@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/esm/CramAdapter/index.js

@@ -1,12 +1,12 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
             displayName: 'CRAM adapter',
             configSchema,
-            getAdapterClass: () => import('./CramAdapter').then(r => r.default),
+            getAdapterClass: () => import("./CramAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/CramAdapter/readFeaturesToNumericCIGAR.d.ts

@@ -0,0 +1,4 @@
+import type { CramRecord } from '@gmod/cram';
+type ReadFeatures = CramRecord['readFeatures'];
+export declare function readFeaturesToNumericCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number): ArrayLike<number>;
+export {};

package/esm/CramAdapter/readFeaturesToNumericCIGAR.js

@@ -0,0 +1,112 @@
+import { CODE_B, CODE_D, CODE_H, CODE_I, CODE_N, CODE_P, CODE_S, CODE_X, CODE_b, CODE_i, } from "./const.js";
+const CIGAR_CODE_TO_INDEX = {
+    77: 0,
+    73: 1,
+    68: 2,
+    78: 3,
+    83: 4,
+    72: 5,
+    80: 6,
+    61: 7,
+    88: 8,
+};
+export function readFeaturesToNumericCIGAR(readFeatures, alignmentStart, readLen) {
+    const cigarParts = [];
+    let op = 77;
+    let oplen = 0;
+    let lastPos = alignmentStart;
+    let insLen = 0;
+    let seqLen = 0;
+    if (readFeatures !== undefined) {
+        for (let i = 0, l = readFeatures.length; i < l; i++) {
+            const { code, refPos, data } = readFeatures[i];
+            const sublen = refPos - lastPos;
+            seqLen += sublen;
+            lastPos = refPos;
+            if (insLen && sublen) {
+                const opIndex = CIGAR_CODE_TO_INDEX[73];
+                cigarParts.push((insLen << 4) | opIndex);
+                insLen = 0;
+            }
+            if (oplen && op !== 77) {
+                const opIndex = CIGAR_CODE_TO_INDEX[op];
+                cigarParts.push((oplen << 4) | opIndex);
+                oplen = 0;
+            }
+            if (sublen) {
+                op = 77;
+                oplen += sublen;
+            }
+            const codeChar = code.charCodeAt(0);
+            if (codeChar === CODE_b) {
+                const addedLen = data.split(',').length;
+                seqLen += addedLen;
+                lastPos += addedLen;
+                oplen += addedLen;
+            }
+            else if (codeChar === CODE_B || codeChar === CODE_X) {
+                seqLen++;
+                lastPos++;
+                oplen++;
+            }
+            else if (codeChar === CODE_D || codeChar === CODE_N) {
+                lastPos += data;
+                if (oplen) {
+                    const opIndex = CIGAR_CODE_TO_INDEX[op];
+                    cigarParts.push((oplen << 4) | opIndex);
+                    oplen = 0;
+                }
+                const opIndex = CIGAR_CODE_TO_INDEX[codeChar];
+                cigarParts.push((data << 4) | opIndex);
+            }
+            else if (codeChar === CODE_I || codeChar === CODE_S) {
+                const dataLen = data.length;
+                seqLen += dataLen;
+                if (oplen) {
+                    const opIndex = CIGAR_CODE_TO_INDEX[op];
+                    cigarParts.push((oplen << 4) | opIndex);
+                    oplen = 0;
+                }
+                const opIndex = CIGAR_CODE_TO_INDEX[codeChar];
+                cigarParts.push((dataLen << 4) | opIndex);
+            }
+            else if (codeChar === CODE_i) {
+                if (oplen) {
+                    const opIndex = CIGAR_CODE_TO_INDEX[op];
+                    cigarParts.push((oplen << 4) | opIndex);
+                    oplen = 0;
+                }
+                insLen++;
+                seqLen++;
+            }
+            else if (codeChar === CODE_P || codeChar === CODE_H) {
+                if (oplen) {
+                    const opIndex = CIGAR_CODE_TO_INDEX[op];
+                    cigarParts.push((oplen << 4) | opIndex);
+                    oplen = 0;
+                }
+                const opIndex = CIGAR_CODE_TO_INDEX[codeChar];
+                cigarParts.push((data << 4) | opIndex);
+            }
+        }
+    }
+    const remaining = readLen - seqLen;
+    if (remaining) {
+        if (oplen && op !== 77) {
+            const opIndex = CIGAR_CODE_TO_INDEX[op];
+            cigarParts.push((oplen << 4) | opIndex);
+            oplen = 0;
+        }
+        op = 77;
+        oplen += remaining;
+    }
+    if (remaining && insLen) {
+        const opIndex = CIGAR_CODE_TO_INDEX[73];
+        cigarParts.push((insLen << 4) | opIndex);
+    }
+    if (oplen) {
+        const opIndex = CIGAR_CODE_TO_INDEX[op];
+        cigarParts.push((oplen << 4) | opIndex);
+    }
+    return cigarParts;
+}

