@jbrowse/plugin-alignments 2.17.0 → 2.18.0

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 declare const AlignmentsFeatureDetails: (props: {
     model: AlignmentFeatureWidgetModel;
 }) => React.JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,28 +1,22 @@
 import React, { lazy } from 'react';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import clone from 'clone';
-import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
-// locals
-import { getTag } from './util';
-import { tags } from './tagInfo';
-// local components
 import Flags from './Flags';
-import PairLink from './PairLink';
 import Formatter from './Formatter';
-// lazies
+import PairLink from './PairLink';
+import { tags } from './tagInfo';
+import { getTag } from './util';
 const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'));
 const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'));
 const AlignmentsFeatureDetails = observer(function (props) {
     const { model } = props;
     const { featureData } = model;
-    const feat = clone(featureData);
+    const feat = structuredClone(featureData);
     const SA = getTag('SA', feat);
     const { flags } = feat;
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
-        React.createElement(FeatureDetails, { ...props, 
-            // @ts-expect-error
-            descriptions: { ...tags, tags: tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
+        React.createElement(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
         SA !== undefined ? (React.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
         flags & 1 ? (React.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
         flags !== undefined ? React.createElement(Flags, { feature: feat, ...props }) : null));

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1,2 +1 @@
-// re-exported for react lazy
 export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1,2 +1 @@
-// re-exported for react lazy
 export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -1,8 +1,8 @@
 import React from 'react';
-import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
+import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,

package/esm/AlignmentsFeatureDetail/Formatter.js

@@ -1,8 +1,5 @@
 import React, { useState } from 'react';
 import copy from 'copy-to-clipboard';
-// this 'show more...' used specifically as a formatter on alignments feature
-// details because long SEQ or CRAM files, even a single div full of a ton of
-// data from a long read, can slow down the rest of the app
 export default function Formatter({ value }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
 }): React.JSX.Element;

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,10 +1,9 @@
 import React, { lazy } from 'react';
-import { Typography, Link } from '@mui/material';
-import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
-// lazies
+import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { Link, Typography } from '@mui/material';
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }) {
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = getSession(model);
     const f1 = {
         uniqueId: feature.uniqueId,
@@ -38,10 +37,8 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
                             BreakendMultiLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },
@@ -54,10 +51,8 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
                             BreakendSingleLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
 }): React.JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -1,18 +1,15 @@
 import React, { lazy, useEffect, useState } from 'react';
-import { Typography, Link } from '@mui/material';
-import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
 import { ErrorMessage } from '@jbrowse/core/ui';
+import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { Link, Typography } from '@mui/material';
 import { getSAFeatures } from './getSAFeatures';
-// lazies
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
-export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const session = getSession(model);
+export default function LaunchBreakpointSplitViewPanel({ model, feature, }) {
     const { view } = model;
     const [res, setRes] = useState();
     const [error, setError] = useState();
     useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -49,36 +46,40 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
                 ":",
                 toLocale(f2.strand === 1 ? f2.start : f2.end),
                 ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
+                React.createElement(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }),
                 ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")));
+                React.createElement(SideBySideViewLink, { model: model, f1: f1, f2: f2 })));
         })))) : null;
 }
+function TopBottomSplitViewLink({ model, f1, f2, }) {
+    return (React.createElement(Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = getSession(model);
+            session.queueDialog(handleClose => [
+                BreakendMultiLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        } }, "(top/bottom)"));
+}
+function SideBySideViewLink({ model, f1, f2, }) {
+    return (React.createElement(Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = getSession(model);
+            session.queueDialog(handleClose => [
+                BreakendSingleLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        } }, "(single row)"));
+}

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -6,12 +6,11 @@ export default function SuppAlignments(props) {
     const { model, feature } = props;
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" }, viewType ? (React.createElement(LaunchPairedEndBreakpointSplitViewPanel, { viewType: viewType, model: model, feature: feature })) : null));
+    return (React.createElement(BaseCard, { ...props, title: "Paired alignments" }, hasBreakendSplitView ? (React.createElement(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature })) : null));
 }

package/esm/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function PairLink({ locString, model, }: {
     locString: string;
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/PairLink.js

@@ -4,7 +4,6 @@ import { navToLoc } from './util';
 export default function PairLink({ locString, model, }) {
     return (React.createElement(Link, { onClick: event => {
             event.preventDefault();
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             navToLoc(locString, model);
         }, href: "#" }, locString));
 }

