@jbrowse/plugin-sequence 3.1.0 → 3.3.0
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/BgzipFastaAdapter/configSchema.js +22 -1
- package/dist/ChromSizesAdapter/configSchema.js +14 -1
- package/dist/IndexedFastaAdapter/configSchema.js +18 -1
- package/dist/ReferenceSequenceTrack/configSchema.js +7 -3
- package/dist/TwoBitAdapter/configSchema.js +26 -2
- package/dist/UnindexedFastaAdapter/configSchema.js +14 -1
- package/esm/BgzipFastaAdapter/configSchema.js +22 -1
- package/esm/ChromSizesAdapter/configSchema.js +14 -1
- package/esm/IndexedFastaAdapter/configSchema.js +18 -1
- package/esm/ReferenceSequenceTrack/configSchema.js +7 -3
- package/esm/TwoBitAdapter/configSchema.js +26 -2
- package/esm/UnindexedFastaAdapter/configSchema.js +14 -1
- package/package.json +6 -6
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@@ -29,5 +29,26 @@ const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAd
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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faiLocation: {
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uri: `${snap.uri}.fai`,
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baseUri: snap.baseUri,
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},
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gziLocation: {
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uri: `${snap.uri}.gzi`,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = BgzipFastaAdapter;
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@@ -10,5 +10,18 @@ const ChromSizesAdapter = (0, configuration_1.ConfigurationSchema)('ChromSizesAd
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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chromSizesLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = ChromSizesAdapter;
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@@ -19,5 +19,22 @@ const IndexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('IndexedFas
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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faiLocation: {
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uri: `${snap.uri}.fai`,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = IndexedFastaAdapter;
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@@ -46,16 +46,20 @@ function createReferenceSeqTrackConfig(pluginManager) {
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const displayTypes = new Set();
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const { displays = [] } = snap;
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if (snap.trackId !== 'placeholderId') {
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-
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for (const d of displays) {
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if (d) {
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displayTypes.add(d.type);
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}
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}
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const trackType = pluginManager.getTrackType(snap.type);
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trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes
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for (const displayType of (trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes) || []) {
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if (!displayTypes.has(displayType.name)) {
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displays.push({
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displayId: `${snap.trackId}-${displayType.name}`,
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type: displayType.name,
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});
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}
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}
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}
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}
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return { ...snap, displays };
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},
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@@ -5,7 +5,10 @@ function x() { }
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const TwoBitAdapter = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
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twoBitLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.2bit',
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locationType: 'UriLocation',
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},
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},
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chromSizesLocation: {
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type: 'fileLocation',
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@@ -15,5 +18,26 @@ const TwoBitAdapter = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter',
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},
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description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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twoBitLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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...(snap.chromSizes
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? {
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chromSizesLocation: {
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uri: snap.chromSizes,
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baseUri: snap.baseUri,
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},
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}
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: {}),
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}
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: snap;
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},
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});
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exports.default = TwoBitAdapter;
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@@ -23,5 +23,18 @@ const UnindexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('Unindexe
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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exports.default = UnindexedFastaAdapter;
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@@ -27,5 +27,26 @@ const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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faiLocation: {
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uri: `${snap.uri}.fai`,
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baseUri: snap.baseUri,
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},
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gziLocation: {
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uri: `${snap.uri}.gzi`,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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export default BgzipFastaAdapter;
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@@ -8,5 +8,18 @@ const ChromSizesAdapter = ConfigurationSchema('ChromSizesAdapter', {
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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chromSizesLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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export default ChromSizesAdapter;
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@@ -17,5 +17,22 @@ const IndexedFastaAdapter = ConfigurationSchema('IndexedFastaAdapter', {
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locationType: 'UriLocation',
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},
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},
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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faiLocation: {
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uri: `${snap.uri}.fai`,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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export default IndexedFastaAdapter;
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@@ -43,16 +43,20 @@ export function createReferenceSeqTrackConfig(pluginManager) {
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const displayTypes = new Set();
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const { displays = [] } = snap;
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if (snap.trackId !== 'placeholderId') {
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for (const d of displays) {
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if (d) {
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displayTypes.add(d.type);
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}
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}
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const trackType = pluginManager.getTrackType(snap.type);
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trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes
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for (const displayType of (trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes) || []) {
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if (!displayTypes.has(displayType.name)) {
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displays.push({
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displayId: `${snap.trackId}-${displayType.name}`,
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type: displayType.name,
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});
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}
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}
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}
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}
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return { ...snap, displays };
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},
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@@ -3,7 +3,10 @@ function x() { }
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const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
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twoBitLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.2bit',
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locationType: 'UriLocation',
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},
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},
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chromSizesLocation: {
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type: 'fileLocation',
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@@ -13,5 +16,26 @@ const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
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},
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description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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twoBitLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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...(snap.chromSizes
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? {
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chromSizesLocation: {
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uri: snap.chromSizes,
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baseUri: snap.baseUri,
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},
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}
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: {}),
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}
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: snap;
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},
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});
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export default TwoBitAdapter;
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@@ -21,5 +21,18 @@ const UnindexedFastaAdapter = ConfigurationSchema('UnindexedFastaAdapter', {
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locationType: 'UriLocation',
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},
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},
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}, {
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}, {
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explicitlyTyped: true,
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preProcessSnapshot: snap => {
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return snap.uri
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? {
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...snap,
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fastaLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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}
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: snap;
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},
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});
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export default UnindexedFastaAdapter;
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package/package.json
CHANGED
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{
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"name": "@jbrowse/plugin-sequence",
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"version": "3.
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"version": "3.3.0",
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"description": "JBrowse 2 sequence adapters, tracks, etc.",
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"keywords": [
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"jbrowse",
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@@ -39,10 +39,10 @@
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"@gmod/abortable-promise-cache": "^2.0.0",
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"@gmod/indexedfasta": "^3.0.0",
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"@gmod/twobit": "^4.0.1",
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"@jbrowse/core": "^3.
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"@jbrowse/plugin-linear-genome-view": "^3.
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"@jbrowse/plugin-wiggle": "^3.
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"@mui/material": "^
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"@jbrowse/core": "^3.3.0",
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"@jbrowse/plugin-linear-genome-view": "^3.3.0",
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"@jbrowse/plugin-wiggle": "^3.3.0",
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"@mui/material": "^7.0.0",
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"mobx": "^6.0.0",
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"mobx-react": "^9.0.0",
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"mobx-state-tree": "^5.0.0",
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@@ -57,5 +57,5 @@
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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": "
|
|
60
|
+
"gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
|
|
61
61
|
}
|