@jbrowse/plugin-arc 2.16.1 → 2.18.0

package/esm/LinearPairedArcDisplay/renderSvg.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearArcDisplayModel } from './model';
+import type { LinearArcDisplayModel } from './model';
 export declare function renderArcSvg(model: LinearArcDisplayModel, _opts: {
     rasterizeLayers?: boolean;
 }): Promise<React.JSX.Element>;

package/esm/LinearPairedArcDisplay/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 getTag(feature: Feature, tag: string): any;
 export declare function getTagAlt(feature: Feature, tag: string, alt: string): any;
 export declare const orientationTypes: {

package/esm/LinearPairedArcDisplay/util.js

@@ -1,21 +1,14 @@
-import { toArray } from 'rxjs/operators';
-import { firstValueFrom } from 'rxjs';
-import { addDisposer, isAlive } from 'mobx-state-tree';
 import { autorun } from 'mobx';
-// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
-// BAM does not
+import { addDisposer, isAlive } from 'mobx-state-tree';
+import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export function getTag(feature, tag) {
-    const tags = feature.get('tags');
-    return tags !== undefined ? tags[tag] : feature.get(tag);
+    return feature.get('tags')[tag];
 }
-// use fallback alt tag, used in situations where upper case/lower case tags
-// exist e.g. Mm/MM for base modifications
 export function getTagAlt(feature, tag, alt) {
     var _a;
     return (_a = getTag(feature, tag)) !== null && _a !== void 0 ? _a : getTag(feature, alt);
 }
-// orientation definitions from igv.js, see also
-// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations
 export const orientationTypes = {
     fr: {
         F1R2: 'LR',
@@ -73,8 +66,6 @@ export function getColorWGBS(strand, base) {
     }
     return '#888';
 }
-// fetches region sequence augmenting by +/- 1bp for CpG on either side of
-// requested region
 export async function fetchSequence(region, adapter) {
     var _a;
     const { start, end, originalRefName, refName } = region;
@@ -88,12 +79,9 @@ export async function fetchSequence(region, adapter) {
         .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
-// has to check underlying C-G (aka CpG) on the reference sequence
 export function shouldFetchReferenceSequence(type) {
     return type === 'methylation';
 }
-// adapted from IGV
-// https://github.com/igvteam/igv/blob/e803e3af2d8c9ea049961dfd4628146bdde9a574/src/main/java/org/broad/igv/sam/mods/BaseModificationColors.java#L27
 export const modificationColors = {
     m: 'rgb(255,0,0)',
     h: 'rgb(11, 132, 165)',

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class ArcPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,8 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
+import { set1 } from '@jbrowse/core/ui/colors';
+import ArcRendererF from './ArcRenderer';
 import LinearArcDisplayF from './LinearArcDisplay';
 import LinearPairedArcDisplayF from './LinearPairedArcDisplay';
-import ArcRendererF from './ArcRenderer';
-import { set1 } from '@jbrowse/core/ui/colors';
 export default class ArcPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -30,7 +30,7 @@ export default class ArcPlugin extends Plugin {
                 return set1[4];
             }
             else {
-                return set1[6]; // skip 5, yellow
+                return set1[6];
             }
         });
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -53,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }