@jbrowse/plugin-linear-comparative-view 3.6.2 → 3.6.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/LGVSyntenyDisplay/components/util.js +13 -9
- package/dist/LGVSyntenyDisplay/configSchemaF.js +18 -2
- package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js +6 -4
- package/esm/LGVSyntenyDisplay/components/util.js +13 -9
- package/esm/LGVSyntenyDisplay/configSchemaF.js +18 -2
- package/esm/LinearSyntenyDisplay/components/SyntenyContextMenu.js +6 -4
- package/package.json +5 -5
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@@ -60,16 +60,28 @@ async function navToSynteny({ feature, windowSize: ws, session, trackId, region,
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rMateStart = mateStart;
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rMateEnd = mateEnd;
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}
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const
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const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
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const m1 = Math.min(rMateStart, rMateEnd);
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const m2 = Math.max(rMateStart, rMateEnd);
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const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
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session.addView('LinearSyntenyView', {
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type: 'LinearSyntenyView',
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views: [
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{
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type: 'LinearGenomeView',
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hideHeader: true,
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init: {
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assembly: featAsm,
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loc: l1,
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},
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},
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{
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type: 'LinearGenomeView',
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hideHeader: true,
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init: {
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assembly: mateAsm,
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loc: l2,
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},
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},
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],
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tracks: [
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@@ -85,12 +97,4 @@ async function navToSynteny({ feature, windowSize: ws, session, trackId, region,
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},
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],
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});
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const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
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const m1 = Math.min(rMateStart, rMateEnd);
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const m2 = Math.max(rMateStart, rMateEnd);
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const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
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await Promise.all([
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view2.views[0].navToLocString(l1, featAsm),
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view2.views[1].navToLocString(l2, mateAsm),
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]);
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}
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@@ -1,11 +1,27 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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const configuration_1 = require("@jbrowse/core/configuration");
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const util_1 = require("@jbrowse/core/util");
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const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
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function configSchemaF(pluginManager) {
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pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
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const
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const mate = f.get('mate');
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const l1name = f.get('name') || f.get('id');
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const l2name = (mate === null || mate === void 0 ? void 0 : mate.name) || (mate === null || mate === void 0 ? void 0 : mate.id);
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return [
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l1name ? `Name1: ${l1name}` : '',
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l2name ? `Name1: ${l2name}` : '',
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`Loc1: ${(0, util_1.assembleLocString)({
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refName: f.get('refName'),
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start: f.get('start'),
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end: f.get('end'),
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})} (${(0, util_1.toLocale)(f.get('end') - f.get('start'))}bp)`,
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`Loc2: ${(0, util_1.assembleLocString)({
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refName: mate.refName,
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start: mate.start,
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end: mate.end,
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})} (${(0, util_1.toLocale)(mate.end - mate.start)}bp)`,
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]
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.filter(f => !!f)
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.join('<br/>');
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});
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@@ -38,14 +38,16 @@ function SyntenyContextMenu({ model, onClose, anchorEl, }) {
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const mate = f.get('mate');
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const l1 = view.views[model.level];
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const l2 = view.views[model.level + 1];
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const l1asm = l1.assemblyNames[0];
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const l2asm = l2.assemblyNames[0];
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l1.navToLocString(`${refName}:${start}-${end}`).catch((e) => {
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const err = `${
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console.error(err);
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const err = `${l1asm}:${e}`;
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console.error(l1asm, err);
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(0, util_1.getSession)(model).notifyError(err, e);
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});
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l2.navToLocString(`${mate.refName}:${mate.start}-${mate.end}`).catch((e) => {
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const err = `${
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console.error(err);
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const err = `${l2asm}:${e}`;
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console.error(l2asm, err);
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(0, util_1.getSession)(model).notifyError(err, e);
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});
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},
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@@ -57,16 +57,28 @@ export async function navToSynteny({ feature, windowSize: ws, session, trackId,
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rMateStart = mateStart;
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rMateEnd = mateEnd;
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}
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const
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const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
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const m1 = Math.min(rMateStart, rMateEnd);
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const m2 = Math.max(rMateStart, rMateEnd);