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,12 +1,8 @@
-import BamAdapter from '../BamAdapter/BamAdapter';
+import BamAdapter from '../BamAdapter/BamAdapter.ts';
+import BamSlightlyLazyFeature from '../BamAdapter/BamSlightlyLazyFeature.ts';
 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;
-        sequenceAdapter: BaseFeatureDataAdapter;
-    } | {
-        bam: BamFile;
-        sequenceAdapter?: undefined;
-    }>;
+    protected configure(): {
+        bam: BamFile<BamSlightlyLazyFeature>;
+    };
 }

package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -1,21 +1,19 @@
 import { HtsgetFile } from '@gmod/bam';
-import BamAdapter from '../BamAdapter/BamAdapter';
+import BamAdapter from "../BamAdapter/BamAdapter.js";
+import BamSlightlyLazyFeature from "../BamAdapter/BamSlightlyLazyFeature.js";
 export default class HtsgetBamAdapter extends BamAdapter {
-    async configurePre() {
-        const htsgetBase = this.getConf('htsgetBase');
-        const htsgetTrackId = this.getConf('htsgetTrackId');
-        const bam = new HtsgetFile({
-            baseUrl: htsgetBase,
-            trackId: htsgetTrackId,
-        });
-        const adapterConfig = this.getConf('sequenceAdapter');
-        if (adapterConfig && this.getSubAdapter) {
-            const adapter = await this.getSubAdapter(adapterConfig);
-            return {
-                bam,
-                sequenceAdapter: adapter.dataAdapter,
+    configure() {
+        if (!this.configureResult) {
+            const htsgetBase = this.getConf('htsgetBase');
+            const htsgetTrackId = this.getConf('htsgetTrackId');
+            this.configureResult = {
+                bam: new HtsgetFile({
+                    baseUrl: htsgetBase,
+                    trackId: htsgetTrackId,
+                    recordClass: BamSlightlyLazyFeature,
+                }),
             };
         }
-        return { bam };
+        return this.configureResult;
     }
 }

package/esm/HtsgetBamAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const HtsgetBamAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     htsgetBase: {
         type: string;
         description: string;
@@ -9,10 +9,5 @@ declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configuratio
         description: string;
         defaultValue: string;
     };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HtsgetBamAdapter;

package/esm/HtsgetBamAdapter/configSchema.js

@@ -11,10 +11,5 @@ const HtsgetBamAdapter = ConfigurationSchema('HtsgetBamAdapter', {
         description: 'the trackId, which is appended to the base URL',
         defaultValue: '',
     },
-    sequenceAdapter: {
-        type: 'frozen',
-        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
-        defaultValue: null,
-    },
 }, { explicitlyTyped: true });
 export default HtsgetBamAdapter;

