@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -1,111 +0,0 @@
-import type { ColorBy, FilterBy } from '../shared/types';
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-declare function stateModelFactory(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
-    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").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    }, {
-        stopToken: string | undefined;
-        filled: boolean;
-        reactElement: React.ReactElement | undefined;
-        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        layout: any;
-        status: string;
-        error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean;
-        ReactComponent: ({ model, }: {
-            model: {
-                error?: unknown;
-                reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
-                reactElement?: React.ReactElement;
-            };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
-        renderProps: any;
-    } & {
-        doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
-        setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
-        setError(error: unknown): void;
-        reload(): void;
-        beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: 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">>;
-} & {
-    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
-        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    configuration: AnyConfigurationSchemaType;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
-    invertedSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    showInterbaseIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    showArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-}, never, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
-export default stateModelFactory;

package/dist/LinearSNPCoverageDisplay/model.js

@@ -1,273 +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 });
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-const util_1 = require("@jbrowse/core/util");
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const getUniqueModifications_1 = require("../shared/getUniqueModifications");
-const util_2 = require("../util");
-const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
-const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
-function stateModelFactory(pluginManager, configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-        showInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        showInterbaseIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        showArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        filterBySetting: mobx_state_tree_1.types.frozen(),
-        colorBySetting: mobx_state_tree_1.types.frozen(),
-        jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
-    }))
-        .volatile(() => ({
-        visibleModifications: mobx_1.observable.map({}),
-        simplexModifications: new Set(),
-        modificationsReady: false,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-    }))
-        .actions(self => ({
-        setConfig(configuration) {
-            self.configuration = configuration;
-        },
-        setFilterBy(filter) {
-            self.filterBySetting = {
-                ...filter,
-            };
-        },
-        setColorScheme(colorBy) {
-            self.colorBySetting = colorBy
-                ? {
-                    ...colorBy,
-                }
-                : undefined;
-        },
-        setJexlFilters(filters) {
-            self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
-        },
-        updateVisibleModifications(uniqueModifications) {
-            for (const modification of uniqueModifications) {
-                if (!self.visibleModifications.has(modification.type)) {
-                    self.visibleModifications.set(modification.type, {
-                        ...modification,
-                        color: (0, util_2.getColorForModification)(modification.type),
-                    });
-                }
-            }
-        },
-        setSimplexModifications(simplex) {
-            self.simplexModifications = new Set(simplex);
-        },
-    }))
-        .views(self => {
-        const { adapterProps: superAdapterProps } = self;
-        return {
-            get modificationThreshold() {
-                var _a, _b, _c;
-                return (_c = (_b = (_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.modifications) === null || _b === void 0 ? void 0 : _b.threshold) !== null && _c !== void 0 ? _c : 10;
-            },
-            get rendererConfig() {
-                const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-                const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
-                return self.rendererType.configSchema.create({
-                    ...configBlob,
-                    showInterbaseCounts: showInterbaseCounts !== null && showInterbaseCounts !== void 0 ? showInterbaseCounts : configBlob.showInterbaseCounts,
-                    showInterbaseIndicators: showInterbaseIndicators !== null && showInterbaseIndicators !== void 0 ? showInterbaseIndicators : configBlob.showInterbaseIndicators,
-                    showArcs: showArcs !== null && showArcs !== void 0 ? showArcs : configBlob.showArcs,
-                }, (0, mobx_state_tree_1.getEnv)(self));
-            },
-            get showArcsSetting() {
-                var _a;
-                return ((_a = self.showArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showArcs'));
-            },
-            get showInterbaseCountsSetting() {
-                var _a;
-                return ((_a = self.showInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseCounts'));
-            },
-            get showInterbaseIndicatorsSetting() {
-                var _a;
-                return ((_a = self.showInterbaseIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseIndicators'));
-            },
-            get autorunReady() {
-                const view = (0, util_1.getContainingView)(self);
-                return (view.initialized &&
-                    self.statsReadyAndRegionNotTooLarge &&
-                    !self.error);
-            },
-            adapterProps() {
-                const superProps = superAdapterProps();
-                const { filters, filterBy } = self;
-                return {
-                    ...superProps,
-                    filters,
-                    filterBy,
-                    modificationThreshold: this.modificationThreshold,
-                };
-            },
-        };
-    })
-        .actions(self => ({
-        setModificationsReady(flag) {
-            self.modificationsReady = flag;
-        },
-        setShowInterbaseIndicators(arg) {
-            self.showInterbaseIndicators = arg;
-        },
-        setShowInterbaseCounts(arg) {
-            self.showInterbaseCounts = arg;
-        },
-        setShowArcs(arg) {
-            self.showArcs = arg;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, util_2.createAutorun)(self, async () => {
-                self.setModificationsReady(false);
-                if (!self.autorunReady) {
-                    return;
-                }
-                const view = (0, util_1.getContainingView)(self);
-                const { staticBlocks } = view;
-                const { colorBy } = self;
-                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                    const { modifications, simplexModifications } = await (0, getUniqueModifications_1.getUniqueModifications)({
-                        model: self,
-                        adapterConfig: (0, configuration_1.getConf)(self.parentTrack, 'adapter'),
-                        blocks: staticBlocks,
-                    });
-                    if ((0, mobx_state_tree_1.isAlive)(self)) {
-                        self.updateVisibleModifications(modifications);
-                        self.setSimplexModifications(simplexModifications);
-                        self.setModificationsReady(true);
-                    }
-                }
-                else {
-                    self.setModificationsReady(true);
-                }
-            }, { delay: 1000 });
-        },
-    }))
-        .views(self => {
-        const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
-        return {
-            renderReady() {
-                const superProps = superRenderProps();
-                return !superProps.notReady && self.modificationsReady;
-            },
-            renderProps() {
-                const { colorBy, visibleModifications, simplexModifications } = self;
-                return {
-                    ...superRenderProps(),
-                    notReady: !this.renderReady(),
-                    colorBy,
-                    visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
-                    simplexModifications: [...simplexModifications],
-                };
-            },
-            get TooltipComponent() {
-                return Tooltip;
-            },
-            get adapterConfig() {
-                const subadapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-                return {
-                    type: 'SNPCoverageAdapter',
-                    subadapter,
-                };
-            },
-            get rendererTypeName() {
-                return rendererTypes.get('snpcoverage');
-            },
-            get graphType() {
-                return true;
-            },
-            contextMenuItems() {
-                return [];
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Show insertion/clipping indicators',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showInterbaseIndicatorsSetting,
-                        onClick: () => {
-                            self.setShowInterbaseIndicators(!self.showInterbaseIndicatorsSetting);
-                        },
-                    },
-                    {
-                        label: 'Show insertion/clipping counts',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showInterbaseCountsSetting,
-                        onClick: () => {
-                            self.setShowInterbaseCounts(!self.showInterbaseCountsSetting);
-                        },
-                    },
-                    {
-                        label: 'Show arcs',
-                        icon: Visibility_1.default,
-                        type: 'checkbox',
-                        checked: self.showArcsSetting,
-                        onClick: () => {
-                            self.setShowArcs(!self.showArcsSetting);
-                        },
-                    },
-                ];
-            },
-            get filters() {
-                return new serializableFilterChain_1.default({ filters: self.jexlFilters });
-            },
-        };
-    });
-}
-exports.default = stateModelFactory;

