@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/dist/shared/components/BaseDisplayComponent.js

@@ -1,44 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    loading: {
-        backgroundColor: theme.palette.background.default,
-        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
-        position: 'absolute',
-        bottom: 0,
-        height: 50,
-        width: 300,
-        right: 0,
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
-const BlockError = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { error } = model;
-    return ((0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Reload", children: (0, jsx_runtime_1.jsx)(material_1.Button, { "data-testid": "reload_button", onClick: () => {
-                    model.reload();
-                }, children: "Reload" }) }) }));
-});
-const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
-    const { error, regionTooLarge } = model;
-    return error ? ((0, jsx_runtime_1.jsx)(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : ((0, jsx_runtime_1.jsx)(DataDisplay, { model: model, children: children }));
-});
-const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
-    const { drawn, loading } = model;
-    const view = (0, util_1.getContainingView)(model);
-    const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
-    return ((0, jsx_runtime_1.jsxs)("div", { "data-testid": `drawn-${drawn}`, children: [(0, jsx_runtime_1.jsx)("div", { style: { position: 'absolute', left }, children: children }), left !== 0 || loading ? (0, jsx_runtime_1.jsx)(LoadingBar, { model: model }) : null] }));
-});
-const LoadingBar = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes } = useStyles();
-    const { message } = model;
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.loading, children: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: message }) }));
-});
-exports.default = BaseDisplayComponent;

package/dist/shared/components/FilterByTagDialog.d.ts

@@ -1,9 +0,0 @@
-import type { FilterBy } from '../types';
-declare const FilterByTagDialog: (props: {
-    model: {
-        filterBy: FilterBy;
-        setFilterBy: (arg: FilterBy) => void;
-    };
-    handleClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default FilterByTagDialog;

package/dist/shared/components/FilterByTagDialog.js

@@ -1,88 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    paper: {
-        padding: theme.spacing(2),
-        margin: theme.spacing(2),
-    },
-    field: {
-        margin: theme.spacing(2),
-    },
-}));
-const flagNames = [
-    'read paired',
-    'read mapped in proper pair',
-    'read unmapped',
-    'mate unmapped',
-    'read reverse strand',
-    'mate reverse strand',
-    'first in pair',
-    'second in pair',
-    'not primary alignment',
-    'read fails platform/vendor quality checks',
-    'read is PCR or optical duplicate',
-    'supplementary alignment',
-];
-function Bitmask(props) {
-    const { flag = 0, setFlag } = props;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.TextField, { type: "number", value: flag, onChange: event => {
-                    setFlag(+event.target.value);
-                } }), flagNames.map((name, index) => {
-                const val = flag & (1 << index);
-                const key = `${name}_${val}`;
-                return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("input", { type: "checkbox", checked: Boolean(val), onChange: event => {
-                                if (event.target.checked) {
-                                    setFlag(flag | (1 << index));
-                                }
-                                else {
-                                    setFlag(flag & ~(1 << index));
-                                }
-                            } }), (0, jsx_runtime_1.jsx)("label", { htmlFor: key, children: name })] }, key));
-            })] }));
-}
-const FilterByTagDialog = (0, mobx_react_1.observer)(function (props) {
-    var _a, _b;
-    const { model, handleClose } = props;
-    const { classes } = useStyles();
-    const { filterBy } = model;
-    const [flagInclude, setFlagInclude] = (0, react_1.useState)(filterBy.flagInclude);
-    const [flagExclude, setFlagExclude] = (0, react_1.useState)(filterBy.flagExclude);
-    const [tag, setTag] = (0, react_1.useState)(((_a = filterBy.tagFilter) === null || _a === void 0 ? void 0 : _a.tag) || '');
-    const [tagValue, setTagValue] = (0, react_1.useState)(((_b = filterBy.tagFilter) === null || _b === void 0 ? void 0 : _b.value) || '');
-    const [readName, setReadName] = (0, react_1.useState)(filterBy.readName || '');
-    const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    const site = 'https://broadinstitute.github.io/picard/explain-flags.html';
-    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["Set filter bitmask options. Refer to ", (0, jsx_runtime_1.jsx)(material_1.Link, { href: site, children: site }), ' ', "for details"] }), (0, jsx_runtime_1.jsx)(material_1.Paper, { className: classes.paper, variant: "outlined", children: (0, jsx_runtime_1.jsxs)("div", { style: { display: 'flex' }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Read must have ALL these flags" }), (0, jsx_runtime_1.jsx)(Bitmask, { flag: flagInclude, setFlag: setFlagInclude })] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Read must have NONE of these flags" }), (0, jsx_runtime_1.jsx)(Bitmask, { flag: flagExclude, setFlag: setFlagExclude })] })] }) }), (0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.paper, variant: "outlined", children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: tag, onChange: event => {
-                                setTag(event.target.value);
-                            }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', slotProps: {
-                                htmlInput: {
-                                    maxLength: 2,
-                                },
-                            } }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: tagValue, onChange: event => {
-                                setTagValue(event.target.value);
-                            }, placeholder: "Enter tag value" })] }), (0, jsx_runtime_1.jsxs)(material_1.Paper, { className: classes.paper, variant: "outlined", children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Filter by read name" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.field, value: readName, onChange: event => {
-                                setReadName(event.target.value);
-                            }, placeholder: "Enter read name" })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", autoFocus: true, type: "submit", onClick: () => {
-                                model.setFilterBy({
-                                    flagInclude,
-                                    flagExclude,
-                                    readName,
-                                    tagFilter: tag !== ''
-                                        ? {
-                                            tag,
-                                            value: tagValue,
-                                        }
-                                        : undefined,
-                                });
-                                handleClose();
-                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                                handleClose();
-                            }, children: "Cancel" })] })] }) }));
-});
-exports.default = FilterByTagDialog;

