@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/CramAdapter/util.js

@@ -1,213 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.readFeaturesToMismatches = readFeaturesToMismatches;
-exports.readFeaturesToCIGAR = readFeaturesToCIGAR;
-function readFeaturesToMismatches(readFeatures, start, qual) {
-    if (!readFeatures) {
-        return [];
-    }
-    const mismatches = new Array(readFeatures.length);
-    let j = 0;
-    let insLen = 0;
-    let refPos = 0;
-    let sublen = 0;
-    let lastPos = start;
-    for (const { refPos: p, code, pos, data, sub, ref } of readFeatures) {
-        sublen = refPos - lastPos;
-        lastPos = refPos;
-        if (sublen && insLen > 0) {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${insLen}`,
-                length: 0,
-            };
-            insLen = 0;
-        }
-        refPos = p - 1 - start;
-        if (code === 'X') {
-            mismatches[j++] = {
-                start: refPos,
-                length: 1,
-                base: sub,
-                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
-                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
-                type: 'mismatch',
-            };
-        }
-        else if (code === 'I') {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${data.length}`,
-                length: 0,
-            };
-        }
-        else if (code === 'N') {
-            mismatches[j++] = {
-                type: 'skip',
-                length: data,
-                start: refPos,
-                base: 'N',
-            };
-        }
-        else if (code === 'S') {
-            const len = data.length;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'softclip',
-                base: `S${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'P') {
-        }
-        else if (code === 'H') {
-            const len = data;
-            mismatches[j++] = {
-                start: refPos,
-                type: 'hardclip',
-                base: `H${len}`,
-                cliplen: len,
-                length: 1,
-            };
-        }
-        else if (code === 'D') {
-            mismatches[j++] = {
-                type: 'deletion',
-                length: data,
-                start: refPos,
-                base: '*',
-            };
-        }
-        else if (code === 'b') {
-        }
-        else if (code === 'q') {
-        }
-        else if (code === 'B') {
-        }
-        else if (code === 'i') {
-            insLen++;
-        }
-        else if (code === 'Q') {
-        }
-    }
-    if (sublen && insLen > 0) {
-        mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: `${insLen}`,
-            length: 0,
-        };
-        insLen = 0;
-    }
-    return mismatches.slice(0, j);
-}
-function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
-    let seq = '';
-    let cigar = '';
-    let op = 'M';
-    let oplen = 0;
-    if (!refRegion) {
-        return '';
-    }
-    const ref = refRegion.seq;
-    const refStart = refRegion.start;
-    let lastPos = alignmentStart;
-    let sublen = 0;
-    let insLen = 0;
-    if (readFeatures !== undefined) {
-        for (const { code, refPos, sub, data } of readFeatures) {
-            sublen = refPos - lastPos;
-            seq += ref.slice(lastPos - refStart, refPos - refStart);
-            lastPos = refPos;
-            if (insLen > 0 && sublen) {
-                cigar += `${insLen}I`;
-                insLen = 0;
-            }
-            if (oplen && op !== 'M') {
-                cigar += `${oplen}${op}`;
-                oplen = 0;
-            }
-            if (sublen) {
-                op = 'M';
-                oplen += sublen;
-            }
-            if (code === 'b') {
-                const ret = data.split(',');
-                const added = String.fromCharCode(...ret);
-                seq += added;
-                lastPos += added.length;
-                oplen += added.length;
-            }
-            else if (code === 'B') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'X') {
-                seq += sub;
-                lastPos++;
-                oplen++;
-            }
-            else if (code === 'D' || code === 'N') {
-                lastPos += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data + code;
-                oplen = 0;
-            }
-            else if (code === 'I' || code === 'S') {
-                seq += data;
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += data.length + code;
-                oplen = 0;
-            }
-            else if (code === 'i') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                insLen++;
-                seq += data;
-                oplen = 0;
-            }
-            else if (code === 'P') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}P`;
-            }
-            else if (code === 'H') {
-                if (oplen) {
-                    cigar += `${oplen}${op}`;
-                }
-                cigar += `${data}H`;
-                oplen = 0;
-            }
-        }
-    }
-    else {
-        sublen = readLen - seq.length;
-    }
-    if (seq.length !== readLen) {
-        sublen = readLen - seq.length;
-        seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
-        if (oplen && op !== 'M') {
-            cigar += `${oplen}${op}`;
-            oplen = 0;
-        }
-        op = 'M';
-        oplen += sublen;
-    }
-    if (sublen && insLen > 0) {
-        cigar += `${insLen}I`;
-    }
-    if (oplen) {
-        cigar += `${oplen}${op}`;
-    }
-    return cigar;
-}

