@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/shared/renderSvgUtil.js

@@ -1,66 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.renderSvg = renderSvg;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-function getId(id) {
-    const isJest = typeof jest === 'undefined';
-    return `arc-clip-${isJest ? id : 'jest'}`;
-}
-async function renderSvg(self, opts, cb) {
-    const view = (0, util_1.getContainingView)(self);
-    const width = view.dynamicBlocks.totalWidthPx;
-    const height = self.height;
-    if (opts.rasterizeLayers) {
-        const canvas = document.createElement('canvas');
-        canvas.width = width * 2;
-        canvas.height = height * 2;
-        const ctx = canvas.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.scale(2, 2);
-        cb(self, ctx, width, height);
-        return ((0, jsx_runtime_1.jsx)("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
-    }
-    else {
-        const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
-        const ctx = new C2S.default(width, height);
-        cb(self, ctx, width, height);
-        const clipid = getId(self.id);
-        return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: height }) }) }), (0, jsx_runtime_1.jsx)("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })] }));
-    }
-}

package/dist/shared/types.d.ts

@@ -1,96 +0,0 @@
-export type SkipMap = Record<string, {
-    score: number;
-    feature: unknown;
-    start: number;
-    end: number;
-    strand: number;
-    effectiveStrand: number;
-}>;
-export interface BinEntry {
-    entryDepth: number;
-    '-1': number;
-    '0': number;
-    '1': number;
-    avgProbability?: number;
-}
-type BinType = Record<string, BinEntry>;
-export interface BaseCoverageBin {
-    refbase?: string;
-    depth: number;
-    readsCounted: number;
-    ref: BinEntry;
-    snps: BinType;
-    mods: BinType;
-    nonmods: BinType;
-    delskips: BinType;
-    noncov: BinType;
-}
-export interface PreBinEntry {
-    entryDepth: number;
-    '-1': number;
-    '0': number;
-    '1': number;
-    probabilities: number[];
-}
-type PreBinType = Record<string, PreBinEntry>;
-export interface PreBaseCoverageBin extends PreBaseCoverageBinSubtypes {
-    refbase?: string;
-    depth: number;
-    readsCounted: number;
-    ref: PreBinEntry;
-}
-export interface PreBaseCoverageBinSubtypes {
-    snps: PreBinType;
-    mods: PreBinType;
-    nonmods: PreBinType;
-    delskips: PreBinType;
-    noncov: PreBinType;
-}
-export interface ModificationType {
-    type: string;
-    base: string;
-    strand: string;
-}
-export interface ModificationTypeWithColor {
-    color: string;
-    type: string;
-    base: string;
-    strand: string;
-}
-export interface ColorBy {
-    type: string;
-    tag?: string;
-    modifications?: {
-        twoColor?: boolean;
-        isolatedModification?: string;
-        threshold?: number;
-    };
-}
-export interface FilterBy {
-    flagExclude: number;
-    flagInclude: number;
-    readName?: string;
-    tagFilter?: {
-        tag: string;
-        value?: string;
-    };
-}
-export interface SortedBy {
-    type: string;
-    pos: number;
-    refName: string;
-    assemblyName: string;
-    tag?: string;
-}
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    insertedBases?: string;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
-export {};

package/dist/shared/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/shared/util.d.ts

@@ -1,22 +0,0 @@
-import type { ChainData } from './fetchChains';
-export declare function hasPairedReads(features: ChainData): boolean;
-export declare function alphaColor(baseColor: string, p: number): string;
-export declare const defaultFilterFlags: {
-    flagInclude: number;
-    flagExclude: number;
-};
-export declare const negFlags: {
-    flagInclude: number;
-    flagExclude: number;
-};
-export declare const posFlags: {
-    flagInclude: number;
-    flagExclude: number;
-};
-export declare function cacheGetter<T>(ctor: {
-    prototype: T;
-}, prop: keyof T): void;
-export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
-export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
-export declare function shouldRenderChevrons(bpPerPx: number, featureHeight: number): boolean;
-export declare const CHEVRON_WIDTH = 5;

