@jbrowse/plugin-alignments 2.13.1 → 2.14.0

package/esm/LinearReadArcsDisplay/model.js

@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
 // locals
 import { FilterModel } from '../shared';
 // async
-const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
+const FilterByTagDialog = lazy(() => import('../shared/FilterByTagDialog'));
 /**
  * #stateModel LinearReadArcsDisplay
  * the arc display is a non-block-based track, so draws to a single canvas and
@@ -202,15 +202,21 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Thin',
-                                onClick: () => self.setLineWidth(1),
+                                onClick: () => {
+                                    self.setLineWidth(1);
+                                },
                             },
                             {
                                 label: 'Bold',
-                                onClick: () => self.setLineWidth(2),
+                                onClick: () => {
+                                    self.setLineWidth(2);
+                                },
                             },
                             {
                                 label: 'Extra bold',
-                                onClick: () => self.setLineWidth(5),
+                                onClick: () => {
+                                    self.setLineWidth(5);
+                                },
                             },
                         ],
                     },
@@ -221,19 +227,25 @@ function stateModelFactory(configSchema) {
                                 type: 'checkbox',
                                 checked: self.jitterVal === 0,
                                 label: 'None',
-                                onClick: () => self.setJitter(0),
+                                onClick: () => {
+                                    self.setJitter(0);
+                                },
                             },
                             {
                                 type: 'checkbox',
                                 checked: self.jitterVal === 2,
                                 label: 'Small',
-                                onClick: () => self.setJitter(2),
+                                onClick: () => {
+                                    self.setJitter(2);
+                                },
                             },
                             {
                                 type: 'checkbox',
                                 checked: self.jitterVal === 10,
                                 label: 'Large',
-                                onClick: () => self.setJitter(10),
+                                onClick: () => {
+                                    self.setJitter(10);
+                                },
                             },
                         ],
                     },
@@ -241,13 +253,17 @@ function stateModelFactory(configSchema) {
                         label: 'Draw inter-region vertical lines',
                         type: 'checkbox',
                         checked: self.drawInter,
-                        onClick: () => self.setDrawInter(!self.drawInter),
+                        onClick: () => {
+                            self.setDrawInter(!self.drawInter);
+                        },
                     },
                     {
                         label: 'Draw long range connections',
                         type: 'checkbox',
                         checked: self.drawLongRange,
-                        onClick: () => self.setDrawLongRange(!self.drawLongRange),
+                        onClick: () => {
+                            self.setDrawLongRange(!self.drawLongRange);
+                        },
                     },
                     {
                         label: 'Color scheme',
@@ -255,19 +271,27 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Insert size ± 3σ and orientation',
-                                onClick: () => self.setColorScheme({ type: 'insertSizeAndOrientation' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'insertSizeAndOrientation' });
+                                },
                             },
                             {
                                 label: 'Insert size ± 3σ',
-                                onClick: () => self.setColorScheme({ type: 'insertSize' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'insertSize' });
+                                },
                             },
                             {
                                 label: 'Orientation',
-                                onClick: () => self.setColorScheme({ type: 'orientation' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'orientation' });
+                                },
                             },
                             {
                                 label: 'Insert size gradient',
-                                onClick: () => self.setColorScheme({ type: 'gradient' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'gradient' });
+                                },
                             },
                         ],
                     },

package/esm/LinearReadCloudDisplay/components/ReactComponent.js

@@ -6,7 +6,10 @@ const Cloud = observer(function ({ model, }) {
     const view = getContainingView(model);
     const width = Math.round(view.dynamicBlocks.totalWidthPx);
     const height = model.height;
-    const cb = useCallback((ref) => model.setRef(ref), 
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
+    const cb = useCallback((ref) => {
+        model.setRef(ref);
+    }, 
     // eslint-disable-next-line react-hooks/exhaustive-deps
     [model, width, height]);
     // note: the position absolute below avoids scrollbar from appearing on track

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -75,13 +75,13 @@ export function getPairedColor({ type, v0, v1, stats, }) {
     if (type === 'insertSizeAndOrientation') {
         return getPairedInsertSizeAndOrientationColor(v0, v1, stats);
     }
-    else if (type === 'orientation') {
+    if (type === 'orientation') {
         return getPairedOrientationColor(v0);
     }
-    else if (type === 'insertSize') {
+    if (type === 'insertSize') {
         return getPairedInsertSizeColor(v0, v1, stats);
     }
-    else if (type === 'gradient') {
+    if (type === 'gradient') {
         const s = Math.min(v0.start, v1.start);
         const e = Math.max(v0.end, v1.end);
         return [