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SupplementaryAlignments(props: {
     tag: string;
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -1,20 +1,19 @@
 import React from 'react';
-import { getEnv, getSession } from '@jbrowse/core/util';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
+import { getEnv, getSession } from '@jbrowse/core/util';
 import LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel';
+import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
 export default function SupplementaryAlignments(props) {
     const { model, tag, feature } = props;
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
     return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
         React.createElement(SupplementaryAlignmentsLocStrings, { model: model, tag: tag }),
-        viewType ? (React.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, feature: feature })) : null));
+        hasBreakendSplitView ? (React.createElement(LaunchBreakpointSplitViewPanel, { model: model, feature: feature })) : null));
 }

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
     tag: string;
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,6 +1,5 @@
 import React from 'react';
-import { Typography, Link } from '@mui/material';
-// locals
+import { Link, Typography } from '@mui/material';
 import { getLengthOnRef } from '../MismatchParser';
 import { navToLoc } from './util';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }) {
@@ -21,12 +20,9 @@ export default function SupplementaryAlignmentsLocStrings({ tag, model, }) {
             const displayStart = start.toLocaleString('en-US');
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-            return (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            React.createElement("li", { key: `${locString}-${idx}` },
+            return (React.createElement("li", { key: `${locString}-${idx}` },
                 React.createElement(Link, { href: "#", onClick: async (event) => {
                         event.preventDefault();
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         navToLoc(locString, model);
                     } }, displayString)));
         }))));

package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts

@@ -1,5 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export interface ReducedFeature {
     refName: string;
     start: number;

package/esm/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,5 +1,4 @@
 import { getSession } from '@jbrowse/core/util';
-// locals
 import { featurizeSA, getClip, getLengthSansClipping } from '../MismatchParser';
 export async function getSAFeatures({ view, feature, }) {
     var _a;
@@ -9,9 +8,6 @@ export async function getSAFeatures({ view, feature, }) {
     const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
     const readName = feature.get('name');
     const clipPos = getClip(cigar, 1);
-    // get the canonical refname for the read because if the read.get('refName')
-    // is chr1 and the actual fasta refName is 1 then no tracks can be opened on
-    // the top panel of the linear read vs ref
     const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
     if (!assembly) {
         throw new Error('assembly not found');

package/esm/AlignmentsFeatureDetail/index.d.ts

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

package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,5 +1,5 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ReducedFeature } from './getSAFeatures';
+import type { ReducedFeature } from './getSAFeatures';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function getBreakpointSplitView({ f1, f2, view, }: {
     f1: ReducedFeature;
     f2: ReducedFeature;

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { Instance } from 'mobx-state-tree';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;

package/esm/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,5 +1,5 @@
-import { types } from 'mobx-state-tree';
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
+import { types } from 'mobx-state-tree';
 export function stateModelFactory(pluginManager) {
     const baseModel = baseModelFactory(pluginManager);
     return types.compose(baseModel, types.model('AlignmentsFeatureWidget', {

package/esm/AlignmentsFeatureDetail/tagInfo.js

@@ -17,7 +17,7 @@ export const tags = {
     E2: 'The 2nd most likely base calls',
     FI: 'The index of segment in the template',
     FS: 'Segment suffix',
-    FZ: 'Flow signal intensities',
+    FZ: 'Flow stopToken intensities',
     GC: 'Reserved for backwards compatibility reasons',
     GQ: 'Reserved for backwards compatibility reasons',
     GS: 'Reserved for backwards compatibility reasons',

package/esm/AlignmentsFeatureDetail/util.d.ts

@@ -1,4 +1,4 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
     tags?: Record<string, unknown>;
     [key: string]: unknown;

package/esm/AlignmentsTrack/configSchemaF.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;

package/esm/AlignmentsTrack/configSchemaF.js

@@ -1,15 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 export default function configSchemaFactory(pluginManager) {
     return ConfigurationSchema('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: createBaseTrackConfig(pluginManager),
     });
 }

package/esm/AlignmentsTrack/index.d.ts

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

package/esm/AlignmentsTrack/index.js

@@ -11,9 +11,6 @@ export default function register(pm) {
             stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
         });
         const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay');
-        // Add LinearAlignmentsDisplay here so that it has priority over the other
-        // linear displays (defaults to order the displays are added, but we have
-        // to add the Pileup and SNPCoverage displays first).
         track.addDisplayType(linearAlignmentsDisplay);
         return track;
     });

package/esm/BamAdapter/BamAdapter.d.ts

@@ -1,8 +1,9 @@
 import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { FilterBy } from '../shared/types';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { FilterBy } from '../shared/types';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -23,7 +24,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;