package/dist/shared/fetchChains.d.ts

@@ -1,28 +0,0 @@
-import type { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
-import type { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
-export interface ReducedFeature {
-    name: string;
-    strand: number;
-    refName: string;
-    start: number;
-    end: number;
-    id: string;
-    flags: number;
-    tlen: number;
-    pair_orientation: string;
-    next_ref?: string;
-    next_pos?: number;
-    clipPos: number;
-    SA?: string;
-}
-export interface ChainStats {
-    max: number;
-    min: number;
-    upper: number;
-    lower: number;
-}
-export interface ChainData {
-    chains: ReducedFeature[][];
-    stats?: ChainStats;
-}
-export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/dist/shared/fetchChains.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchChains = fetchChains;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-async function fetchChains(self) {
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const view = (0, util_1.getContainingView)(self);
-    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
-        return;
-    }
-    self.setLoading(true);
-    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-        filterBy: self.filterBy,
-        adapterConfig: self.adapterConfig,
-    }));
-    self.setChainData(ret);
-    self.setLoading(false);
-}

package/dist/shared/getMaximumModificationAtEachPosition.d.ts

@@ -1,8 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-interface MaximumProbabilityMod {
-    type: string;
-    prob: number;
-    allProbs: number[];
-}
-export declare function getMaxProbModAtEachPosition(feature: Feature, cigarOps?: string[]): MaximumProbabilityMod[] | undefined;
-export {};

package/dist/shared/getMaximumModificationAtEachPosition.js

@@ -1,42 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMaxProbModAtEachPosition = getMaxProbModAtEachPosition;
-const MismatchParser_1 = require("../MismatchParser");
-const getModPositions_1 = require("../ModificationParser/getModPositions");
-const getModProbabilities_1 = require("../ModificationParser/getModProbabilities");
-const util_1 = require("../util");
-function getMaxProbModAtEachPosition(feature, cigarOps) {
-    const fstrand = feature.get('strand');
-    const seq = feature.get('seq');
-    const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
-    const ops = cigarOps || (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-    if (seq) {
-        const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
-        const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
-        const maxProbModForPosition = [];
-        let probIndex = 0;
-        for (const { type, positions } of modifications) {
-            for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx)]) || 0;
-                if (!maxProbModForPosition[ref]) {
-                    maxProbModForPosition[ref] = {
-                        type,
-                        prob,
-                        allProbs: [prob],
-                    };
-                }
-                else {
-                    const old = maxProbModForPosition[ref];
-                    maxProbModForPosition[ref] = {
-                        allProbs: [...old.allProbs, prob],
-                        prob: Math.max(old.prob, prob),
-                        type: old.prob > prob ? old.type : type,
-                    };
-                }
-            }
-            probIndex += positions.length;
-        }
-        return maxProbModForPosition;
-    }
-    return undefined;
-}