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -29,7 +29,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -53,9 +53,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree" /**
              * #property
@@ -65,7 +63,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{
@@ -85,9 +83,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;

package/esm/LinearReadCloudDisplay/model.js

@@ -10,7 +10,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll';
 // locals
 import { FilterModel } from '../shared';
 // async
-const FilterByTagDialog = lazy(() => import('../shared/FilterByTag'));
+const FilterByTagDialog = lazy(() => import('../shared/FilterByTagDialog'));
 /**
  * #stateModel LinearReadCloudDisplay
  * it is not a block based track, hence not BaseLinearDisplay
@@ -135,7 +135,9 @@ function stateModelFactory(configSchema) {
                         label: 'Draw singletons',
                         type: 'checkbox',
                         checked: self.drawSingletons,
-                        onClick: () => self.setDrawSingletons(!self.drawSingletons),
+                        onClick: () => {
+                            self.setDrawSingletons(!self.drawSingletons);
+                        },
                     },
                     {
                         label: 'Filter by',
@@ -153,19 +155,27 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Insert size ± 3σ and orientation',
-                                onClick: () => self.setColorScheme({ type: 'insertSizeAndOrientation' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'insertSizeAndOrientation' });
+                                },
                             },
                             {
                                 label: 'Insert size ± 3σ',
-                                onClick: () => self.setColorScheme({ type: 'insertSize' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'insertSize' });
+                                },
                             },
                             {
                                 label: 'Orientation',
-                                onClick: () => self.setColorScheme({ type: 'orientation' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'orientation' });
+                                },
                             },
                             {
                                 label: 'Insert size gradient',
-                                onClick: () => self.setColorScheme({ type: 'gradient' }),
+                                onClick: () => {
+                                    self.setColorScheme({ type: 'gradient' });
+                                },
                             },
                         ],
                     },

package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -3,7 +3,7 @@ import { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
     model: {
-        featureUnderMouse: Feature;
+        featureUnderMouse?: Feature;
     };
     height: number;
     offsetMouseCoord: Coord;

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -50,7 +50,7 @@ const TooltipContents = React.forwardRef(function TooltipContents2({ feature },
                         score['1'] ? `${score['1']}(+)` : ''),
                     React.createElement("td", null, key)))))))));
 });
-const SNPCoverageTooltip = observer((props) => {
+const SNPCoverageTooltip = observer(function (props) {
     const { model } = props;
     const { featureUnderMouse: feat } = model;
     return feat && feat.get('type') === 'skip' ? null : (React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props }));

package/esm/LinearSNPCoverageDisplay/models/model.d.ts

@@ -142,7 +142,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             tag: import("mobx-state-tree").ISimpleType<string>;
-            value: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
     /**

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -159,7 +159,7 @@ function stateModelFactory(pluginManager, configSchema) {
                     // must use getSnapshot because otherwise changes to e.g. just the
                     // colorBy.type are not read
                     colorBy: colorBy ? getSnapshot(colorBy) : undefined,
-                    filterBy: filterBy ? getSnapshot(filterBy) : undefined,
+                    filterBy: getSnapshot(filterBy),
                 };
             },
         };
@@ -202,7 +202,11 @@ function stateModelFactory(pluginManager, configSchema) {
                 const { colorBy } = self;
                 if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
                     const adapter = getConf(self.parentTrack, 'adapter');
-                    const vals = await getUniqueModificationValues(self, adapter, colorBy, staticBlocks);
+                    const vals = await getUniqueModificationValues({
+                        self,
+                        adapterConfig: adapter,
+                        blocks: staticBlocks,
+                    });
                     if (isAlive(self)) {
                         self.updateModificationColorMap(vals);
                         self.setModificationsReady(true);
@@ -261,19 +265,25 @@ function stateModelFactory(pluginManager, configSchema) {
                         label: 'Draw insertion/clipping indicators',
                         type: 'checkbox',
                         checked: self.drawIndicatorsSetting,
-                        onClick: () => self.toggleDrawIndicators(),
+                        onClick: () => {
+                            self.toggleDrawIndicators();
+                        },
                     },
                     {
                         label: 'Draw insertion/clipping counts',
                         type: 'checkbox',
                         checked: self.drawInterbaseCountsSetting,
-                        onClick: () => self.toggleDrawInterbaseCounts(),
+                        onClick: () => {
+                            self.toggleDrawInterbaseCounts();
+                        },
                     },
                     {
                         label: 'Draw arcs',
                         type: 'checkbox',
                         checked: self.drawArcsSetting,
-                        onClick: () => self.toggleDrawArcs(),
+                        onClick: () => {
+                            self.toggleDrawArcs();
+                        },
                     },
                 ];
             },

