@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/shared/getMaximumModificationAtEachPosition.js

@@ -1,6 +1,5 @@
-// locals
-import { getModPositions, getModProbabilities } from '../ModificationParser';
 import { getNextRefPos, parseCigar } from '../MismatchParser';
+import { getModPositions, getModProbabilities } from '../ModificationParser';
 import { getTagAlt } from '../util';
 export function getMaxProbModAtEachPosition(feature, cigarOps) {
     const fstrand = feature.get('strand');

package/esm/shared/getUniqueModifications.d.ts

@@ -1,14 +1,14 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { ModificationType } from './types';
+import type { ModificationType } from './types';
+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 getUniqueModifications({ self, adapterConfig, blocks, opts, }: {
     self: IAnyStateTreeNode;
     adapterConfig: AnyConfigurationModel;
     blocks: BlockSet;
     opts?: {
         headers?: Record<string, string>;
-        signal?: AbortSignal;
+        stopToken?: string;
         filters: string[];
     };
 }): Promise<ModificationType[]>;

package/esm/shared/getUniqueTags.d.ts

@@ -1,6 +1,6 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+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;
@@ -9,7 +9,7 @@ export declare function getUniqueTags({ self, tag, blocks, opts, }: {
     blocks: BlockSet;
     opts?: {
         headers?: Record<string, string>;
-        signal?: AbortSignal;
+        stopToken?: string;
         filters: string[];
     };
 }): Promise<string[]>;

package/esm/shared/renderSvgUtil.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 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<React.JSX.Element | undefined>;
+}, cb: (model: T, ctx: CanvasRenderingContext2D, width: number, height: number) => void): Promise<import("react/jsx-runtime").JSX.Element | undefined>;

package/esm/shared/renderSvgUtil.js

@@ -1,6 +1,5 @@
-import React from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
-// stabilize clipid under test for snapshot
 function getId(id) {
     const isJest = typeof jest === 'undefined';
     return `arc-clip-${isJest ? id : 'jest'}`;
@@ -19,18 +18,13 @@ export async function renderSvg(self, opts, cb) {
         }
         ctx.scale(2, 2);
         cb(self, ctx, width, height);
-        return (React.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+        return (_jsx("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
     }
     else {
-        // @ts-ignore
         const C2S = await import('canvas2svg');
         const ctx = new C2S.default(width, height);
         cb(self, ctx, width, height);
         const clipid = getId(self.id);
-        return (React.createElement(React.Fragment, null,
-            React.createElement("defs", null,
-                React.createElement("clipPath", { id: clipid },
-                    React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
-            React.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+        return (_jsxs(_Fragment, { children: [_jsx("defs", { children: _jsx("clipPath", { id: clipid, children: _jsx("rect", { x: 0, y: 0, width: width, height: height }) }) }), _jsx("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })] }));
     }
 }

package/esm/shared/util.d.ts

@@ -1,10 +1,20 @@
-import { ChainData } from './fetchChains';
+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/esm/shared/util.js

@@ -18,6 +18,14 @@ export const defaultFilterFlags = {
     flagInclude: 0,
     flagExclude: 1540,
 };
+export const negFlags = {
+    flagInclude: 16,
+    flagExclude: 1540,
+};
+export const posFlags = {
+    flagInclude: 0,
+    flagExclude: 1556,
+};
 export function cacheGetter(ctor, prop) {
     const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
     const getter = desc.get;
@@ -29,3 +37,19 @@ export function cacheGetter(ctor, prop) {
         },
     });
 }
+export function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    else if (flags & flagExclude) {
+        return true;
+    }
+    else {
+        return false;
+    }
+}
+export function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}

package/esm/util.d.ts

@@ -1,7 +1,7 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, AugmentedRegion } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { IAutorunOptions } from 'mobx';
+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>;

package/esm/util.js

@@ -1,16 +1,12 @@
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-// use fallback alt tag, used in situations where upper case/lower case tags
-// exist e.g. Mm/MM for base modifications
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export function getTagAlt(feature, tag, alt) {
     var _a;
     const tags = feature.get('tags');
     return (_a = tags[tag]) !== null && _a !== void 0 ? _a : tags[alt];
 }
-// orientation definitions from igv.js, see also
-// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 export const orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -81,8 +77,6 @@ export async function fetchSequence(region, adapter) {
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// adapted from IGV
-// https://github.com/igvteam/igv/blob/af07c3b1be8806cfd77343ee04982aeff17d2beb/src/main/resources/org/broad/igv/prefs/preferences.tab#L230-L242
 export const modificationData = {
     m: { color: 'rgb(255,0,0)', name: '5mC' },
     h: { color: 'rgb(255,0,255)', name: '5hmC' },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,15 +36,14 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bam": "^4.0.1",
-    "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.17.0",
+    "@gmod/bam": "^5.0.0",
+    "@gmod/cram": "^4.0.1",
+    "@jbrowse/sv-core": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
-    "clone": "^2.1.2",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^3.0.0"
+    "generic-filehandle2": "^1.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -64,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }