@jbrowse/plugin-bed 2.9.0 → 2.10.1
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.
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@@ -8,6 +8,7 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
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const io_1 = require("@jbrowse/core/util/io");
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const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const tabix_1 = require("@gmod/tabix");
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+
// locals
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const util_1 = require("../util");
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class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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constructor(config, getSubAdapter, pluginManager) {
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package/dist/util.js
CHANGED
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@@ -7,6 +7,7 @@ function ucscProcessedTranscript(feature) {
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// split the blocks into UTR, CDS, and exons
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const thickStart = feature.get('thickStart');
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const thickEnd = feature.get('thickEnd');
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+
const refName = feature.get('refName');
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if (!thickStart && !thickEnd) {
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return feature;
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}
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@@ -15,7 +16,6 @@ function ucscProcessedTranscript(feature) {
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.filter(child => child.get('type') === 'block')
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.sort((a, b) => a.get('start') - b.get('start'))
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: [];
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-
// eslint-disable-next-line @typescript-eslint/no-explicit-any
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const newChildren = [];
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blocks.forEach(block => {
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const start = block.get('start');
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@@ -27,6 +27,7 @@ function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end,
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+
refName,
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});
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}
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else if (thickStart > start && thickStart < end && thickEnd >= end) {
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@@ -36,10 +37,12 @@ function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end: thickStart,
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+
refName,
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}, {
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type: 'CDS',
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start: thickStart,
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end,
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+
refName,
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});
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}
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else if (thickStart <= start && thickEnd >= end) {
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@@ -48,6 +51,7 @@ function ucscProcessedTranscript(feature) {
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type: 'CDS',
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start,
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end,
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+
refName,
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});
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}
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else if (thickStart > start && thickStart < end && thickEnd < end) {
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@@ -58,14 +62,17 @@ function ucscProcessedTranscript(feature) {
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type: `${leftPrime}_prime_UTR`,
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start,
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end: thickStart,
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refName,
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}, {
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type: `CDS`,
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start: thickStart,
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end: thickEnd,
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+
refName,
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}, {
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type: `${rightPrime}_prime_UTR`,
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start: thickEnd,
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end,
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refName,
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});
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}
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else if (thickStart <= start && thickEnd > start && thickEnd < end) {
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@@ -75,10 +82,12 @@ function ucscProcessedTranscript(feature) {
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type: `CDS`,
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start,
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end: thickEnd,
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refName,
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}, {
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type: `${prime}_prime_UTR`,
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start: thickEnd,
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end,
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refName,
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});
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}
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else if (thickEnd <= start) {
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@@ -88,6 +97,7 @@ function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end,
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refName,
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});
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}
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});
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@@ -135,6 +145,7 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
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uniqueId: `${uniqueId}-${b}`,
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start: bmin,
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end: bmax,
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+
refName,
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type: 'block',
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});
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}
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@@ -3,6 +3,7 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
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import { openLocation } from '@jbrowse/core/util/io';
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import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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import { TabixIndexedFile } from '@gmod/tabix';
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// locals
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import { featureData } from '../util';
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class BedTabixAdapter extends BaseFeatureDataAdapter {
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constructor(config, getSubAdapter, pluginManager) {
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package/esm/util.js
CHANGED
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@@ -4,6 +4,7 @@ export function ucscProcessedTranscript(feature) {
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// split the blocks into UTR, CDS, and exons
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const thickStart = feature.get('thickStart');
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const thickEnd = feature.get('thickEnd');
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const refName = feature.get('refName');
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if (!thickStart && !thickEnd) {
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return feature;
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}
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@@ -12,7 +13,6 @@ export function ucscProcessedTranscript(feature) {
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.filter(child => child.get('type') === 'block')
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.sort((a, b) => a.get('start') - b.get('start'))
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: [];
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-
// eslint-disable-next-line @typescript-eslint/no-explicit-any
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const newChildren = [];
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blocks.forEach(block => {
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const start = block.get('start');
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@@ -24,6 +24,7 @@ export function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end,
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refName,
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});
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}
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else if (thickStart > start && thickStart < end && thickEnd >= end) {
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@@ -33,10 +34,12 @@ export function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end: thickStart,
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refName,
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}, {
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type: 'CDS',
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start: thickStart,
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end,
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+
refName,
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});
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}
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else if (thickStart <= start && thickEnd >= end) {
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@@ -45,6 +48,7 @@ export function ucscProcessedTranscript(feature) {
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type: 'CDS',
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start,
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end,
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+
refName,
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});
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}
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else if (thickStart > start && thickStart < end && thickEnd < end) {
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@@ -55,14 +59,17 @@ export function ucscProcessedTranscript(feature) {
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type: `${leftPrime}_prime_UTR`,
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start,
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end: thickStart,
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+
refName,
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}, {
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type: `CDS`,
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start: thickStart,
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end: thickEnd,
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+
refName,
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}, {
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type: `${rightPrime}_prime_UTR`,
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start: thickEnd,
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end,
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+
refName,
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});
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}
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else if (thickStart <= start && thickEnd > start && thickEnd < end) {
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@@ -72,10 +79,12 @@ export function ucscProcessedTranscript(feature) {
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type: `CDS`,
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start,
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end: thickEnd,
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refName,
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}, {
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type: `${prime}_prime_UTR`,
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start: thickEnd,
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end,
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+
refName,
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});
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}
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else if (thickEnd <= start) {
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@@ -85,6 +94,7 @@ export function ucscProcessedTranscript(feature) {
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type: `${prime}_prime_UTR`,
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start,
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end,
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refName,
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});
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}
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});
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@@ -131,6 +141,7 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
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uniqueId: `${uniqueId}-${b}`,
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start: bmin,
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end: bmax,
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+
refName,
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type: 'block',
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});
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}
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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{
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"name": "@jbrowse/plugin-bed",
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"version": "2.
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"version": "2.10.1",
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"description": "JBrowse 2 bed adapters, tracks, etc.",
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"keywords": [
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"jbrowse",
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@@ -55,5 +55,5 @@
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"distModule": "esm/index.js",
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"srcModule": "src/index.ts",
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"module": "esm/index.js",
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"gitHead": "
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"gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
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}
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