package/esm/MismatchParser/index.js

@@ -267,7 +267,7 @@ export function getModificationPositions(mm, fseq, fstrand) {
     for (const mod of mods) {
         const [basemod, ...skips] = mod.split(',');
         // regexes based on parse_mm.pl from hts-specs
-        const matches = basemod.match(modificationRegex);
+        const matches = modificationRegex.exec(basemod);
         if (!matches) {
             throw new Error('bad format for MM tag');
         }
@@ -314,8 +314,8 @@ export function getModificationTypes(mm) {
         .split(';')
         .filter(mod => !!mod)
         .flatMap(mod => {
-        const [basemod] = mod.split(',');
-        const matches = basemod.match(modificationRegex);
+        const basemod = mod.split(',')[0];
+        const matches = modificationRegex.exec(basemod);
         if (!matches) {
             throw new Error(`bad format for MM tag: ${mm}`);
         }
@@ -341,9 +341,7 @@ export function getOrientedCigar(flip, cigar) {
         }
         return ret;
     }
-    else {
-        return cigar;
-    }
+    return cigar;
 }
 export function getOrientedMismatches(flip, cigar) {
     const p = parseCigar(cigar);
@@ -387,8 +385,8 @@ export function getLengthSansClipping(cigar) {
 }
 export function getClip(cigar, strand) {
     return strand === -1
-        ? +(cigar.match(startClip) || [])[1] || 0
-        : +(cigar.match(endClip) || [])[1] || 0;
+        ? +(startClip.exec(cigar) || [])[1] || 0
+        : +(endClip.exec(cigar) || [])[1] || 0;
 }
 export function getTag(f, tag) {
     const tags = f.get('tags');
@@ -402,7 +400,11 @@ export function getTag(f, tag) {
 // usage can keep this false
 export function featurizeSA(SA, id, strand, readName, normalize) {
     return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
-        const [saRef, saStart, saStrand, saCigar] = aln.split(',');
+        const ret = aln.split(',');
+        const saRef = ret[0];
+        const saStart = ret[1];
+        const saStrand = ret[2];
+        const saCigar = ret[3];
         const saLengthOnRef = getLengthOnRef(saCigar);
         const saLength = getLength(saCigar);
         const saLengthSansClipping = getLengthSansClipping(saCigar);

package/esm/PileupRPC/base.d.ts

@@ -4,5 +4,5 @@ export default abstract class PileupBaseRPC extends RpcMethodType {
     serializeArguments(args: RenderArgs & {
         signal?: AbortSignal;
         statusCallback?: (arg: string) => void;
-    }, rpcDriver: string): Promise<{}>;
+    }, rpcDriver: string): Promise<Record<string, unknown>>;
 }

package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts

@@ -4,7 +4,7 @@ import PileupBaseRPC from '../base';
 export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
     name: string;
     execute(args: {
-        adapterConfig: {};
+        adapterConfig: Record<string, unknown>;
         signal?: RemoteAbortSignal;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -4,14 +4,14 @@ import PileupBaseRPC from '../base';
 export default class PileupGetReducedFeatures extends PileupBaseRPC {
     name: string;
     execute(args: {
-        adapterConfig: {};
+        adapterConfig: Record<string, unknown>;
         signal?: RemoteAbortSignal;
         headers?: Record<string, string>;
         regions: Region[];
         sessionId: string;
         tag: string;
     }, rpcDriver: string): Promise<{
-        chains: ({
+        chains: {
             id: string;
             refName: string;
             name: any;
@@ -25,7 +25,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
             next_pos: any;
             clipPos: any;
             SA: any;
-        }[] | undefined)[];
+        }[][];
         stats: {
             upper: number;
             lower: number;

package/esm/PileupRPC/methods/GetVisibleModifications.d.ts

@@ -4,7 +4,7 @@ import PileupBaseRPC from '../base';
 export default class PileupGetVisibleModifications extends PileupBaseRPC {
     name: string;
     execute(args: {
-        adapterConfig: {};
+        adapterConfig: Record<string, unknown>;
         signal?: RemoteAbortSignal;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/PileupRenderer/PileupLayoutSession.d.ts