package/esm/BamAdapter/BamAdapter.js

@@ -1,27 +1,21 @@
 import { BamFile } from '@gmod/bam';
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-// jbrowse
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { bytesForRegions, updateStatus } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
-// locals
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
+import { filterReadFlag, filterTagValue } from '../shared/util';
 export default class BamAdapter extends BaseFeatureDataAdapter {
     constructor() {
         super(...arguments);
-        // used for avoiding re-creation new BamSlightlyLazyFeatures, keeping
-        // mismatches in cache. at an average of 100kb-300kb, keeping even just 500
-        // of these in memory is memory intensive but can reduce recomputation on
-        // these objects
         this.ultraLongFeatureCache = new QuickLRU({
             maxSize: 500,
         });
     }
-    // derived classes may not use the same configuration so a custom configure
-    // method allows derived classes to override this behavior
     async configurePre() {
         const bamLocation = this.getConf('bamLocation');
         const location = this.getConf(['index', 'location']);
@@ -53,23 +47,20 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         }
         return this.configureP;
     }
-    async getHeader(opts) {
+    async getHeader(_opts) {
         const { bam } = await this.configure();
-        return bam.getHeaderText(opts);
+        return bam.getHeaderText();
     }
     async setupPre(opts) {
         const { statusCallback = () => { } } = opts || {};
         const { bam } = await this.configure();
         this.samHeader = await updateStatus('Downloading index', statusCallback, async () => {
-            const samHeader = await bam.getHeader(opts);
-            // use the @SQ lines in the header to figure out the
-            // mapping between ref ref ID numbers and names
+            const samHeader = await bam.getHeader();
             const idToName = [];
             const nameToId = {};
             samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
                 const SN = sqLine.data.find(item => item.tag === 'SN');
                 if (SN) {
-                    // this is the ref name
                     const refName = SN.value;
                     nameToId[refName] = refId;
                     idToName[refId] = refName;
@@ -127,11 +118,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(region, opts) {
         const { refName, start, end, originalRefName } = region;
-        const { signal, filterBy, statusCallback = () => { } } = opts || {};
+        const { stopToken, filterBy, statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
             const { bam } = await this.configure();
             await this.setup(opts);
-            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end, opts));
+            checkStopToken(stopToken);
+            const records = await updateStatus('Downloading alignments', statusCallback, () => bam.getRecordsForRange(refName, start, end));
+            checkStopToken(stopToken);
             await updateStatus('Processing alignments', statusCallback, async () => {
                 const { flagInclude = 0, flagExclude = 0, tagFilter, readName, } = filterBy || {};
                 for (const record of records) {
@@ -139,25 +132,16 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
                     if (!record.tags.MD) {
                         ref = await this.seqFetch(originalRefName || refName, record.start, record.end);
                     }
-                    const flags = record.flags;
-                    if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
+                    if (filterReadFlag(record.flags, flagInclude, flagExclude)) {
                         continue;
                     }
-                    if (tagFilter) {
-                        const readVal = record.tags[tagFilter.tag];
-                        const filterVal = tagFilter.value;
-                        if (filterVal === '*'
-                            ? readVal === undefined
-                            : `${readVal}` !== `${filterVal}`) {
-                            continue;
-                        }
+                    if (tagFilter &&
+                        filterTagValue(record.tags[tagFilter.tag], tagFilter.value)) {
+                        continue;
                     }
                     if (readName && record.name !== readName) {
                         continue;
                     }
-                    // retrieve a feature from our feature cache if it is available, the
-                    // features in the cache have pre-computed mismatches objects that
-                    // can be re-used across blocks
                     const ret = this.ultraLongFeatureCache.get(`${record.id}`);
                     if (!ret) {
                         const elt = new BamSlightlyLazyFeature(record, this, ref);
@@ -170,11 +154,10 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
                 }
                 observer.complete();
             });
-        }, signal);
+        });
     }
     async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
-        // this is a method to avoid calling on htsget adapters
         if (bam.index) {
             const bytes = await bytesForRegions(regions, bam);
             const fetchSizeLimit = this.getConf('fetchSizeLimit');
@@ -182,8 +165,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         }
         return super.getMultiRegionFeatureDensityStats(regions, opts);
     }
-    freeResources( /* { region } */) { }
-    // depends on setup being called before the BAM constructor
+    freeResources() { }
     refIdToName(refId) {
         var _a;
         return (_a = this.samHeader) === null || _a === void 0 ? void 0 : _a.idToName[refId];

package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -1,6 +1,6 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import { BamRecord } from '@gmod/bam';
-import BamAdapter from './BamAdapter';
+import type BamAdapter from './BamAdapter';
+import type { BamRecord } from '@gmod/bam';
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 export default class BamSlightlyLazyFeature implements Feature {
     private record;
     private adapter;