package/dist/shared/util.js

@@ -1,68 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.CHEVRON_WIDTH = exports.posFlags = exports.negFlags = exports.defaultFilterFlags = void 0;
-exports.hasPairedReads = hasPairedReads;
-exports.alphaColor = alphaColor;
-exports.cacheGetter = cacheGetter;
-exports.filterReadFlag = filterReadFlag;
-exports.filterTagValue = filterTagValue;
-exports.shouldRenderChevrons = shouldRenderChevrons;
-const colord_1 = require("@jbrowse/core/util/colord");
-function hasPairedReads(features) {
-    for (const f of features.chains.values()) {
-        if (f[0].flags & 1) {
-            return true;
-        }
-    }
-    return false;
-}
-function alphaColor(baseColor, p) {
-    return p !== 1
-        ? (0, colord_1.colord)(baseColor)
-            .alpha(Math.min(1, p * p + 0.1))
-            .toHslString()
-        : baseColor;
-}
-exports.defaultFilterFlags = {
-    flagInclude: 0,
-    flagExclude: 1540,
-};
-exports.negFlags = {
-    flagInclude: 16,
-    flagExclude: 1540,
-};
-exports.posFlags = {
-    flagInclude: 0,
-    flagExclude: 1556,
-};
-function cacheGetter(ctor, prop) {
-    const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
-    const getter = desc.get;
-    Object.defineProperty(ctor.prototype, prop, {
-        get() {
-            const ret = getter.call(this);
-            Object.defineProperty(this, prop, { value: ret });
-            return ret;
-        },
-    });
-}
-function filterReadFlag(flags, flagInclude, flagExclude) {
-    if ((flags & flagInclude) !== flagInclude) {
-        return true;
-    }
-    else if (flags & flagExclude) {
-        return true;
-    }
-    else {
-        return false;
-    }
-}
-function filterTagValue(readVal, filterVal) {
-    return filterVal === '*'
-        ? readVal === undefined
-        : `${readVal}` !== `${filterVal}`;
-}
-function shouldRenderChevrons(bpPerPx, featureHeight) {
-    return bpPerPx < 50 && featureHeight >= 3;
-}
-exports.CHEVRON_WIDTH = 5;

package/dist/util.d.ts

@@ -1,25 +0,0 @@
-import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { AugmentedRegion, Feature } from '@jbrowse/core/util';
-import type { IAutorunOptions } from 'mobx';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
-export declare const orientationTypes: {
-    fr: Record<string, string>;
-    rf: Record<string, string>;
-    ff: Record<string, string>;
-};
-export declare const pairMap: {
-    readonly LR: "color_pair_lr";
-    readonly LL: "color_pair_ll";
-    readonly RR: "color_pair_rr";
-    readonly RL: "color_pair_rl";
-};
-export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
-export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
-type DisplayModel = IAnyStateTreeNode & {
-    setError: (arg: unknown) => void;
-};
-export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
-export declare function randomColor(str: string): string;
-export declare function getColorForModification(str: string): string;
-export { modificationData } from './shared/modificationData';

package/dist/util.js

@@ -1,114 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.modificationData = exports.pairMap = exports.orientationTypes = void 0;
-exports.getTagAlt = getTagAlt;
-exports.getColorWGBS = getColorWGBS;
-exports.fetchSequence = fetchSequence;
-exports.createAutorun = createAutorun;
-exports.randomColor = randomColor;
-exports.getColorForModification = getColorForModification;
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const rxjs_1 = require("rxjs");
-const operators_1 = require("rxjs/operators");
-const modificationData_1 = require("./shared/modificationData");
-function getTagAlt(feature, tag, alt) {
-    var _a;
-    const tags = feature.get('tags');
-    return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
-}
-exports.orientationTypes = {
-    fr: {
-        F1R2: 'LR',
-        F2R1: 'LR',
-        F1F2: 'LL',
-        F2F1: 'LL',
-        R1R2: 'RR',
-        R2R1: 'RR',
-        R1F2: 'RL',
-        R2F1: 'RL',
-    },
-    rf: {
-        R1F2: 'LR',
-        R2F1: 'LR',
-        R1R2: 'LL',
-        R2R1: 'LL',
-        F1F2: 'RR',
-        F2F1: 'RR',
-        F1R2: 'RL',
-        F2R1: 'RL',
-    },
-    ff: {
-        F2F1: 'LR',
-        R1R2: 'LR',
-        F2R1: 'LL',
-        R1F2: 'LL',
-        R2F1: 'RR',
-        F1R2: 'RR',
-        R2R1: 'RL',
-        F1F2: 'RL',
-    },
-};
-exports.pairMap = {
-    LR: 'color_pair_lr',
-    LL: 'color_pair_ll',
-    RR: 'color_pair_rr',
-    RL: 'color_pair_rl',
-};
-function getColorWGBS(strand, base) {
-    if (strand === 1) {
-        if (base === 'C') {
-            return '#f00';
-        }
-        if (base === 'T') {
-            return '#00f';
-        }
-    }
-    else if (strand === -1) {
-        if (base === 'G') {
-            return '#f00';
-        }
-        if (base === 'A') {
-            return '#00f';
-        }
-    }
-    return '#888';
-}
-async function fetchSequence(region, adapter) {
-    var _a;
-    const { start, end, originalRefName, refName } = region;
-    const feats = await (0, rxjs_1.firstValueFrom)(adapter
-        .getFeatures({
-        ...region,
-        refName: originalRefName || refName,
-        end,
-        start,
-    })
-        .pipe((0, operators_1.toArray)()));
-    return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
-}
-function createAutorun(self, cb, opts) {
-    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-        try {
-            await cb();
-        }
-        catch (e) {
-            if ((0, mobx_state_tree_1.isAlive)(self)) {
-                self.setError(e);
-            }
-        }
-    }, opts));
-}
-function randomColor(str) {
-    let sum = 0;
-    for (let i = 0; i < str.length; i++) {
-        sum += str.charCodeAt(i);
-    }
-    return `hsl(${sum * 10}, 20%, 50%)`;
-}
-function getColorForModification(str) {
-    var _a;
-    return ((_a = modificationData_1.modificationData[str]) === null || _a === void 0 ? void 0 : _a.color) || randomColor(str);
-}
-var modificationData_2 = require("./shared/modificationData");
-Object.defineProperty(exports, "modificationData", { enumerable: true, get: function () { return modificationData_2.modificationData; } });