package/dist/MismatchParser/cigarToMismatches.d.ts

@@ -1,2 +0,0 @@
-import type { Mismatch } from '../shared/types';
-export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];

package/dist/MismatchParser/getNextRefPos.d.ts

@@ -1,4 +0,0 @@
-export declare function getNextRefPos(cigarOps: string[], positions: number[]): {
-    ref: number;
-    idx: number;
-}[];

package/dist/MismatchParser/getNextRefPos.js

@@ -1,38 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNextRefPos = getNextRefPos;
-function getNextRefPos(cigarOps, positions) {
-    let readPos = 0;
-    let refPos = 0;
-    let currPos = 0;
-    const ret = [];
-    for (let i = 0; i < cigarOps.length && currPos < positions.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op === 'S' || op === 'I') {
-            for (let i = 0; i < len && currPos < positions.length; i++) {
-                if (positions[currPos] === readPos + i) {
-                    currPos++;
-                }
-            }
-            readPos += len;
-        }
-        else if (op === 'D' || op === 'N') {
-            refPos += len;
-        }
-        else if (op === 'M' || op === 'X' || op === '=') {
-            for (let i = 0; i < len && currPos < positions.length; i++) {
-                if (positions[currPos] === readPos + i) {
-                    ret.push({
-                        ref: refPos + i,
-                        idx: currPos,
-                    });
-                    currPos++;
-                }
-            }
-            readPos += len;
-            refPos += len;
-        }
-    }
-    return ret;
-}

package/dist/MismatchParser/index.d.ts

@@ -1,27 +0,0 @@
-import type { Mismatch } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(s?: string): string[];
-export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
-export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
-export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
-export declare function getLengthOnRef(cigar: string): number;
-export declare function getLength(cigar: string): number;
-export declare function getLengthSansClipping(cigar: string): number;
-export declare function getClip(cigar: string, strand: number): number;
-export declare function getTag(feature: Feature, tag: string): any;
-export declare function featurizeSA(SA: string | undefined, id: string, strand: number, readName: string, normalize?: boolean): {
-    refName: string;
-    start: number;
-    end: number;
-    seqLength: number;
-    clipPos: number;
-    CIGAR: string;
-    strand: number;
-    uniqueId: string;
-    mate: {
-        start: number;
-        end: number;
-        refName: string;
-    };
-}[];
-export { getNextRefPos } from './getNextRefPos';