package/dist/GuessAlignmentsTypes/index.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessAlignmentsTypesF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessAlignmentsTypesF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            const indexName = index && (0, tracks_1.getFileName)(index);
-            if ((0, util_1.testAdapter)(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
-                return {
-                    type: 'BamAdapter',
-                    bamLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                    },
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
-                return {
-                    type: 'CramAdapter',
-                    cramLocation: file,
-                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-        return (adapterName) => {
-            if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
-                return 'AlignmentsTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,12 +0,0 @@
-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;
-        sequenceAdapter: BaseFeatureDataAdapter;
-    } | {
-        bam: BamFile;
-        sequenceAdapter?: undefined;
-    }>;
-}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -1,27 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const bam_1 = require("@gmod/bam");
-const BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
-class HtsgetBamAdapter extends BamAdapter_1.default {
-    async configurePre() {
-        const htsgetBase = this.getConf('htsgetBase');
-        const htsgetTrackId = this.getConf('htsgetTrackId');
-        const bam = new bam_1.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,
-            };
-        }
-        return { bam };
-    }
-}
-exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.d.ts

@@ -1,18 +0,0 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    htsgetBase: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    htsgetTrackId: {
-        type: string;
-        description: string;
-        defaultValue: string;
-    };
-    sequenceAdapter: {
-        type: string;
-        description: string;
-        defaultValue: null;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
-    htsgetBase: {
-        type: 'string',
-        description: 'the base URL to fetch from',
-        defaultValue: '',
-    },
-    htsgetTrackId: {
-        type: 'string',
-        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 });
-exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/dist/HtsgetBamAdapter/index.js

@@ -1,54 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = HtsgetBamAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function HtsgetBamAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'HtsgetBamAdapter',
-            displayName: 'Htsget BAM adapter',
-            adapterMetadata: {
-                hiddenFromGUI: true,
-            },
-            configSchema: configSchema_1.default,
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/LinearAlignmentsDisplay/alignmentsModel.d.ts

@@ -1,12 +0,0 @@
-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">;
-    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>;

package/dist/LinearAlignmentsDisplay/alignmentsModel.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LinearAlignmentsDisplayMixin = LinearAlignmentsDisplayMixin;
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("./util");
-function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
-    return mobx_state_tree_1.types.model({
-        PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...(0, util_1.getLowerPanelDisplays)(pluginManager).map(f => f.stateModel))),
-        SNPCoverageDisplay: mobx_state_tree_1.types.maybe(pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel),
-        snpCovHeight: 45,
-        type: mobx_state_tree_1.types.literal('LinearAlignmentsDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        heightPreConfig: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        userFeatureScreenDensity: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-        lowerPanelType: 'LinearPileupDisplay',
-    });
-}

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

@@ -1,5 +0,0 @@
-import type { LinearAlignmentsDisplayModel } from '../model';
-declare const AlignmentsDisplay: ({ model, }: {
-    model: LinearAlignmentsDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,31 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const configuration_1 = require("@jbrowse/core/configuration");
-const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()({
-    resizeHandle: {
-        height: 5,
-        position: 'absolute',
-        zIndex: 2,
-    },
-});
-const AlignmentsDisplay = (0, mobx_react_1.observer)(function AlignmentsDisplay({ model, }) {
-    var _a;
-    const { PileupDisplay, SNPCoverageDisplay } = model;
-    const { classes } = useStyles();
-    if (!SNPCoverageDisplay) {
-        return null;
-    }
-    const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
-    return ((0, jsx_runtime_1.jsxs)("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)("div", { "data-testid": "Blockset-snpcoverage", children: (0, jsx_runtime_1.jsx)(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay }) }), (0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { onDrag: delta => {
-                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                    return delta;
-                }, className: classes.resizeHandle, style: { top: top - 4 } }), (0, jsx_runtime_1.jsx)("div", { "data-testid": "Blockset-pileup", style: {
-                    position: 'absolute',
-                    top,
-                }, children: (0, jsx_runtime_1.jsx)(PileupDisplay.RenderingComponent, { model: PileupDisplay }) })] }));
-});
-exports.default = AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/configSchema.d.ts

@@ -1,36 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function configModelFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    height: {
-        type: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearAlignmentsDisplay/configSchema.js

@@ -1,19 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = configModelFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-function configModelFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
-        pileupDisplay: pluginManager.getDisplayType('LinearPileupDisplay')
-            .configSchema,
-        snpCoverageDisplay: pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema,
-        height: {
-            type: 'number',
-            defaultValue: 250,
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/dist/LinearAlignmentsDisplay/index.js

@@ -1,24 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LinearAlignmentsDisplayF;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function LinearAlignmentsDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearAlignmentsDisplay',
-            displayName: 'Alignments display (combination)',
-            configSchema,
-            stateModel: (0, model_1.default)(pluginManager, configSchema),
-            trackType: 'AlignmentsTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: AlignmentsDisplay_1.default,
-        });
-    });
-}