@jbrowse/plugin-bed 5.0.0-beta.1 → 5.0.0-beta.2
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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@@ -16,6 +16,11 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
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* ```
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*/
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declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly densityAdapter: {
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readonly type: 'frozen';
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readonly defaultValue: null;
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readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it';
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};
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/**
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* #slot
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* location of the bgzip-compressed BED, sorted by position. Must be bgzip
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@@ -1,4 +1,5 @@
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import { ConfigurationSchema, expandTabixShorthand, tabixIndexFields, } from '@jbrowse/core/configuration';
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import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
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export function normalizeSnapshot(snap) {
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return expandTabixShorthand(snap, 'bedGzLocation');
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}
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@@ -63,6 +64,7 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
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description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
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defaultValue: false,
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},
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...densityAdapterConfigSchemaFields,
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}, {
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explicitlyTyped: true,
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/**
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@@ -14,6 +14,11 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
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* ```
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*/
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declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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readonly densityAdapter: {
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readonly type: 'frozen';
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readonly defaultValue: null;
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readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it';
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};
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/**
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* #slot
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* location of the BigBed file. It carries its own index and summary zoom
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@@ -1,4 +1,5 @@
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import { ConfigurationSchema } from '@jbrowse/core/configuration';
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import { densityAdapterConfigSchemaFields } from '@jbrowse/core/data_adapters/BaseAdapter';
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export function normalizeSnapshot(snap) {
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return snap.uri
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? {
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@@ -60,6 +61,7 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
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description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
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defaultValue: false,
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},
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...densityAdapterConfigSchemaFields,
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}, {
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explicitlyTyped: true,
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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": "5.0.0-beta.
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"version": "5.0.0-beta.2",
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"type": "module",
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"description": "JBrowse 2 bed adapters, tracks, etc.",
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"keywords": [
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@@ -27,7 +27,7 @@
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"@jbrowse/mobx-state-tree": "^6.5.1",
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"mobx": "^7.0.3",
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"rxjs": "^7.8.2",
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"@jbrowse/core": "^5.0.0-beta.
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"@jbrowse/core": "^5.0.0-beta.2"
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},
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"publishConfig": {
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"access": "public"
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