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const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
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session.addView('LinearSyntenyView', {
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type: 'LinearSyntenyView',
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views: [
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{
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type: 'LinearGenomeView',
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hideHeader: true,
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init: {
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assembly: featAsm,
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loc: l1,
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},
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},
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{
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type: 'LinearGenomeView',
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hideHeader: true,
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init: {
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assembly: mateAsm,
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loc: l2,
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},
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},
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],
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tracks: [
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@@ -82,12 +94,4 @@ export async function navToSynteny({ feature, windowSize: ws, session, trackId,
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},
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],
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});
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const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
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-
const m1 = Math.min(rMateStart, rMateEnd);
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const m2 = Math.max(rMateStart, rMateEnd);
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const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
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await Promise.all([
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view2.views[0].navToLocString(l1, featAsm),
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view2.views[1].navToLocString(l2, mateAsm),
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]);
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}
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@@ -1,9 +1,25 @@
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import { ConfigurationSchema } from '@jbrowse/core/configuration';
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import { assembleLocString, toLocale } from '@jbrowse/core/util';
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import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments';
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function configSchemaF(pluginManager) {
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pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
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const
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const mate = f.get('mate');
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const l1name = f.get('name') || f.get('id');
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const l2name = (mate === null || mate === void 0 ? void 0 : mate.name) || (mate === null || mate === void 0 ? void 0 : mate.id);
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return [
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l1name ? `Name1: ${l1name}` : '',
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l2name ? `Name1: ${l2name}` : '',
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`Loc1: ${assembleLocString({
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refName: f.get('refName'),
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start: f.get('start'),
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end: f.get('end'),
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})} (${toLocale(f.get('end') - f.get('start'))}bp)`,
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`Loc2: ${assembleLocString({
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refName: mate.refName,
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start: mate.start,
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end: mate.end,
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})} (${toLocale(mate.end - mate.start)}bp)`,
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]
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.filter(f => !!f)
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.join('<br/>');
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});
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@@ -35,14 +35,16 @@ export default function SyntenyContextMenu({ model, onClose, anchorEl, }) {
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const mate = f.get('mate');
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const l1 = view.views[model.level];
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const l2 = view.views[model.level + 1];
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const l1asm = l1.assemblyNames[0];
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const l2asm = l2.assemblyNames[0];
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l1.navToLocString(`${refName}:${start}-${end}`).catch((e) => {
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const err = `${
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console.error(err);
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const err = `${l1asm}:${e}`;
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console.error(l1asm, err);
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getSession(model).notifyError(err, e);
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});
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l2.navToLocString(`${mate.refName}:${mate.start}-${mate.end}`).catch((e) => {
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const err = `${
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console.error(err);
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const err = `${l2asm}:${e}`;
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console.error(l2asm, err);
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getSession(model).notifyError(err, e);
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});
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},
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package/package.json
CHANGED
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{
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"name": "@jbrowse/plugin-linear-comparative-view",
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"version": "3.6.
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"version": "3.6.4",
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"description": "JBrowse 2 linear comparative view",
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"keywords": [
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"jbrowse",
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"clean": "rimraf dist esm *.tsbuildinfo"
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},
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"dependencies": {
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"@jbrowse/core": "^3.6.
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"@jbrowse/plugin-alignments": "^3.6.
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"@jbrowse/plugin-linear-genome-view": "^3.6.
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"@jbrowse/core": "^3.6.4",
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"@jbrowse/plugin-alignments": "^3.6.4",
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"@jbrowse/plugin-linear-genome-view": "^3.6.4",
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"@mui/icons-material": "^7.0.0",
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"@mui/material": "^7.0.0",
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"copy-to-clipboard": "^3.3.1",
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"publishConfig": {
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"access": "public"
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},
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"gitHead": "
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"gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
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}
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