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.d.ts

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1 +0,0 @@
-export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/esm/CramAdapter/readFeaturesToCIGAR.d.ts

@@ -1,9 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export declare function readFeaturesToCIGAR(readFeatures: ReadFeatures, alignmentStart: number, readLen: number, refRegion?: {
-    seq: string;
-    start: number;
-}): string;
-export {};

package/esm/CramAdapter/readFeaturesToCIGAR.js

@@ -1,208 +0,0 @@
-export function readFeaturesToMismatches(readFeatures = [], start, qual) {
-    const mismatches = new Array(readFeatures.length);
-    let j = 0;
-    let insLen = 0;
-    let refPos = 0;
-    let sublen = 0;
-    let lastPos = start;
-    for (const ret of readFeatures) {
-        const { refPos: p, code, pos, data, sub, ref } = ret;
-        sublen = refPos - lastPos;
-        lastPos = refPos;
-        if (sublen && insLen > 0) {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${insLen}`,
-                insertedBases: data,
-                length: 0,
-            };
-            insLen = 0;
-        }
-        refPos = p - 1 - start;
-        if (code === 'X') {
-            mismatches[j++] = {
-                start: refPos,
-                length: 1,
-                base: sub,
-                qual: qual === null || qual === void 0 ? void 0 : qual[pos - 1],
-                altbase: ref === null || ref === void 0 ? void 0 : ref.toUpperCase(),
-                type: 'mismatch',
-            };
-        }
-        else if (code === 'I') {
-            mismatches[j++] = {
-                start: refPos,
-                type: 'insertion',
-                base: `${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: `${insLen}`,
-            length: 0,
-        };
-        insLen = 0;
-    }
-    return mismatches.slice(0, j);
-}
-export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
-    let seq = '';
-    let cigar = '';
-    let op = 'M';
-    let oplen = 0;
-    if (!refRegion) {
-        return '';
-    }
-    const ref = refRegion.seq;
-    const refStart = refRegion.start;
-    let lastPos = alignmentStart;
-    let sublen = 0;
-    let insLen = 0;
-    if (readFeatures !== undefined) {
-        for (const { code, refPos, sub, data } of readFeatures) {
-            sublen = refPos - lastPos;
-            seq += ref.slice(lastPos - refStart, refPos - refStart);
-            lastPos = refPos;
-            if (insLen > 0 && sublen) {
-                cigar += `${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/esm/CramAdapter/readFeaturesToMismatches.d.ts

@@ -1,5 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { CramRecord } from '@gmod/cram';
-type ReadFeatures = CramRecord['readFeatures'];
-export declare function readFeaturesToMismatches(readFeatures: ReadFeatures, start: number, qual?: number[] | null): Mismatch[];
-export {};