package/dist/MismatchParser/index.js

@@ -1,145 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getNextRefPos = void 0;
-exports.parseCigar = parseCigar;
-exports.getMismatches = getMismatches;
-exports.getOrientedCigar = getOrientedCigar;
-exports.getOrientedMismatches = getOrientedMismatches;
-exports.getLengthOnRef = getLengthOnRef;
-exports.getLength = getLength;
-exports.getLengthSansClipping = getLengthSansClipping;
-exports.getClip = getClip;
-exports.getTag = getTag;
-exports.featurizeSA = featurizeSA;
-const cigarToMismatches_1 = require("./cigarToMismatches");
-const mdToMismatches_1 = require("./mdToMismatches");
-const startClip = new RegExp(/(\d+)[SH]$/);
-const endClip = new RegExp(/^(\d+)([SH])/);
-function parseCigar(s = '') {
-    let currLen = '';
-    let len;
-    let op;
-    const ret = [];
-    for (let i = 0, l = s.length; i < l; i++) {
-        const c = s[i];
-        if (c >= '0' && c <= '9') {
-            currLen = currLen + c;
-        }
-        else {
-            len = currLen;
-            op = c;
-            currLen = '';
-            ret.push(len, op);
-        }
-    }
-    return ret;
-}
-function getMismatches(cigar, md, seq, ref, qual) {
-    let mismatches = [];
-    const ops = parseCigar(cigar);
-    if (cigar) {
-        mismatches = mismatches.concat((0, cigarToMismatches_1.cigarToMismatches)(ops, seq, ref, qual));
-    }
-    if (md && seq) {
-        mismatches = mismatches.concat((0, mdToMismatches_1.mdToMismatches)(md, ops, mismatches, seq, qual));
-    }
-    return mismatches;
-}
-function getOrientedCigar(flip, cigar) {
-    if (flip) {
-        const ret = [];
-        for (let i = 0; i < cigar.length; i += 2) {
-            const len = cigar[i];
-            let op = cigar[i + 1];
-            if (op === 'D') {
-                op = 'I';
-            }
-            else if (op === 'I') {
-                op = 'D';
-            }
-            ret.push(len, op);
-        }
-        return ret;
-    }
-    return cigar;
-}
-function getOrientedMismatches(flip, cigar) {
-    const p = parseCigar(cigar);
-    return (0, cigarToMismatches_1.cigarToMismatches)(flip ? getOrientedCigar(flip, p) : p);
-}
-function getLengthOnRef(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let lengthOnRef = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'H' && op !== 'S' && op !== 'I') {
-            lengthOnRef += len;
-        }
-    }
-    return lengthOnRef;
-}
-function getLength(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let length = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'D' && op !== 'N') {
-            length += len;
-        }
-    }
-    return length;
-}
-function getLengthSansClipping(cigar) {
-    const cigarOps = parseCigar(cigar);
-    let length = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op !== 'H' && op !== 'S' && op !== 'D' && op !== 'N') {
-            length += len;
-        }
-    }
-    return length;
-}
-function getClip(cigar, strand) {
-    return strand === -1
-        ? +(startClip.exec(cigar) || [])[1] || 0
-        : +(endClip.exec(cigar) || [])[1] || 0;
-}
-function getTag(feature, tag) {
-    return feature.get('tags')[tag];
-}
-function featurizeSA(SA, id, strand, readName, normalize) {
-    return ((SA === null || SA === void 0 ? void 0 : SA.split(';').filter(aln => !!aln).map((aln, index) => {
-        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);
-        const saStrandNormalized = saStrand === '-' ? -1 : 1;
-        const saClipPos = getClip(saCigar, (normalize ? strand : 1) * saStrandNormalized);
-        const saRealStart = +saStart - 1;
-        return {
-            refName: saRef,
-            start: saRealStart,
-            end: saRealStart + saLengthOnRef,
-            seqLength: saLength,
-            clipPos: saClipPos,
-            CIGAR: saCigar,
-            strand: (normalize ? strand : 1) * saStrandNormalized,
-            uniqueId: `${id}_SA${index}`,
-            mate: {
-                start: saClipPos,
-                end: saClipPos + saLengthSansClipping,
-                refName: readName,
-            },
-        };
-    })) || []);
-}
-var getNextRefPos_1 = require("./getNextRefPos");
-Object.defineProperty(exports, "getNextRefPos", { enumerable: true, get: function () { return getNextRefPos_1.getNextRefPos; } });

package/dist/MismatchParser/mdToMismatches.d.ts

@@ -1,2 +0,0 @@
-import type { Mismatch } from '../shared/types';
-export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Uint8Array): Mismatch[];