package/esm/HtsgetBamAdapter/index.js

@@ -1,5 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -9,7 +9,7 @@ export default function HtsgetBamAdapterF(pluginManager) {
                 hiddenFromGUI: true,
             },
             configSchema,
-            getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
+            getAdapterClass: () => import("./HtsgetBamAdapter.js").then(r => r.default),
         });
     });
 }

package/esm/LinearAlignmentsDisplay/alignmentsModel.d.ts

@@ -1,12 +1,12 @@
 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>;
-    snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
-    type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
+export declare function LinearAlignmentsDisplayMixin(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    PileupDisplay: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyType>;
+    SNPCoverageDisplay: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    snpCovHeight: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
     configuration: AnyConfigurationSchemaType;
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userFeatureScreenDensity: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    lowerPanelType: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+}, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/LinearAlignmentsDisplay/alignmentsModel.js

@@ -1,6 +1,6 @@
 import { ConfigurationReference } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
-import { getLowerPanelDisplays } from './util';
+import { types } from '@jbrowse/mobx-state-tree';
+import { getLowerPanelDisplays } from "./util.js";
 export function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
     return types.model({
         PileupDisplay: types.maybe(types.union(...getLowerPanelDisplays(pluginManager).map(f => f.stateModel))),

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

@@ -1,4 +1,4 @@
-import type { LinearAlignmentsDisplayModel } from '../model';
+import type { LinearAlignmentsDisplayModel } from '../model.ts';
 declare const AlignmentsDisplay: ({ model, }: {
     model: LinearAlignmentsDisplayModel;
 }) => import("react/jsx-runtime").JSX.Element | null;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     resizeHandle: {
         height: 5,
@@ -15,19 +15,25 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 const AlignmentsDisplay = observer(function AlignmentsDisplay({ model, }) {
-    var _a;
-    const { PileupDisplay, SNPCoverageDisplay } = model;
+    const { PileupDisplay, SNPCoverageDisplay, height, setScrollTop } = model;
     const { classes } = useStyles();
     if (!SNPCoverageDisplay) {
         return null;
     }
-    const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
-    return (_jsxs("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' }, children: [_jsx("div", { "data-testid": "Blockset-snpcoverage", children: _jsx(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay }) }), _jsx(ResizeHandle, { onDrag: delta => {
+    const coverageHeight = SNPCoverageDisplay.height ?? 100;
+    const pileupHeight = height - coverageHeight;
+    return (_jsxs("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative', height }, 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: {
+                }, className: classes.resizeHandle, style: { top: coverageHeight - 4 } }), _jsx("div", { "data-testid": "Blockset-pileup", style: {
                     position: 'absolute',
-                    top,
+                    top: coverageHeight,
+                    height: pileupHeight,
+                    width: '100%',
+                    overflowY: 'auto',
+                    overflowX: 'hidden',
+                }, onScroll: evt => {
+                    setScrollTop(evt.currentTarget.scrollTop);
                 }, children: _jsx(PileupDisplay.RenderingComponent, { model: PileupDisplay }) })] }));
 });
 export default AlignmentsDisplay;

package/esm/LinearAlignmentsDisplay/configSchema.d.ts

@@ -1,12 +1,12 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function configModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configModelFactory(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     height: {
         type: string;
         defaultValue: number;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;
         description: string;
@@ -33,4 +33,4 @@ export default function configModelFactory(pluginManager: PluginManager): import
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/LinearAlignmentsDisplay/index.js

@@ -1,7 +1,7 @@
+import { lazy } from 'react';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
-import ReactComponent from './components/AlignmentsDisplay';
-import configSchemaFactory from './configSchema';
-import modelFactory from './model';
+import configSchemaFactory from "./configSchema.js";
+import modelFactory from "./model.js";
 export default function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
@@ -12,7 +12,7 @@ export default function LinearAlignmentsDisplayF(pluginManager) {
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',
             viewType: 'LinearGenomeView',
-            ReactComponent,
+            ReactComponent: lazy(() => import("./components/AlignmentsDisplay.js")),
         });
     });
 }