@jbrowse/plugin-bed 3.0.5 → 3.1.0
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/BedAdapter/configSchema.js +18 -2
- package/dist/BedGraphAdapter/configSchema.js +14 -1
- package/dist/BedGraphTabixAdapter/configSchema.js +20 -1
- package/dist/BedTabixAdapter/configSchema.js +24 -2
- package/dist/BedpeAdapter/configSchema.js +14 -1
- package/dist/BigBedAdapter/configSchema.js +18 -2
- package/esm/BedAdapter/configSchema.js +18 -2
- package/esm/BedGraphAdapter/configSchema.js +14 -1
- package/esm/BedGraphTabixAdapter/configSchema.js +20 -1
- package/esm/BedTabixAdapter/configSchema.js +24 -2
- package/esm/BedpeAdapter/configSchema.js +14 -1
- package/esm/BigBedAdapter/configSchema.js +18 -2
- package/package.json +3 -3
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@@ -5,7 +5,10 @@ function x() { }
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const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
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bedLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bed.gz',
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locationType: 'UriLocation',
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},
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},
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columnNames: {
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type: 'stringArray',
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@@ -37,5 +40,18 @@ const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
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description: 'The column to use as a "end" attribute',
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defaultValue: 2,
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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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bedLocation: {
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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 = BedAdapter;
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@@ -15,5 +15,18 @@ const BedGraphAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphAdapte
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description: 'List of column names',
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defaultValue: [],
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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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bedGraphLocation: {
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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 = BedGraphAdapter;
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@@ -30,5 +30,24 @@ const BedGraphTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedGraphT
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description: 'List of column names',
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defaultValue: [],
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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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bedGraphGzLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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index: {
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location: {
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uri: `${snap.uri}.tbi`,
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baseUri: snap.baseUri,
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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 = BedGraphTabixAdapter;
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@@ -6,7 +6,10 @@ function x() { }
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const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
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bedGzLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bed.gz',
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locationType: 'UriLocation',
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},
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},
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index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
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indexType: {
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@@ -37,5 +40,24 @@ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapte
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description: 'The autoSql definition for the data fields in the file',
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defaultValue: '',
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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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bedGzLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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index: {
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location: {
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uri: `${snap.uri}.tbi`,
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baseUri: snap.baseUri,
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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 = BedTabixAdapter;
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@@ -15,5 +15,18 @@ const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
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description: 'List of column names',
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defaultValue: [],
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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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bedpeLocation: {
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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 = BedpeAdapter;
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@@ -5,7 +5,10 @@ function x() { }
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const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
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bigBedLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bb',
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locationType: 'UriLocation',
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},
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},
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scoreColumn: {
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type: 'string',
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@@ -17,5 +20,18 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
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description: 'An attribute to aggregate features with',
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defaultValue: 'geneName2',
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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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bigBedLocation: {
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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 = BigBedAdapter;
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@@ -3,7 +3,10 @@ function x() { }
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const BedAdapter = ConfigurationSchema('BedAdapter', {
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bedLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bed.gz',
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locationType: 'UriLocation',
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},
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},
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columnNames: {
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type: 'stringArray',
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@@ -35,5 +38,18 @@ const BedAdapter = ConfigurationSchema('BedAdapter', {
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description: 'The column to use as a "end" attribute',
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defaultValue: 2,
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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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bedLocation: {
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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 BedAdapter;
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@@ -13,5 +13,18 @@ const BedGraphAdapter = ConfigurationSchema('BedGraphAdapter', {
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description: 'List of column names',
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defaultValue: [],
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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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bedGraphLocation: {
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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 BedGraphAdapter;
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description: 'List of column names',
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defaultValue: [],
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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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bedGraphGzLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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index: {
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location: {
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uri: `${snap.uri}.tbi`,
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baseUri: snap.baseUri,
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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 BedGraphTabixAdapter;
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const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
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bedGzLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bed.gz',
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locationType: 'UriLocation',
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},
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},
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index: ConfigurationSchema('TabixIndex', {
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indexType: {
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@@ -35,5 +38,24 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
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description: 'The autoSql definition for the data fields in the file',
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defaultValue: '',
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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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bedGzLocation: {
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uri: snap.uri,
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baseUri: snap.baseUri,
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},
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index: {
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location: {
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uri: `${snap.uri}.tbi`,
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baseUri: snap.baseUri,
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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 BedTabixAdapter;
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@@ -13,5 +13,18 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
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description: 'List of column names',
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defaultValue: [],
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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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bedpeLocation: {
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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 BedpeAdapter;
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@@ -3,7 +3,10 @@ function x() { }
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const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
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bigBedLocation: {
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type: 'fileLocation',
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defaultValue: {
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defaultValue: {
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uri: '/path/to/my.bb',
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locationType: 'UriLocation',
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},
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},
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scoreColumn: {
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type: 'string',
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@@ -15,5 +18,18 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
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description: 'An attribute to aggregate features with',
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defaultValue: 'geneName2',
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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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bigBedLocation: {
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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 BigBedAdapter;
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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1
1
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{
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"name": "@jbrowse/plugin-bed",
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"version": "3.0
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"version": "3.1.0",
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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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@@ -41,7 +41,7 @@
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41
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"@gmod/bed": "^2.1.2",
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"@gmod/bgzf-filehandle": "^2.0.1",
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"@gmod/tabix": "^2.0.0",
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"@jbrowse/core": "^3.0
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+
"@jbrowse/core": "^3.1.0",
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|
45
45
|
"mobx": "^6.0.0",
|
|
46
46
|
"mobx-react": "^9.0.0",
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|
47
47
|
"mobx-state-tree": "^5.0.0",
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|
@@ -53,5 +53,5 @@
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53
53
|
"distModule": "esm/index.js",
|
|
54
54
|
"srcModule": "src/index.ts",
|
|
55
55
|
"module": "esm/index.js",
|
|
56
|
-
"gitHead": "
|
|
56
|
+
"gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
|
|
57
57
|
}
|