = this._read_group_id();
-        const { tags } = this.record;
-        // avoids a tag copy if no RG, but just copy if there is one
-        return RG !== undefined ? { ...tags, RG } : tags;
+    get tags() {
+        var _a;
+        const RG = (_a = this._store.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[this.record.readGroupId];
+        return RG !== undefined ? { ...this.record.tags, RG } : this.record.tags;
     }
-    _get_seq() {
+    get seq() {
         return this.record.getReadBases();
     }
-    // generate a CIGAR, based on code from jkbonfield
-    _get_CIGAR() {
+    get CIGAR() {
         return readFeaturesToCIGAR(this.record.readFeatures, this.record.alignmentStart, this.record.readLength, this.record._refRegion);
     }
-    tags() {
-        return Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype)
-            .filter(prop => prop.startsWith('_get_') &&
-            prop !== '_get_mismatches' &&
-            prop !== '_get_cram_read_features')
-            .map(methodName => methodName.replace('_get_', ''));
-    }
     id() {
         return `${this._store.id}-${this.record.uniqueId}`;
     }
     get(field) {
-        const methodName = `_get_${field}`;
-        // @ts-expect-error
-        if (this[methodName]) {
-            // @ts-expect-error
-            return this[methodName]();
-        }
-        return undefined;
+        return field === 'mismatches'
+            ? this.mismatches
+            : field === 'qual'
+                ? this.qual
+                : field === 'CIGAR'
+                    ? this.CIGAR
+                    : this.fields[field];
     }
     parent() {
         return undefined;
@@ -105,33 +85,37 @@ export default class CramSlightlyLazyFeature {
     children() {
         return undefined;
     }
-    set() { }
-    pairedFeature() {
-        return false;
-    }
-    _get_clipPos() {
-        const mismatches = this.get('mismatches');
-        if (mismatches.length) {
-            const record = this.get('strand') === -1 ? mismatches.at(-1) : mismatches[0];
-            const { type, cliplen } = record;
-            if (type === 'softclip' || type === 'hardclip') {
-                return cliplen;
-            }
-        }
-        return 0;
+    get mismatches() {
+        return readFeaturesToMismatches(this.record.readFeatures, this.start, this.qualRaw);
     }
-    toJSON() {
+    get fields() {
         return {
-            ...Object.fromEntries(this.tags()
-                .map(t => [t, this.get(t)])
-                .filter(elt => elt[1] !== undefined)),
+            start: this.start,
+            name: this.name,
+            end: this.end,
+            score: this.score,
+            strand: this.strand,
+            template_length: this.template_length,
+            flags: this.flags,
+            tags: this.tags,
+            refName: this.refName,
+            seq: this.seq,
+            type: 'match',
+            pair_orientation: this.pair_orientation,
+            next_ref: this.next_ref,
+            next_pos: this.next_pos,
+            next_segment_position: this.next_segment_position,
             uniqueId: this.id(),
         };
     }
-    _get_mismatches() {
-        const readFeatures = this.record.readFeatures;
-        const qual = this.qualRaw();
-        const start = this.get('start');
-        return readFeaturesToMismatches(readFeatures, start, qual);
+    toJSON() {
+        return {
+            ...this.fields,
+            CIGAR: this.CIGAR,
+            qual: this.qual,
+        };
     }
 }
+cacheGetter(CramSlightlyLazyFeature, 'fields');
+cacheGetter(CramSlightlyLazyFeature, 'CIGAR');
+cacheGetter(CramSlightlyLazyFeature, 'mismatches');

package/esm/CramAdapter/CramTestAdapters.d.ts

@@ -1,7 +1,7 @@
-import { GenericFilehandle } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { Observable } from 'rxjs';
+import type { GenericFilehandle } from 'generic-filehandle';
 export declare function parseSmallFasta(text: string): {
     id: string;
     description: string;

package/esm/CramAdapter/CramTestAdapters.js

@@ -1,8 +1,7 @@
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-// setup for Cram Adapter Testing
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { Observable } from 'rxjs';
 export function parseSmallFasta(text) {
     return text
         .split('>')
@@ -73,5 +72,5 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
             return { unsubscribe: () => { } };
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/CramAdapter/configSchema.d.ts

@@ -1,15 +1,9 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot fetchSizeLimit
-     */
     fetchSizeLimit: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot cramLocation
-     */
     cramLocation: {
         type: string;
         defaultValue: {
@@ -17,9 +11,6 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot craiLocation
-     */
     craiLocation: {
         type: string;
         defaultValue: {
@@ -27,11 +18,6 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot sequenceAdapter
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: string;
         description: string;

package/esm/CramAdapter/configSchema.js

@@ -1,21 +1,11 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config CramAdapter
- * used to configure CRAM adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = ConfigurationSchema('CramAdapter', {
-    /**
-     * #slot fetchSizeLimit
-     */
     fetchSizeLimit: {
         type: 'number',
         description: 'size in bytes over which to display a warning to the user that too much data will be fetched',
         defaultValue: 3000000,
     },
-    /**
-     * #slot cramLocation
-     */
     cramLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -23,9 +13,6 @@ const configSchema = ConfigurationSchema('CramAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot craiLocation
-     */
     craiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -33,11 +20,6 @@ const configSchema = ConfigurationSchema('CramAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot sequenceAdapter
-     * generally refers to the reference genome assembly's sequence adapter
-     * currently needs to be manually added
-     */
     sequenceAdapter: {
         type: 'frozen',
         description: 'sequence data adapter',

package/esm/CramAdapter/index.d.ts

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

package/esm/CramAdapter/index.js

@@ -1,5 +1,4 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-// locals
 import configSchema from './configSchema';
 export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {

package/esm/CramAdapter/util.d.ts

@@ -1,15 +1,6 @@
-import { CramRecord } from '@gmod/cram';
+import type { Mismatch } from '../shared/types';
+import type { CramRecord } from '@gmod/cram';
 type ReadFeatures = CramRecord['readFeatures'];
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string | undefined;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
 export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
 export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
     seq: string;

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

@@ -1,4 +1,4 @@
-import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {

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/{models/alignmentsModel.d.ts → 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/{models/alignmentsModel.js → 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

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

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 { 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,