@@ -15,7 +15,7 @@ type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
 interface CachedPileupLayout {
     layout: MyMultiLayout;
     config: AnyConfigurationModel;
-    filters: SerializableFilterChain;
+    filters?: SerializableFilterChain;
     filterBy: unknown;
     sortedBy: unknown;
     showSoftClip: boolean;

package/esm/PileupRenderer/PileupLayoutSession.js

@@ -1,8 +1,9 @@
 import deepEqual from 'fast-deep-equal';
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { readConfObject } from '@jbrowse/core/configuration';
-// Sorting and revealing soft clip changes the layout of Pileup renderer
-// Adds extra conditions to see if cached layout is valid
+// The pileup layout session adds
+// - sorting and revealing soft clip changes the layout of pileup renderer
+// - extra conditions to see if cached layout is valid
 export class PileupLayoutSession extends LayoutSession {
     constructor(args) {
         super(args);

package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -8,7 +8,7 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
         tag?: string;
     };
     colorTagMap?: Record<string, string>;
-    modificationTagMap?: Record<string, string | undefined>;
+    modificationTagMap?: Record<string, string>;
     sortedBy?: {
         type: string;
         pos: number;

package/esm/PileupRenderer/PileupRenderer.js

@@ -19,7 +19,7 @@ export default class PileupRenderer extends BoxRendererType {
         }
         const pm = this.pluginManager;
         const { dataAdapter } = await getAdapter(pm, sessionId, sequenceAdapter);
-        const [region] = regions;
+        const region = regions[0];
         return fetchSequence(region, dataAdapter);
     }
     getExpandedRegion(region, renderArgs) {
@@ -39,7 +39,7 @@ export default class PileupRenderer extends BoxRendererType {
         const features = await this.getFeatures(renderProps);
         const layout = this.createLayoutInWorker(renderProps);
         const { regions, bpPerPx } = renderProps;
-        const [region] = regions;
+        const region = regions[0];
         const layoutRecords = layoutFeats({
             ...renderProps,
             features,
@@ -53,17 +53,20 @@ export default class PileupRenderer extends BoxRendererType {
         const width = (region.end - region.start) / bpPerPx;
         const height = Math.max(layout.getTotalHeight(), 1);
         const { makeImageData } = await import('./makeImageData');
-        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData({
-            ctx,
-            layoutRecords: layoutRecords.filter(notEmpty),
-            canvasWidth: width,
-            renderArgs: {
-                ...renderProps,
-                layout,
-                features,
-                regionSequence,
-            },
-        }));
+        const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+            makeImageData({
+                ctx,
+                layoutRecords: layoutRecords.filter(notEmpty),
+                canvasWidth: width,
+                renderArgs: {
+                    ...renderProps,
+                    layout,
+                    features,
+                    regionSequence,
+                },
+            });
+            return undefined;
+        });
         const results = await super.render({
             ...renderProps,
             ...res,

package/esm/PileupRenderer/colorBy.js

@@ -39,21 +39,19 @@ function getStranded(feature) {
             return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand';
         }
         // mate missing, separate color
-        else if (flags & 8) {
+        if (flags & 8) {
             return strand * flipper === 1
                 ? 'color_rev_missing_mate'
                 : 'color_fwd_missing_mate';
         }
         // same chrom without proper pairing gets separate color
-        else if (feature.get('refName') === feature.get('next_ref')) {
+        if (feature.get('refName') === feature.get('next_ref')) {
             return strand * flipper === 1
                 ? 'color_rev_strand_not_proper'
                 : 'color_fwd_strand_not_proper';
         }
         // abberant chrom
-        else {
-            return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
-        }
+        return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr';
     }
     return 'color_unknown';
 }

package/esm/PileupRenderer/components/PileupRendering.d.ts

@@ -3,7 +3,7 @@ import { Region } from '@jbrowse/core/util/types';
 import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
 declare const PileupRendering: (props: {
     blockKey: string;
-    displayModel: BaseLinearDisplayModel;
+    displayModel?: BaseLinearDisplayModel;
     width: number;
     height: number;
     regions: Region[];