package/dist/shared/getUniqueModifications.d.ts

@@ -1,15 +0,0 @@
-import { type IAnyStateTreeNode } from 'mobx-state-tree';
-import type { ModificationType } from './types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BlockSet } from '@jbrowse/core/util/blockTypes';
-export interface ModificationOpts {
-    headers?: Record<string, string>;
-    stopToken?: string;
-    filters: string[];
-}
-export declare function getUniqueModifications({ model, adapterConfig, blocks, opts, }: {
-    model: IAnyStateTreeNode;
-    adapterConfig: AnyConfigurationModel;
-    blocks: BlockSet;
-    opts?: ModificationOpts;
-}): Promise<ModificationType[]>;

package/dist/shared/getUniqueModifications.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getUniqueModifications = getUniqueModifications;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const mobx_state_tree_1 = require("mobx-state-tree");
-async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(model);
-    const sessionId = (0, tracks_1.getRpcSessionId)(model);
-    const values = await rpcManager.call(sessionId, 'PileupGetVisibleModifications', {
-        adapterConfig,
-        sessionId,
-        regions: blocks.contentBlocks,
-        statusCallback: (arg) => {
-            if ((0, mobx_state_tree_1.isAlive)(model)) {
-                model.setMessage(arg);
-            }
-        },
-        ...opts,
-    });
-    return values;
-}

package/dist/shared/getUniqueTags.d.ts

@@ -1,15 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { BlockSet } from '@jbrowse/core/util/blockTypes';
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
-export declare function getUniqueTags({ self, tag, blocks, opts, }: {
-    self: IAnyStateTreeNode & {
-        adapterConfig: AnyConfigurationModel;
-    };
-    tag: string;
-    blocks: BlockSet;
-    opts?: {
-        headers?: Record<string, string>;
-        stopToken?: string;
-        filters: string[];
-    };
-}): Promise<string[]>;

package/dist/shared/getUniqueTags.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getUniqueTags = getUniqueTags;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-async function getUniqueTags({ self, tag, blocks, opts, }) {
-    const { rpcManager } = (0, util_1.getSession)(self);
-    const { adapterConfig } = self;
-    const sessionId = (0, tracks_1.getRpcSessionId)(self);
-    const values = await rpcManager.call((0, tracks_1.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', {
-        adapterConfig,
-        tag,
-        sessionId,
-        regions: blocks.contentBlocks,
-        ...opts,
-    });
-    return values;
-}

package/dist/shared/renderSvgUtil.d.ts

@@ -1,6 +0,0 @@
-export declare function renderSvg<T extends {
-    id: string;
-    height: number;
-}>(self: T, opts: {
-    rasterizeLayers?: boolean;
-}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<import("react/jsx-runtime").JSX.Element | undefined>;

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

@@ -1,94 +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;
-    };
-}
-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;
-    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

@@ -1,20 +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;

package/dist/shared/util.js

@@ -1,63 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.posFlags = exports.negFlags = exports.defaultFilterFlags = void 0;
-exports.hasPairedReads = hasPairedReads;
-exports.alphaColor = alphaColor;
-exports.cacheGetter = cacheGetter;
-exports.filterReadFlag = filterReadFlag;
-exports.filterTagValue = filterTagValue;
-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}`;
-}

package/dist/util.d.ts

@@ -1,30 +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>;
-interface ModificationData {
-    color: string;
-    name: string;
-}
-export declare const modificationData: Record<string, ModificationData>;
-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 {};